ARTICLE | doi:10.20944/preprints202202.0097.v1
Subject: Biology And Life Sciences, Endocrinology And Metabolism Keywords: Captive breeding; endangered; red panda; reproductive hormone; stress hormone; welfare
Online: 7 February 2022 (16:07:29 CET)
Animals in human care are affected by stressors that can ultimately reduce fitness. When reproduction is affected, endangered species’ conservation programmes can be severely compromised. Thus, understanding factors related to stress and reproduction, and measures of related hormones, are important to ensure captive breeding success. Red pandas are endangered and populations in the wild are threatened with extinction. A global captive breeding programme has been launched to conserve the species with the goal of reintroduction. However there is little informaiton on how stressors impact reproductive aspects of the species. This study measured fecal glucocorticoid (fGCM), fecal progestagen (fPM) and fecal androgen (fAM) metabolite concentrations in 12 female and 8 male red pandas (Ailurus fulgens fulgens) at three zoos in northeastern India to determine predictors of adrenal and gonadal steroid activity and the influence of fGCM on reproduction. Results indicated that fGCM concentrations were higher in males than females, and positively correlated with number of visitors, while negatively related to frequency of feedings and enclosure area. Sex, visitor number, frequency of feeding, and enclosure area explained 67% of the variations in fGCM concentrations in the study population. Concentrations of fPM were positively associated with tree density in the enclosure, explaining 47% of the variation among females. For fAM, positive associations were found with frequency of feeding, but concentrations were negatively related to age and number of visitors; these three covariates explained 45% of the variation in fAM concentration among males. Comparison of fGCM with fPM showed a negative trend, indicating increasing adrenal hormones may decrease reproductive function among female red pandas. The study thus suggests that zoo management should consider increasing feeding frequency, providing larger enclosures with more trees, and regulating visitor numbers to reduce stress and increase reproductive fitness among red pandas.
ARTICLE | doi:10.20944/preprints201907.0030.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: aquarists; aquarium trade; captive-breeding; IUCN red list; ornamental fish; threatened fish; undescribed species
Online: 2 July 2019 (04:18:04 CEST)
Freshwater fish represent half of all fish species and are the most threatened vertebrate group. Given their considerable passion and knowledge, aquarium hobbyists can play a vital role in their conservation. CARES is made up of many hobbyist organizations, whose purpose is to encourage aquarium hobbyists to the most endangered or extinct-in-the-wild freshwater fish to help ensure their survival. We found the CARES priority list contains nearly six hundred species from twenty families and two dozen species extinct-in-the-wild. The major families were typically the ones with largest hobbyist affiliations such as killifish, livebearers, and cichlids; which alone were half of CARES species. CARES contained every IUCN threatened species of Pseudomugilidae and Valenciidae, but only one percent of threatened Characidae, Cobitidae, and Gobiidae species. No Loricariidae in CARES were in the IUCN red list as they were not scientifically described. Tanzania and Mexico contained the largest amount of species, with the latter containing the most endemics. A large percent of species were classified differently than the IUCN, including a third of extinct-in-the-wild species classified as least concern by the IUCN. The vast disconnect exemplifies the importance of collaboration and information exchange required between hobbyists, the scientific community, and conservation organizations.
ARTICLE | doi:10.20944/preprints202308.0842.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: cheetah; captive diet; wildlife husbandry; gastrointestinal health; stress
Online: 10 August 2023 (12:46:40 CEST)
Unnatural diet composition and frequent feeding regimes may play an aetiological role in the multiple diseases prevalent in captive cheetahs. This study investigated the responses of captive-born (hand-reared) cheetahs (n = 6) to a reduced feeding frequency schedule. During the 3-week treatment period, the study cheetahs were fed four once-daily meals per week and two daily rations six days a week, subsequently, during the control period of equal duration. Total weekly food intake was maintained throughout the study. Variations in body temperature (Tb), heart rate (HR), locomotor activity (LA), behaviour, faecal glucocorticoid metabolite concentration, and faecal consistency score (FCS) were measured. Less frequent feeding resulted in higher FCS (p < 0.01) and LA (p < 0.0001) and lower HR (p < 0.0001) among the studied cheetahs. The study found that their HR was higher when the cheetahs were fed (p < 0.0001) than on days when they were not. Additionally, Tb (p < 0.0001) and HR (p < 0.05) were higher during feeding, suggesting a psychological excitation to food consumption. The results of the FCS analysis indicate that the more natural feeding pattern could have benefited the studied cheetahs’ GI health without a significant behavioural or physiological stress response to the change in feeding frequency.
ARTICLE | doi:10.20944/preprints201808.0538.v1
Subject: Business, Economics And Management, Business And Management Keywords: governance; agricultural value chain; links; captive chain; hierarchy chain
Online: 31 August 2018 (04:35:41 CEST)
The objective of this study is to determine the type of governance of the four main agricultural value chains in Tamaulipas, northeast of Mexico. For the preparation of this research used a qualitative design, using a questionnaire and semi-structured interviews to a sample of representatives of the four selected chains. The results showed that in all the studied networks, control and coordination capacity is limited by the influence that has a link on the rest of the chain. In all cases, was that the industrial link is who leads the chains and exert control over the rest of the links. The results showed that, when the industrial link is located close geographically to the rest of the links (chains of rice and sugar cane), the chains showed a hierarchical type, where the industrial exercised dominion over the rest of the links and captures most of the income. On the other hand, in chains where control is exercised by links that are outside the territory (chains of soybeans and sorghum), they function as captive chains, putting the rest of the chain to its influence and control.
REVIEW | doi:10.20944/preprints202004.0333.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bitter gourd; breeding; genetic diversity; genomics; heterosis; molecular breeding; mutation breeding
Online: 19 April 2020 (06:00:00 CEST)
Bitter gourd is an important vegetable of the family Cucurbitaceae, cultivated mainly in humid and subtropical Asia. Bitter gourd is vegetable with immense health benefits due to the presence of medicinal compounds such as charatin, vicine, and polypeptide-p, which play an essential role in lessening the blood glucose levels. Moreover, bitter gourd fruits are particularly rich in vitamin C, minerals, and carotenes. Here, an effort has been made to critically evaluate the extent of achievements during the enhancement and enactment of bitter gourd breeding programs with the use of latest technologies. Broadening of the genetic base of cultivated bitter groud varieties as a result of enrichment of the existing resources by using the wild species in the breeding programs. Practical seed production technological know-how along with the use of the MS system (male sterility)/chemical-induced sterility procedure is nonetheless vital to cope up with the market demands. Superior yielding bitter gourd hybrids combining early maturity and resistance to biotic and abiotic stresses are regularly needed to cope up with the challenge of bitter gourd production.
ARTICLE | doi:10.20944/preprints202301.0424.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: artificial incubation; captive rearing; apparent survival; hatching rate; fledging rate; conservation.
Online: 24 January 2023 (07:40:29 CET)
Headstarting is a conservation approach that suggests offering an advantage to a population by improving egg production, survival of embryos and/or juveniles. In this article, we are providing the quantitative data obtained during 10-years for different stages of headstarting (production of eggs per pair, hatching and fledging rates) and the resulting impact (survival to maturity, philopatry rate, sex ratio, apparent survival, growth/decline rate) on the local population of the critically endangered spoon-billed sandpiper. We have shown that headstarting gain is reduced over time from fledging to long-term recruitment to the local breeding population. The possible reasons for this reduction are suggested and discussed. The unexpected finding was a drastic difference in sex ratios of the new recruits which was about even for headstaring, but strongly male-biased for wild reared birds. We suggest that to happen due to increased mortality of female chicks in nature. We have also shown only headstarting could stop the global decline of the species, particularly once the suggested improvements are implemented and the number of pairs involved is scaled up. Headstarting also had a significant social effect due to involvement of in-creasing numbers of people both in the local communities in Chukotka and from many countries on the flyway into searching for marked birds and learning about waders, raising awareness about ecological problems on the East Asian-Australasian Flyway, thus, making the need for conservation actions on the flyway more obvious and sensible.
REVIEW | doi:10.20944/preprints202011.0667.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Plant breeding; Genome editing; Molecular breeding; Prime editing; Base editing; CRISPR Cas; Epigenetics; Speed breeding
Online: 26 November 2020 (11:17:56 CET)
Conventional plant breeding methods exploit already existing genomic variation in plants to develop a variety in 8 to 10 years, which can decrease the genetic variability of the plant’s genome. The ever-increasing food demand for cereals crops cannot be met by traditional breeding methods. In order to increase food production in less time, there is a dire need to improve breeding methods. Several conventional and molecular breeding methods are being used to improve the crops traits. Molecular researchers have developed new genome editing tools like CRISPR/Cas9, CRISPR/Cpf1, prime editing, base editing, dcas9 epigenetic modification, and several other transgene-free genomes editing approaches. These genome editing tools can improve the desired traits precisely and efficiently. Moreover, a newly developed breeding method “Speed Breeding” has revolutionized the agriculture by shortening the crop cycle. It can produce 5-6 generations of cereals in a year. In this review, we have summarized all these conventional and molecular breeding approaches to improve cereal crops.
ARTICLE | doi:10.20944/preprints202311.0176.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Crop wild relatives; diploid breeding; pre-breeding; Solanaceae; variability
Online: 3 November 2023 (06:17:57 CET)
Screening of pollen traits in diploid wild potatoes (Solanum sect. Petota, Solanaceae) is desirable to develop heat-tolerant potato (S. tuberosum) cultivars. To accomplish this goal requires exploring potato genetic resources that are conserved in genebanks. The goal of this study was to assess pollen viability and 2n pollen production of the diploid potato wild relatives under heat stress condition. We assessed pollen viability and size of nine potato accessions conserved at the Embrapa Potato Gene Bank, including S. chacoense (BRA 00167447-2, BRA 00167017-3, BRA 00167023-1, BRA 00167028-0), S. commersonii (BRA00167007-4, BRA00167420-9, BRA00183760-8), and S. malmeanum (BRA 00183755-8), along with a control accession from the cultivated species S. tuberosum (BRA 00167251-8). The plant accessions were cultivated in different growth chambers, simulating both control temperature (ranging from 14 to 27°C) and supraoptimal temperature conditions (ranging from 24 to 34°C). At heat stress, the accessions BRA 00167251-8 did not bloom, and BRA 00167023-1 did not produce pollen. The remaining accessions did not exhibit a significant reduction in pollen viability as the temperature increased. Pollen viability at the control temperature had the lowest value in BRA-00167420-9 (S. commersonii) with 68.5% and the highest in BRA 00183755-8 (S. malmeanum) with 100%. At the supraoptimal temperature the lowest value was in BRA 00167420-9 (S. commersonii) with 54.5% and the highest in BRA 00183755-8 (S. malmeanum). The average of pollen size was 20 μm in all wild potato genotypes, and the increase of temperature did not lead to 2n pollen production. Estimated Genotypic Coefficient of Variation (GCV) was lower than Phenotypic Coefficient of Variation (PCV) for pollen viability. The observed heritability values ranged from 58.82% in BRA00167007-4 to 91.32% in BRA 00183755-8. Our results highlight the genetic variability available in wild potato germplasm concerning pollen viability under heat stress. Furthermore, these first insights offer valuable guidance for ongoing and future endeavors in diploid potato breeding.
REVIEW | doi:10.20944/preprints202108.0514.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: radish; breeding; interspecific hybridization; molecular breeding; genomics; genetic engineering
Online: 26 August 2021 (16:46:36 CEST)
Radish is an annual herbaceous root crop, fruit, and oil crop plant belonging to the Cruciferae family. The important traits for radish breeding include high yield, early maturity, late bolting, pungency, cold-hardiness, drought resistance, heat tolerance, and soil adaptability. For successful radish production, need to the understand nature and behavior of the flower, and very important to identify the S haplotypes of parental lines to produce F1 hybrids based on self-incompatibility to get rid of laborious hand emasculation in radish. In radish some desirable genes are not present within varieties. Therefore, further breeding programmes depend on inter-specific and intra-specific hybridization, which has a vital role in genomic studies and crop improvement by introducing desirable agronomic characters. It is essential to acquire detailed genetic information on chromosomes and information on inheritance. Genomics is now at the core of crop improvement, and radish crop is exploited to study the underlying differences in genotypes. But some monogenic characters are improved by genetic engineering. A three-decade span following the first documented instance of genetic engineering has witnessed its application's unprecedented growth. Researchers have successfully produced transgenic radishes with various agronomic characteristics over the last decade.
ARTICLE | doi:10.20944/preprints202309.1295.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: cannabis; breeding; phenotype; correlations
Online: 20 September 2023 (02:35:37 CEST)
Cannabis (Cannabis sativa L.) stands as a historically significant and culturally important plant, embodying economic, social, and medicinal relevance for human societies. However, years of prohibition and stigmatization have hindered the cannabis research community, which is hugely undersized and suffers from a scarcity of understanding of cannabis genetics and how key traits are expressed or inherited. In this study, we conducted a comprehensive phenotypic characteriza-tion of 176 drug-type cannabis accessions, representative of Canada's legal market. We assessed germination methods, evaluated various traits including agronomic, morphological, and canna-binoid profiles, and uncovered significant variation within this population. Notably, yield dis-played a negative correlations with maturity-related traits but positive correlation with fresh biomass. Additionally, the potential THC content showed positive correlation with maturi-ty-related traits but negative correlation with yield. Significant different were observed between plants derived from regular female seeds and feminized seeds, as well as between plants derived from cuttings and seeds for different traits. This study advances our understanding of cannabis cultivation, offering insights into germination practices, agronomic traits, morphological charac-teristics, and biochemical diversity. These findings establish a foundation for precise breeding and cultivar development, enhancing cannabis's potential in the legal market.
ARTICLE | doi:10.20944/preprints202305.0160.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: severity; citrus breeding; varieties
Online: 3 May 2023 (14:44:16 CEST)
Mandarins occupy the third group among citrus produced in Brazil. Primarily aimed at the fresh fruit market, commercial orchards have suffered significant losses in production, due to the high incidence of diseases, such as alternaria brown spot (ABS) and huanglongbing (HLB). The fact that 80% of the orchards are composed of two varieties, Ponkan mandarin and Murcott tangor, are highly susceptible to both diseases, demand intensive chemical control of the diseases in the field, which has resulted in a significant increase in production costs and a negative environmental impact. A total of one hundred and seventy-three mandarin accessions, including several species and hybrids, belonging to the Collections of the Instituto Agronômico de Campinas (IAC), were evaluated in the field, in an endemic location for the diseases. Evaluations of the incidence and severity of the diseases showed that there is a range of genotypes tolerant to ABS with potential to replace the current commercial varieties, mainly within the clementina and Willow leaf mandarin groups. Although with differences in incidence and susceptibility to HLB, there are no varieties tolerant to this disease, which significantly impacts the loss of fruit quality.
ARTICLE | doi:10.20944/preprints202302.0191.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chicory; endive; RADseq; male-sterility; molecular breeding; SNPs; inbred lines; F1 hybrids; predicted breeding value
Online: 10 February 2023 (11:15:16 CET)
Chicory, a horticultural crop cultivated worldwide, presents many botanical varieties and local biotypes. Among these, Italian radicchio group cultivars of pure Cichorium intybus L. and interspecific hybrids with Cichorium endivia L., as the “Red of Chioggia” biotype which in turn includes several phenotypes. This study deals with a pipeline for the marker-assisted breeding of F1 hybrids: it presents the genotyping-by-sequencing results of four elite inbred lines using a RADseq approach and an original molecular assay based on CAPS markers for screening mutants with nuclear male-sterility in radicchio of Chioggia. Two thousand nine hundred fifty-three SNP-carrying RADtags were identified and used to compute the actual estimates of homozygosity, and overall genetic similarity and uniformity of the populations, as well as to determine their genetic distinctiveness and differentiation. Molecular data were further used to investigate the genomic distribution of the RADtags among the two Cichorium species, allowing their mapping in 1,131 and 1,071 coding sequences in chicory and endive, respectively. In parallel, an assay to screen the genotype at the male-sterility locus Cims-1 was developed to discriminate wild-type and mutant alleles of the causative gene myb80-like. Moreover, a RADtag mapped close to this genomic region proved the potential application of this method for future marker-assisted selection tools. Finally, combining the genotype information of the core collection, the best ten individuals from each inbred line were selected to compute the observed genetic similarity as a measure of uniformity as well as the expected homozygosity and heterozygosity estimates scorable by the putative progenies derived from selfing (pollen parent) and full-sibling (seed parent) or pair-wise crossing (F1 hybrids). This predictive approach was conducted as a pilot study for understanding the potential application of RADseq in improving molecular breeding strategies aimed at the development of inbred lines and F1 hybrids in leaf chicory.
COMMUNICATION | doi:10.20944/preprints202305.0879.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: glucosinolate; germplasm; breeding; anticancer; genebank; diversity
Online: 12 May 2023 (04:27:49 CEST)
The aim of this study was to analyze glucosinolates (GSLs) in germplasms that are currently conserved at the RDA-Genebank. The analysis focused on the glucosinolate diversity among the analyzed germplasms, with the goal of identifying those that would be most useful for future breeding efforts to produce nutritionally rich Choy sum plants..Twenty-three accessions of Choy sum which possessed ample background passport information were selected. By analyzing the glucosinolate content for 17 different glucosinolates, we observed aliphatic GSLs to be the most common. We identified one accession, IT228140 to synthesize high quantities of glucobrassi-canapin and progoitrin which have been reported to contain several therapeutic applications. Overall, this study highlights the importance of conserving and analyzing plant genetic re-sources, such as those held in national genebanks, for the purpose of developing new varieties of crops that are both nutritious and beneficial for human health. The identification of excellent germplasms for breeding material and the confirmation of the anticancer effects of glucosin-olates are significant contributions to the field of agricultural research and have the potential to positively impact public health.
REVIEW | doi:10.20944/preprints202211.0489.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Ciherang; agronomics; genetics; breeding; intensive cultivation
Online: 28 November 2022 (03:13:26 CET)
Ciherang rice variety was released in year 2000 and become a superior variety in Indonesia. In a decade, due to the excellent agronomic characteristics and high productivity, Ciherang gradually replace the mega-variety IR-64 and widely cultivate in almost 40% rice production area in Indonesia. In addition to its high grain yield, short straw, early maturity, and high productive tiller number, it had superior grain quality, such as long and slender grain shape, clean yellow color, aromatic, and high milled rice percentage with excellent eating quality, matching with farmers and rice consumers demands. It has intermediate glycemic index and delicious taste. It is intolerance to flooding condition and susceptible to several diseases and pests, including rice blast, bacterial blight, brown planthopper, and yellow stem borer. Because of Ciherang has been well-characterized genetically, many quantitative trait loci (QTLs) and candidate genes which associated with certain traits have been identified. It has also been used as a parent in rice breeding program to develop mapping populations for genetic analysis. In order to increase the flooding tolerant and disease resistant in Ciherang, many valuable genes have been introduced into Ciherang through backcrossing breeding technique and transgenic approach. The optimal rice productivity in Ciherang also supported by the application of intensification system in Ciherang cultivation. Unravelling the complex genetic control of agronomic characteristics, grain yield traits, and other desirable traits which valuable for rice farmers and consumers are very important.
REVIEW | doi:10.20944/preprints202204.0149.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: sweet potato; breeding; genetics; genomics; health
Online: 15 April 2022 (14:58:08 CEST)
Sweet potatoes are a crucial crop for Asian and African countries. Its nutritional content and capacity to keep you healthy have increased in recent years. Moreover, sweet potatoes' fibre also keeps your gut happy. Most sweet potato varieties don't bloom. Due to pollination issues, sweet potatoes are also incompatible with each other. Sweet potato blooms are self-sterile, so they don't mix well in breeding programmes. Traditional and modern breeding procedures didn't always work with sweet potatoes, but some did. Using molecular biology methods, some individuals become more resistant to illnesses by eliminating particular genes. The crop's nature and growth should be improved. All of this should be done to acquire new characteristics in sweet potatoes by crossing them. Sweet potatoes are a superb tuberous crop, but they have issues with pollination and adjusting to new breeding procedures. Modern breeding and biotechnology methods can be used to get the most out of this crop. These are "chronological" ways to get the most out of farming.
ARTICLE | doi:10.20944/preprints202310.1250.v1
Subject: Environmental And Earth Sciences, Other Keywords: yerba mate; breeding; methylxanthines; phenolic compunds; HPLC
Online: 20 October 2023 (08:32:12 CEST)
An especially important species in southern Brazil, yerba mate (Ilex paraguariensis) is traditionally consumed as tea, chimarrão and tererê. Yerba mate consumption has been stimulated by scientific discoveries that have identified high concentrations of bioactive compounds and their health benefits. There are no studies or scientific evidence to certify or guarantee stability of these compounds’ concentrations during different years in the same plants. We were interested in quantifying caffeine, theobromine, total phenolic compounds and proteins concentrations in leaves of yerba mate genotypes and their stability in the same plants over four consecutive years. Mature leaves from yerba mate genotypes selected on a provenance and progenies trial were collected in August of 2015, 2016, 2017 and 2018. Methylxanthines (caffeine and theobromine), total phenolic compounds and total protein contents were quantified. Our results indicate large variations between genotypes regarding caffeine (0.035 to 2.385 g 100 g-1), theobromine (0.0004 to 1.772 g 100 g-1), total phenolic compounds (7.028 to 9.424 g 100 g-1) and proteins (10.39 to 16.58 g 100 g-1) contents, and also high stability of those compounds over the four evaluated years. A great variation of the studied bioactive compounds in different Ilex paraguariensis genotypes was found and its stability over four consecutive years was showed.
COMMUNICATION | doi:10.20944/preprints202310.1131.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Foot injuries; Production systems; Cattle breeding; Amazon.
Online: 18 October 2023 (17:36:16 CEST)
BDD is a hoof disease characterized by inflammation of the second and fifth accessory digits and the skin in this region. This pathology is scarcely described in the literature; however, it has recently been observed in beef cattle in the Amazon Biome region. The objective of this study was to identify the epidemiological factors associated with BDD onset in cattle in the analyzed biome. Samples were collected from eight farms with extensive breeding systems located in Xinguara, Rondon do Pará, Curionópolis, and Ipixuna do Pará, in the state of Pará, Brazil. A total of 706 Nellore and Nellore crossbred with taurine animals of both sexes were evaluated, with males aged between 2–4 years and a mean weight of 650 kg and females aged between 2–11 years and a mean weight of 400 kg. Distal extremities were inspected during cattle management, and in case of accessory digit lesions, a specific examination was carried out after proper restraint. Animals were diagnosed with BDD in all farms analyzed. Of the 706 cattle inspected, 49 (6.94%) showed BDD, of which 19 (38.77%) were Nellore and 30 (61.22%) were crossbred. This was the first study to determine BDD’s occurrence in extensive farming systems in the Amazon region, also showing that pastures with large amounts of stumps and stones, the physical structure of pens, and trauma and injury incidence during animal management are the most important predisposing factors for the onset of BDD.
REVIEW | doi:10.20944/preprints202309.0258.v1
Subject: Biology And Life Sciences, Insect Science Keywords: sweetpotato; weevils; Cylas spp.; resistance; breeding; Uganda
Online: 5 September 2023 (09:13:20 CEST)
In sub-Saharan Africa, sweetpotato weevils are the most devastating pests of cultivated sweetpotato, causing estimated losses of between 60% and 100%, primarily during dry spells. The predominantly cryptic feeding behavior of the Cylas spp within the roots makes their control difficult, thus host plant resistance is one of the most promising lines of protection against these pests. However, progress in breeding for weevil-resistant cultivars has been slow in part due to the complex hexaploid genome of sweetpotato, which complicates conventional breeding in addition to the scarcity of varieties with significant levels of resistance for use as sources of resistance. Pollen sterility, cross incompatibility and poor seed set and germination in sweetpotato are also common challenges to improving weevil resistance. Accurate phenotyping of sweetpotato weevil resistance to enhance efficiency of selection has been equally difficult. Genomics-assisted breeding though in its infancy stages in sweetpotato has the potential application in overcoming some of these barriers. However, it will require the development of more genomic infrastructure; particularly single nucleotide polymorphism markers (SNPs), robust next generation sequencing plat-forms together with relevant statistical procedures for analyses. With the recent advances in genomics, we anticipate that genomic breeding for sweetpotato weevil resistance will be expedited in the coming years. This review sheds light on Uganda's efforts to date to breed against the Cylas puncticollis (Boheman) and Cylas brunneus (Fabricius) species of African sweetpotato weevil.
ARTICLE | doi:10.20944/preprints202307.1716.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Ammonia; CFD; Ventilation; Working and breeding environment
Online: 26 July 2023 (03:23:42 CEST)
Many farms utilize closed-type livestock systems to enhance productivity and facilitate effective environmental management. However, the confined nature of these closed spaces poses an increased risk of exposure to harmful gases and organic dust for both workers and livestock. Additionally, the introduction of outside air through ventilation systems can lead to temperature fluctuations within the breeding environment, resulting in potential productivity issues. This research paper employs computational fluid dynamics (CFD) to develop ventilation operation management plans that address both the working environment and the breeding environment simultaneously. The proposed plans are designed to be easily implemented in practical farm settings. The findings of this study, based on simulation analysis, indicate that while ventilation is effective in reducing harmful gases and improving the working environment, its efficiency decreases after the initial 3 minutes of operation. Furthermore, uncontrolled ventilation can cause sudden temperature changes, which may adversely affect the well-being of the livestock. However, when upgraded ventilation structures are implemented, significant improvements in the working environment (an average of 27.3% improvement) can be achieved while maintaining temperature stability for the livestock. These results highlight the importance of referring to the provided ventilation operation management table before commencing work, as it enables workers to improve the working environment while minimizing the potential impact of ventilation on the breeding environment.
REVIEW | doi:10.20944/preprints202307.1196.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: CRISPR/Cas technology; Crop; Germplasm; Breeding technology
Online: 18 July 2023 (09:27:20 CEST)
Crop breeding is an important global strategy to meet sustainable food demand. CRISPR-Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm, and leads to revolutionary crop breeding innovation. In this review, we summarize recent advance of CRISPR/Cas technology in gene function analyses and generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed.
ARTICLE | doi:10.20944/preprints202303.0328.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Fusion; DCLL; Breeding Blanket; HELIAS; TBR; neutronic
Online: 20 March 2023 (01:08:40 CET)
The Stellarator Power Plant Studies Prospective R&D Work Package among the Eurofusion Programme was settled to bring the stellarator engineering to maturity, so that stellarators and particularly the HELIAS (HELical-axis Advanced Stellarator) configuration could be a possible alternative to tokamaks. However, its complex geometry makes designing a Breeding Blanket (BB) that fully satisfies the requirements for such an HELIAS configuration a difficult task. Taking advantage of the acquired experience in BB design for DEMO tokamak, CIEMAT is leading the development of a Dual Coolant Lithium Lead (DCLL) BB for a HELIAS configuration. To answer the specific HELIAS challenges new and advanced solutions have been proposed, as the use of fully detached First Wall (FW) based on liquid metal Capillary Porous Systems (CPS). These proposed solutions have been studied in a simplified 1D model that can help to estimate the relative variations in Tritium Breeding Ratio (TBR) and displacement per atom (dpa) to verify their effectiveness to simplify the BB integration, improve the machine availability while keeping the main BB nuclear functions (i.e. tritium breeding, heat extraction and shielding). This preliminary study demonstrates that the use of FW CPS would reduce the radiation damage received by the blanket without compromising its tritium breeding performance.
ARTICLE | doi:10.20944/preprints202302.0243.v1
Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: ensemble; wind forecast; dynamical downscaling; breeding; blending
Online: 14 February 2023 (09:36:21 CET)
This work compared the performance of three methods for constructing a regional ensemble prediction system (EPS) for wind speed forecasts: dynamical downscaling, breeding of growth modes (BGM), and blending method. The Weather Research and Forecasting (WRF) model was used to downscale the European Centre for Medium-range Weather Forecast (ECMWF) EPS. In addition, as the BGM method needs observation data for generating scaling factors, an alternative method for generating scaling factors was proposed to eliminate dependence on observation data. One-month tests between October 1st and October 30th, 2020, were implemented to evaluate the performance of three methods in the Gansu province of China. The results demonstrate that the blending method outperforms the other two methods. Furthermore, the difference in performance is evident mainly in early forecast lead time and becomes negligible as forecast time increases.
REVIEW | doi:10.20944/preprints202204.0228.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: vegetables; high throughput phenotyping; genomic assisted breeding
Online: 26 April 2022 (06:00:45 CEST)
Conventional phenotyping breeding approaches for vegetable crops like Solanaceae, Bulb, Root crops, have made a significant contribution by developing many varieties. Despite this, conventional phenotyping approaches are not sufficient due to the longer time taken to develop a variety, low genetic gain, environmental factors and some other externalities that affect the phenotype-based selection. To address the challenges of conventional phenotype, a new recent method of high throughput phenotyping (HTP) is considered a promising tool. The development of high-throughput phenotyping technology began in the preceding decade as advancements in sensor, computer vision, automation, and advanced machine learning technologies. HTP platforms are being utilized to undertake non-destructive assessments of the complete plant system in a range of crops. HTP provides the precise measurements and suggests the collection of high-quality and accurate data which is necessary for standardizing phenotyping for the collection of genetic dissection and genomic assisted breeding such as genome-wide association studies (GWAS), linkage mapping, marker-assisted selection (MAS), genomic selection (GS). The remainder of this chapter discusses how high-throughput phenotyping technologies can be used in genomic-assisted breeding for vegetable crops
REVIEW | doi:10.20944/preprints202202.0181.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: orchid breeding; polyploidy; meiosis; fertility; organ size
Online: 15 February 2022 (04:08:05 CET)
The orchid market is a dynamic horticultural business in which novelty and beauty command high prices. The development of miniature to large and showy flowers, in addition to fragrance, is mainly of interest. Overall organ size might be modified by doubling the chromosome number, which can be accomplished by careful study of meiotic chromosome disjunction in hybrids or species. Meiosis is the process in which diploid (2n) pollen mother cells recombine their DNA sequences and then undergo two rounds of division to give rise to four haploid (n) cells called sporads. Thus, by interfering in chromosome segregation, one can induce the development of diploid recombinant sporads called dyads. These dyads may be used for breeding polyploid progenies with enhanced fertility and large flower size. This review gives an overview of developments in orchid breeding placed in the large context of ploidy breeding in higher plants to facilitate innovation
ARTICLE | doi:10.20944/preprints202105.0560.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: ae mutant; amylose; breeding potential; maize; SBEIIb
Online: 24 May 2021 (10:44:31 CEST)
Maize varieties with high amylose proportion are more valuable for starch industry. The SBEⅡb gene encodes one of the starch branching isozymes (SBEⅠ, SBEⅡa, and SBEⅡb). Its recessive mutant amylose-extender (ae/sbe2b) decreases the total activities of SBEs and increases amylose proportion up to 60%. Here, the breeding potential of introduced germplasm line GEMS-0067 was evaluated by genotyping and phenotyping. The deletion of the ninth exon of the SBEⅡb gene, high amylose proportion, and the typical irregular granules suggested that this germplasm line was derived from the same resource of high amylose line AE11. The gelatinization and thermal properties, and degree of polymerization of starch chain showed its advantages used for high amylose breeding. However, the negative correlation between amylose proportion and starch content, as well as ker-nel filling characteristics should be overcome during breeding process.
ARTICLE | doi:10.20944/preprints201811.0084.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Donkey; breeding; twinning; heritability; REML; risk factors
Online: 5 November 2018 (04:13:35 CET)
Multiple births or twinning in equids are dangerous, undesirable situations that compromise the life of the dam and resulting offspring. However, embryo vitrification and freezing techniques take advantage of individuals whose multiple ovulations allow flushing more fertilised embryos from the oviduct to be collected, increasing the productivity and profitability of such techniques. Embryo preservation is especially important in highly endangered populations such as certain donkey (Equus asinus) breeds; for which conventional reproductive techniques have previously failed. For instance, becoming an effective alternative to artificial insemination with frozen semen to preserve the individuals’ genetic material. The objective of this study was to examine the historical foaling records of Andalusian donkeys to estimate genetic parameters for multiple births, assessing the historical foal number born per animal, maximum foal number per birth and multiple birth number per animal. We designed an Animal Model with single records considering the fixed effects of birthyear, birth season, sex, farm, and husbandry system, and age as a linear and quadratic covariate. Restricted maximum likelihood reported heritability estimates ranging from 0.18±0.01 to 0.24±0.01. Genetic and phenotypic correlations ranged from 0.01±0.01 to 0.83±0.01 and 0.12±0.01 and 0.53±0.01, respectively. These estimates enable the potential for selection against/for these traits, offering a new perspective for donkey breeding and conservation.
ARTICLE | doi:10.20944/preprints202307.1622.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Blumeria graminis; resistance genes; resistance; germplasm; gene bank; biodiversity; plant breeding; plant genetic resources; crop wild relatives; pre-breeding
Online: 24 July 2023 (12:21:45 CEST)
Sources of resistance to powdery mildew in wild barley (Hordeum vulgare subsp. spontaneum) collected in Jordan, Lebanon, and Libya Jerzy H. Czembor 1, *, Elżbieta Czembor 1 1 Plant Breeding and Acclimatization Institute – National Research Institute (IHAR-PIB), Radzikow, 05-870 Błonie, Poland; firstname.lastname@example.org (E.C.) *Correspondence: email@example.com) Abstract Barley powdery mildew (BPM) is caused by the pathogen Blumeria graminis f.sp. hordei (Bgh). It is an economically important disease and plant pathologists are looking for new sources of resistance to BPM. Barley genetic resources present in gene banks are often a rich source of disease resistance to be used by breeders. These new sources of resistance to BPM are often used in combination (pyramiding) with those that are already used in modern cultivars. Barley accessions, including the wild subspecies Hordeum vulgare subsp. spontaneum (Hvs), are stored in many gene banks and often are a valuable source of economically important characteristics. This source of biodiversity should be more efficiently used to improve barley in the process of plant breeding. However, their proper characterization and availability are urgently needed. The resistance to BPM in 81 accessions of wild barley (Hvs) collected in Jordan (47), Lebanon (23), and Libya (11) was investigated. The seed samples of these accessions were obtained from the ICARDA gene bank and collected in 10 expeditions from 1981 to 1995. Twenty European differential isolates of BPM were used to select accessions with efficient resistance. Thirty-one resistant single plant lines were selected from 15 accessions from Jordan and Libya based on tests performed with the most avirulent isolate of Bgh available. These resistant single plant lines were tested for the presence of specific resistance genes using a differential set of Bgh isolates. After analysis of obtained results, it was concluded that all tested 31 single plant lines of wild barley have genes for resistance that are not represented in the Pallas isolines differential s. Twenty-six lines of Hvs selected from accessions originated in Jordan and Libya showed resistance reaction to all isolates used. Identified new sources of effective resistance to BPM in single plant lines of Hvs will be further tested and used in barley pre-breeding programs. Keywords: Blumeria graminis; resistance genes; resistance; germplasm; gene bank;
REVIEW | doi:10.20944/preprints202202.0048.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Plant Breeding; Speed Breeding; Training Population; Field Design; Multi-Environment; Multi-Trait; Deep Learning; High-Throughput Phenotyping; Genetic Gain
Online: 3 February 2022 (10:41:44 CET)
Plant geneticists and breeders have used marker technology since the 1980s in quantitative trait locus (QTL) identification. Marker-assisted selection is effective for large-effect QTL but has been challenging to use with quantitative traits controlled by multiple minor effect alleles. Therefore, genomic selection (GS) was proposed to estimate all markers simultaneously, thereby capturing all their effects. However, breeding programs are still struggling to identify the best strategy to implement it into their programs. Traditional breeding programs need to be optimized to implement GS effectively. This review explores the optimization of breeding programs for variety release based on aspects of the breeder’s equation. Optimizations include reorganizing field designs, training populations, increasing the number of lines evaluated, and leveraging the large amount of genomic and phenotypic data collected across different growing seasons and environments to increase heritability estimates, selection intensity, and selection accuracy. Breeding programs can leverage their phenotypic and genotypic data to maximize genetic gain and selection accuracy through GS methods utilizing multi-trait and, multi-environment models, high-throughput phenotyping, and deep learning approaches. Overall, this review describes various methods that plant breeders can utilize to increase genetic gains and effectively implement GS in breeding .
REVIEW | doi:10.20944/preprints202310.0243.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Lupinus mutabilis; genetic diversity; breeding; anthracnose resistance; alkaloids
Online: 5 October 2023 (02:38:00 CEST)
Lupinus mutabilis, also known as tarwi or chocho, is an important agricultural species cultivated in South America since ancient times. Tarwi is native from the Andean regions of Peru, Bolivia, and Ecuador and has a very high protein content. Despite its high nutritional value and promotion efforts by regional researchers and breeders, tarwi is not a widely cultivated crop in its center of origin. In this review, we present the work carried out by public breeding programs of L. mutabilis at national agricultural research institutes, universities, and other institutions in Ecuador, Peru, and Bolivia. The main breeding method used in the Andes to improve local landraces has been mass selection to adapt lines to specific environments. At least 25 cultivars or ecotypes have been selected and released over the last 40 years using this breeding system. Notwithstanding, breeders are currently struggling to develop new varieties that are high yielding, suitable for mechanized harvesting, have a low content of alkaloids or other anti-nutritional properties, and to anthracnose (Colletotrichum acutatum). Therefore, it is necessary to reassess the potential of this crop and invest in its research to incorporate new techniques and breeding strategies to optimize the development of new varieties in the Andes which address the current cultivation challenges of the species.
ARTICLE | doi:10.20944/preprints202109.0095.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: prion; deer; PRNP; selective breeding; resistance; susceptibility; CWD
Online: 6 September 2021 (13:13:47 CEST)
Chronic wasting disease is a fatal transmissible spongiform encephalopathy (TSE) of cervids caused by a misfolded variant of the normal cellular prion protein, and is closely related to sheep scrapie. Variations in a host’s prion gene, PRNP, and its primary protein structure, dramatically affect susceptibility to specific prion disorders, and breeding for PRNP variants that prevent scrapie infection has led to steep declines in the disease in North American and European sheep. While resistant alleles have been identified in cervids, a PRNP variant that completely prevents CWD has not yet been identified. Thus, control of the disease in farmed herds traditionally relies on quarantine and depopulation. In CWD-endemic areas, depopulation of private herds becomes challenging to justify, leading to opportunities to manage the disease in situ. In the present study, we developed a selective breeding program for farmed white-tailed deer in a CWD-endemic area, focused on reducing frequencies of highly susceptible PRNP variants and introducing animals with less-susceptible variants into historically high prevalence areas. We found that breeding followed predictable Mendelian inheritance, and early data support our project’s utility in reducing CWD prevalence. This project represents a novel approach to CWD management, with future efforts building on these findings.
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: wheat; reticulate evolution; introgression; speciation; hybridization; adaptation; breeding
Online: 21 April 2021 (08:55:42 CEST)
Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (Triticum aestivum subsp. aestivum) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera Triticum and Aegilops. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of Triticum species should be beneficial to future genetic study and breeding of bread wheat.
ARTICLE | doi:10.20944/preprints202101.0543.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Blueberry; Pre-breeding; hybridization; V. elliottii; Fruit quality
Online: 26 January 2021 (15:55:14 CET)
Wild germplasm can be classified as the raw material essential for crop improvement. Introgression of wild germplasm is normally used in breeding to increase crop quality or resilience to evolving biotic and abiotic threats. Here, we explore the potential of introgressing Vaccinium elliottii into commercial blueberry germplasm. Vaccinium elliottii is a wild diploid blueberry species endemic to the southeastern United States that possesses highly desirable and economically important traits for blueberry breeding such as: short bloom to ripe period, adaptation to upland sandy soils, disease resistance, firmness, and pleasant flavor. To examine the potential of hybridization, we evaluated populations of interspecific hybrids across multiples stages of breeding (i.e., F1, F2, and backcrosses) in two crop seasons. We used our extensive pedigree data to generate breeding values for pre-breeding blueberry hybrid populations. Hybrid performance was evaluated considering fitness (i.e., plant vigor and plant height) in addition to evaluating six fruit-quality and marketable-related traits (i.e., size, firmness, acidity, soluble solids, weight, and yield). Overall, F2 and backcrosses rapidly achieved market thresholds, presenting values not significantly different from commercial blueberry germplasm. Our results confirmed the potential of exploiting the high genetic variability contained in V. elliotii for interspecific hybridization. Additionally, we developed germplasm resources that can be further evaluated and utilized in the breeding process, advancing selections for fruit quality and environmental adaptation.
REVIEW | doi:10.20944/preprints202010.0460.v2
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: plant breeding; genomic selection; Bayes; BLUP; machine learning
Online: 18 November 2020 (11:21:50 CET)
Estimation of breeding values through Best Linear Unbiased Prediction (BLUP) using pedigree-based kinship and Marker-Assisted Selection (MAS) are the two fundamental breeding methods used before and after the introduction of genetic markers, respectively. The emergence of high-density genome-wide markers has led to the development of two parallel series of approaches inspired by BLUP and MAS, which are collectively referred to as Genomic Selection (GS). The first series of GS methods alters pedigree-based BLUP by replacing pedigree-based kinship with marker-based kinship in a variety of ways, including weighting markers by their effects in genome-wide association study (GWAS), joining both pedigree and marker-based kinship together in a single-step BLUP, and substituting individuals with groups in a compressed BLUP. The second series of GS methods estimates the effects for all genetic markers simultaneously. For the second series methods, the marker effects are summed together regardless of their individual significance. Instead of fitting individuals as random effects like in the BLUP series, the second series fits markers as random effects. Differing assumptions regarding the underlying distribution of these marker effects have resulted in the development of many Bayesian-based GS methods. This review highlights critical concept developments for both of these series and explores ongoing GS developments in machine learning, multiple trait selection, and adaptation for hybrid breeding. Furthermore, considering the increasing use and variety of GS methods in plant breeding programs, this review addresses important concerns for future GS development and application, such as the use of GWAS-assisted GS, the long-term effectiveness of GS methods, and the valid assessment of prediction accuracy.
REVIEW | doi:10.20944/preprints201912.0158.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: QTLs; biofortification; malnutrition; hidden hunger; marker-assisted breeding
Online: 12 December 2019 (03:52:07 CET)
Rice (Oryza sativa L.) supplies nourishment to about half of the population of the world's inhabitants. Of them, more than 2 billion people suffer from "hidden hunger" in which they are unable to meet the recommended nutrients or micronutrients from their daily dietary intake. Bio-fortification refers to developing micronutrient-rich diet foods using traditional breeding methods and modern biotechnology, a promising approach to nutrition enrichment as part of an integrated strategy for food systems. To improve the profile of rice grain for the biofortification related traits, understanding the genetics of important biofortification traits is required. Moreover, these attributes are quantitative in nature and are influenced by several genes and environmental variables. In the course of past decades, several endeavours such, as finding the important quantitative trait loci (QTLs) for improving the nutrient profile of rice seeds were successfully undertaken. In this review, we have presented the information regarding the QTLs identified for the biofortification traits in the rice.
ARTICLE | doi:10.20944/preprints201906.0293.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: kiwifruit; genomics; polyploidy; breeding; ascorbic acid; vitamin C
Online: 28 June 2019 (08:09:04 CEST)
During analysis of kiwifruit derived from hybrids between the high AsA species Actinidia eriantha and A. chinensis var chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis we performed whole-genome sequencing on pools of high and low AsA fruit from tetraploid A. chinensis var. deliciosa x A. eriantha backcross families. Pool-GWAS revealed a single QTL spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis x A. eriantha) x A. chinensis backcross families, showing that the eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNASEQ. This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harboring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.
REVIEW | doi:10.20944/preprints202311.1311.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Triticum durum; breeding; grain yield; grain quality; physiological traits
Online: 21 November 2023 (10:20:15 CET)
The leading role of Italy in the cultivation of durum wheat stimulated intense breeding activities in the country from the beginning of the 20th century, much earlier than any other country involved in durum wheat production. Older, genetically more heterogeneous landraces became replaced with new highly productive, superior quality varieties, and this led an inevitable reduction in overall genetic diversity among new cultivars, which makes the genetic variability of the old cultivars preserved particularly valuable and important. The aim of this paper was to assist future breeding programmes by providing a detailed description of the history of durum wheat breeding in Italy and of the changes in yield, quality and related traits that subsequently occurred, starting from the most diffuse landraces present between 1900 and 1920 up until the present day. The parallel evolution of breeding techniques, breeding goals and agricultural systems in this period is also described, and some future breeding goals suggested. In the current context of climate change and of rapidly mutating pathogen populations, preserving the yield level with the continuous introduction of new cultivars by exploiting the reservoir of largely unused genetic variation stored in old cultivars and landraces could be as important as increasing grain yield and quality.
ARTICLE | doi:10.20944/preprints202308.0630.v1
Subject: Engineering, Energy And Fuel Technology Keywords: WCLL; breeding blanket; DEMO; thermomechanics; FEM analysis; Bottom Cap
Online: 8 August 2023 (07:18:48 CEST)
The Water-Cooled Lead Lithium (WCLL) Breeding Blanket (BB) is one of the two BB concepts candidate to be selected as driver blanket for the EU-DEMO fusion reactor. In this regards, the development of a sound architecture of the WCLL Central Outboard Blanket (COB) Segment, ensuring the fulfilment of the thermal and structural design requirements, is one of the main goals of the EUROfusion consortium. To this purpose, an exploratory research campaign has been launched to preliminarily investigate the thermo-mechanical performances of the Bottom Cap (BC) region of the WCLL COB segment, because of its peculiarities making its design different from the other regions. The assessment has been carried out considering the nominal BB operating conditions, the Normal Operation (NO) scenario, as well as a steady-state scenario derived from the in-box LOCA accident, the Over-Pressurization (OP) scenario. Starting from the reference geometric layout of the WCLL COB BC region, a first set of analysis has been launched in order to evaluate its structural performances under a previously calculated thermal field and to select potential geometric improvements. Then, the analysis of a more complete BC region has been conducted from both the thermal and structural standpoints, evaluating its structural behaviour in compliance with the RCC-MRx code. Finally, after some iterations and geometric updates, a promising geometric layout of the BC region has been obtained even though some criticalities still persist in the internal Stiffening Plates and First Wall. However, the obtained results clearly showed that the proposed layout is worthy to be further assessed to achieve a robust enough configuration. The work has been performed following a theoretical-numerical approach based on the Finite Element Method (FEM) and adopting the quoted Ansys commercial FEM code.
ARTICLE | doi:10.20944/preprints202212.0584.v1
Subject: Biology And Life Sciences, Forestry Keywords: miRNA156; micropropagation; tree breeding; recalcitrant; woody plants; perennial plants
Online: 30 December 2022 (10:18:33 CET)
In plants, phase change from the juvenile stage to maturity is a tightly controlled process at the physiological and genetic level, which is controlled by evolutionary highly conserved microRNAs. These phase changes are more pronounced in woody plant species, but the majority of molecular genetic studies on the regulation of this transition has been done in annual model or crop species. This process is of particular significance for the in vitro propagation of woody plant species, as individuals or tissues that have undergone the transition to vegetative maturity are recalcitrant to propagation. Development of effective methodologies for silver birch vegetative propagation are required to increase the efficiency of breeding programs. Conserved miRNAs that were differentially expressed between juvenile and mature silver birch tissues were identified using high-throughput sequencing of small RNA libraries. These differentially expressed miRNAs could potentially be utilized to develop markers indicating the juvenility or maturity of silver birch explants and in vitro cultures. In addition, the obtained results will provide an insight into the molecular mechanisms regulating vegetative phase change in silver birch and other perennial woody plant species.
REVIEW | doi:10.20944/preprints202210.0373.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Rojolele; aromatic rice; intensification system; mutation breeding; transgenic lines
Online: 25 October 2022 (03:10:49 CEST)
Rojolele is an Indonesian traditional rice variety from Klaten (Central Java) that classified as tropical japonica and low land rice which become a premium rice variety and have higher price in the market due to a delicious taste and a fragrance aroma. The agronomic characteristics of Rojolele are having high plant stature with sturdy stems and upright plant shape, thick and rough leaves, strong and deeper root systems, long panicle length, and long duration of life. Rojolele rice cultivation is facing important challenges from drought, diseases, long duration, and lodging. Thus, breeding Rojolele cultivars with resistance to drought, diseases, lodging, and short duration is the major focus for Rojolele rice improvement. Indonesian farmer have learned to successfully cultivate Rojolele by applying practical skills, leading to increase the rice productivity. Molecular breeding program, including quantitative trait loci (QTL), genome-wide association study (GWAS), genomic selection, and genome editing can be applied to improve Rojolele characteristics. In this review, important agronomic and quality traits, intensification system for irrigation and pest control, mutation breeding, transgenic lines, and also future perspectives for Rojolele research were presented. Rojolele is useful for rice breeding program in order to guarantee the food security to overcome increasing population and climate change.
TECHNICAL NOTE | doi:10.20944/preprints202202.0341.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Ctenophora; breeding; comb jelly; cultivation; husbandry; protocol; sea walnut
Online: 25 February 2022 (15:26:33 CET)
Ctenophores are marine organisms attracting significant attention from evolutionary, molecular biology and ecological research. Here we describe an easy and affordable set-up to maintain a stable culture of the ctenophore Mnemiopsis leidyi. The challenging delicacy of the lobate ctenophores can be met by monitoring the water quality, providing the right nutrition, and adapting the handling and tank set-up to their fragile gelatinous body plan. Following this protocol allows stable laboratory lines, a continuous supply of embryos for molecular biological studies, and independence from population responses to environmental fluctuations.
REVIEW | doi:10.20944/preprints202112.0338.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Brinjal; Chlorogenic acid content; Climate smart; Breeding; Molecular markers
Online: 21 December 2021 (13:44:30 CET)
Brinjal is a beautiful vegetable crop with strong nutritional properties specifically folate concentration and total chlorogenic acid content. These vitamins and minerals are very much effective in building up the immune system, whilst chlorogenic acid content protects the human body against heart illnesses, liver issues and diabetes. The quantity of these chemicals changes from cultivar to cultivar largely based upon the location of growth and changing environmental circumstances. Many plant breeding strategies are used to alleviate the losses but have proved to be less successful. Whereas the use of molecular markers and other biotechnology technologies have created a road for creating climate smart brinjal with maximum yields and nutritious contents.
ARTICLE | doi:10.20944/preprints202111.0574.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Zantedeschia aethiopica; X-ray mutagenesis; cultivation; Pectobacterium; mutation breeding
Online: 30 November 2021 (14:42:05 CET)
The development of new cultivars is important for the profitability of the floriculture industry. There are a limited number of cultivars of Zantedeschia aethiopica, an iconic ornamental cut flower, garden plant, and potted plant, due to the incompatibility of interspecific crossings within the genus. Most present-day varieties are the result of spontaneous mutations or classical breeding within the species, followed by a long selection process. Breeders are very interested in the development of a time- and cost-effective method for producing new Z. aethiopica cultivars with novel characteristics. Here, Z. aethiopica mutants were generated by treating seeds with 100 Gy of X-ray radiation. The resulting putative mutants were selected based on particular flowering parameters and compared to non-irradiated, control plants. Over two growing seasons, characteristics such as early flowering, flower size and shape, yield and response to soft-rot disease were monitored and considerable variation was observed among the mutated lines. Out of 319 mutants, 20 lines were selected based on their phenotypes and then propagated and further analyzed. Within this group, only two phenotypes displayed at least five improved flowering properties under natural, Mediterranean conditions. The rest displayed two to four desired combinations of flowering traits, some with great commercial potential.
REVIEW | doi:10.20944/preprints202012.0372.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Vicia faba; genomic resources; mapping population; gene discovery; breeding
Online: 15 December 2020 (10:38:24 CET)
Faba bean (Vicia faba L.), a member of the Fabaceae family, is one of the important food legumes cultivated in cool temperate regions. It holds great importance for human consumption and livestock feed because of its high protein content, dietary fibre, and nutritional value. Major faba bean breeding challenges include its mixed breeding system, unknown wild progenitor, and genome size of ~13 Gb, which is the largest among diploid field crops. The key breeding objectives in faba bean include improved resistance to biotic and abiotic stress and enhanced seed quality traits. Major progress on reduction of vicine-convicine and seed coat tannins, the main anti-nutritional factors limiting faba bean seed usage, have been recently achieved through gene discovery. Genomic resources are relatively less advanced compared to other grain legume species, but significant improvements are underway due to a recent significant increase in research activities. A number of bi-parental populations have been constructed and mapped for targeted traits in the last decade. Faba bean now benefits from saturated synteny‐based genetic maps, along with next-generation sequencing and high-throughput genotyping technologies that are paving the way for marker-assisted selection. Developing a reference genome, and ultimately a pan-genome, will provide a foundational resource for molecular breeding. In this review, we cover the recent development and deployment of genomic tools for faba bean breeding.
REVIEW | doi:10.20944/preprints202010.0149.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: breeding; diversity; genetic engineering; genomics; male sterility; melon; QTLs
Online: 7 October 2020 (09:22:33 CEST)
Melon (Cucumis melo L.) a member of family Cucurbitaceae is extensively cultivated for its fleshy fruits. Based on the specific agro-climatic zones of cultivation as well as concerning the regional preferences, melon displays significant variability phenotypic and biochemical attributes. Below, an effort is put forth to considerably evaluate the scope of achievements while in the growth as well as the enactment of melon breeding programs by employing the newest solutions. Melon breeding has achieved critical milestones throughout the previous century, and we hope this trend will go on to persist down the road. However, studies have to determine new genetic information for genes associated with the challenges imposed by climate change. The identification of valuable hereditary and also metabolic variability in the form of landraces and melon wild relatives will be useful for harvest diversification and also for the broadening of the cultivated melon genetic base. Whereas, considerable information on genomics, and melon metabolomics, is beneficial for dissecting the basis of the inheritance of important traits and their impact on the former characteristics. Overall, we hope the manuscript is going to serve as a crucial resource for the melon breeders.
CONCEPT PAPER | doi:10.20944/preprints202007.0390.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Farmer’s right; food sovereignty; seed production system; conventional breeding
Online: 17 July 2020 (15:22:09 CEST)
Farmer’s right and their sovereignty is an important issue related with intellectual property rights and agrobiodiversity management. To boost farmer’s right, a conceptual hypothesis is proposed where they choose either a new high yielding variety or the existing one and apply conventional breeding approaches to select the seed for next years in their own fields. Although farmers produce seeds traditionally from several years, they have not been guided with scientific discipline to produce sufficient amount of quality seeds. This new concept suggests trained farmers can use breeding approaches to produce quality seed for their own use.
REVIEW | doi:10.20944/preprints202006.0016.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: abiotic stress; biotic stress; biofortification; breeding; French bean; QTLs
Online: 3 June 2020 (09:43:01 CEST)
French bean (Phaseolus vulgaris L.) a member of family Leguminosae is a useful source of protein (∼22%), minerals (folate), vitamins and fibre. Abiotic and biotic stresses are the constraints to high yield and production of French bean. Varieties reluctant to diseases as well as abiotic stresses is among the top breeding objectives for the French bean. Mendelian ratios could know the genetically reliable forms of resistance, whereas it's more robust to understand the intricate kinds, often referred to as quantitative trait loci (QTL). Here, we review and compile the information from the studies related to the identification of QTLs for critical biofortification traits, biotic and abiotic stresses in French bean. Successful map-based cloning requires QTLs represent single genes which could be isolated in near-isogenic lines, and also the genotypes could be unambiguously inferred by progeny testing. Overall, this information will be useful for directing the French bean breeders to select a suitable method for the inheritance evaluation of quantitative traits and determining the novel genes in germplasm resources to ensure that much more potential of genetic information may be uncovered.
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: rice; yield; HYV; Tongil; indica; japonica; SNP; molecular breeding
Online: 12 May 2020 (05:56:38 CEST)
The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.
ARTICLE | doi:10.20944/preprints201903.0115.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: machine learning; agroclimactic modelling; crop breeding and genetics; GxE
Online: 11 March 2019 (07:59:22 CET)
Crop breeding is as ancient as the invention of cultivation. In essence, the objective of crop breeding is to improve plant fitness under human cultivation conditions, making crops more productive while maintaining consistency in life cycle and quality. The applications of predictive breeding has been gaining momentum in agricultural industry and public breeding programs for the last decade, in the aftermath of genomic selection being recognized and widely applied for accelerating genetic gain in breeding programs. The massive amounts of data that has been generated by industry and farmers year after year through several decades has finally been recognized as an asset. A wide range of analytical methods such as machine learning, deep learning and artificial intelligence that were initially developed for diverse quantitative disciplines are now being adopted to crop breeding decision making processes. New technologies are currently being developed that would enable integration of data from various domains such as geospatial variables and a multitude of phenotypic responses as well as genetic information, in order to identify, develop and improve crop faster via partial or full automation of the decisions that pertain to variety development. Here we will discuss and summarize efforts from public and private domains for predictive analytics, and its applications to crop breeding and agricultural product development, and provide suggestions for future research.
ARTICLE | doi:10.20944/preprints201805.0144.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: citrus breeding; diversity; genetic similarity; Lime; molecular markers; PCR
Online: 9 May 2018 (11:05:37 CEST)
Acid lime [Citrus aurantifolia (Christm.) Swingle] is a fruit crop, enriched with high commercial value and is cultivated in 60 out of 75 districts representing all geographical landscapes of Nepal. Lack of high yielding cultivars is probably one of the main reason for its extremely reduced productivity which warrants a deep understanding of genetic diversity in existing germplasm. Hereby, we aim to access the genetic diversity of acid lime germplasm cultivated at 3-different ecological gradients of eastern Nepal employing PCR-based Inter-Simple Sequence Repeats markers (ISSR). Altogether, 21 polymorphic ISSR markers were used to assess the genetic diversity in 60 acid lime cultivars sampled from different geographical locations. Analysis of binary data matrix was performed on the basis of bands obtained, scoring of the data was done accordingly, and principal coordinate analysis and phenogram were constructed using different computer algorithms. ISSR profiling yielded 234 amplicons, of which 87.18% were found to be polymorphic. The number of amplified fragments ranged from 7-18 with amplicon size ranging from 250-3200 bp. The NTSYS based Cluster analysis using UPGMA algorithm taking Dice Similarity coefficient separated 60 accessions into 2-major and 3-minor clusters. The genetic diversity analysis revealed the highest for Terai and the lowest for High-hill zone. Cluster I comprised of accessions from High-hill and Mid-hill regions revealing the close genetic relationship, whereas cluster II comprised of accessions from all three agro-ecological zones and the exotic varieties. Furthermore, our results revealed the accessions harvested from different geographical gradients were not genetically distinct, but highest diversity was observed in Terai accessions in comparison to the regions belonging to the High and Mid-hills. Thus, our data indicate that the ISSR provides a better option for evaluating the genetic diversity of Nepalese Acid Lime cultivars and furnished significant information, assisting parental selection in current and future breeding programs and germplasm conservation which ultimately may help to provide a technological breakthrough for the farmers of the developing country like Nepal.
ARTICLE | doi:10.20944/preprints202311.1565.v1
Subject: Biology And Life Sciences, Horticulture Keywords: goji berry; breeding; plant resistance; Whole Genome Sequencing; BODYGUARD genes.
Online: 26 November 2023 (05:17:31 CET)
Goji berries, long valued in Chinese medicine and cuisine for their wide range of medicinal benefits, are considered a 'superfruit' and functional food. Out of the nearly 100 Lycium species known for their genetic diversity, L. barbarum and L. chinense currently dominate the market. Due to increasing market demand and concerns about food safety and sustainability, Europe and the Americas are expanding the local goji berry production, using as starting material plants originated from China. European breeding programs are focusing on Lycium to develop varieties adapted to local conditions, especially in response to climate change. By 2023, Romania registered seven goji berry varieties, both from L. barbarum and L. chinense species, without incorporating local germplasm. Advanced genomic studies, including NGS sequencing of five cultivated and three wild goji berry plant genomes, have been conducted to analyse their genetic variation, with a particular focus on the BODYGUARD 3 and 4 genes. This research uncovered significant differences between cultivated and wild genotypes, both in the entire genome and specifically in the BODYGUARD genes, providing crucial insights for goji berry breeders to support the development of goji berry cultivation in Romania.
ARTICLE | doi:10.20944/preprints202304.1098.v2
Subject: Engineering, Energy And Fuel Technology Keywords: European DEMO; Helium Cooled Pebble Bed; Tritium Breeding Blanket; Fusion
Online: 25 June 2023 (04:44:52 CEST)
Significant design efforts were undertaken during the Pre-Concept Design (PCD) phase of the European DEMO programme to optimize the Helium Cooled Pebble Bed (HCPB) breeding blanket. A gate review was conducted for the entire European DEMO programme at the conclusion of the PCD phase. This article presents a summary of the design evolution and the rationale behind the HCPB breeding blanket concept for the European DEMO. The main performance metrics, including nuclear, thermal hydraulics, thermal mechanical, and tritium permeation behaviors, are reported. These figures demonstrate that the HCPB breeding blanket is a highly effective tritium-breeding and robust driver blanket concept for the European DEMO. In addition, three alternative concepts of interest were explored. Furthermore, this article outlines the upcoming design and R&D activities for the HCPB breeding blanket during the Concept Design phase (2021-2027).
ARTICLE | doi:10.20944/preprints202305.1530.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Abiotic stresses; Molecular breeding; Machine learning; Responsive genes; Adapted crops
Online: 22 May 2023 (15:29:12 CEST)
Plants have a natural protective process of altering their genetic molecules in response to changing environments. To uncover the genetic potential of plants, it is crucial to understand how they adapt to adverse conditions by analyzing their genetic molecules. In the study, we focused on understanding the responsive genes of tomatoes under drought conditions. We analyzed RNASeq data from different Tomato genotypes, tissue types, and different drought durations. We used a time series scale to identify early and late drought-responsive gene modules and applied a machine learning method to identify the best responsive genes. We found six candidate genes of Tomato (ASCT, FLA2, BAG5, DCL2b, NFP7.3, and ADC1) that were responsive to drought. We further constructed their protein-protein interaction network to identify their potential interactors and found them drought responsive proteins. The candidate genes can help to explore the adaptation of tomato plants under drought conditions. The identification of these candidate genes and modules can have far-reaching implications for molecular breeding and genome editing in Tomato, providing insights into the molecular mechanisms that underlie drought adaptation. This research underscores the importance of the genetic basis of plant adaptation, particularly in changing climates and growing populations.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Mollusc; selective breeding; gene editing; disease resistance; transgenesis; CRISPR/Cas9
Online: 15 October 2020 (16:06:27 CEST)
Molluscan aquaculture is a major contributor to global seafood production, but is hampered by infectious disease outbreaks which can cause serious economic losses. Selective breeding has been widely used to improve disease resistance in major agricultural and aquaculture species, and has clear potential in molluscs, albeit its commercial application remains at a formative stage. Advances in genomic technologies, especially development of cost-efficient genomic selection, have potential to accelerate genetic improvement. However, tailored approaches are required due to the distinctive reproductive and lifecycle characteristics of molluscan species. Transgenesis and genome editing, in particular CRISPR/Cas systems, have been successfully trialled in molluscs, and may further understanding and improvement of genetic resistance to disease through targeted changes to the host genome. Whole organism genome editing is achievable on a much greater scale compared to other farmed species, making genome-wide CRISPR screening approaches plausible. This review discusses the current state and future potential of selective breeding, genomic tools, and genome editing approaches to understand and improve host resistance to infectious disease in molluscs.
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Saiga; antelope; conservation breeding; reintroduction; Convention on Migratory Species (CMS)
Online: 26 February 2020 (10:49:20 CET)
Saiga (Saiga tatarica) was extirpated in China. Since Mid-1980s, attempts have been made for revival the species in the country, however, only a breeding herd of Saiga was successfully established at Wuwei, Gansu, China. The reintroduced Saiga population experienced a bumpy growth. Then, the population collapsed following the catastrophe die-off in the Saiga ranging countries in Central Asia, then population started to rebound when 6 new lams were born in 2019. After reviewing the population trend and conservation breeding of Saiga in China, we concluded that to establish a migratory species that needs vast range size like Saiga on central Asia steppe, an international collaboration is needed for introducing new genes. We recommend China to ratify the CMS in order to facilitate international conservation efforts to restoring the species in its former range.
REVIEW | doi:10.20944/preprints201808.0093.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Triticum durum, cropping systems, microbiome, fertilization, tillage, breeding, environmental footprint
Online: 5 August 2018 (12:04:57 CEST)
The global demands for various grains including durum wheat (Triticum durum Desf.) are expected to increase substantially in the coming years due to ever-growing human population’s needs for food, feed and fuel. Thus, providing consistent or increased durum grain to the world market is one of the priorities for policy-makers, researchers, and farmers. What are the major achievements in agronomic advancement for durum wheat cultivation in recent decades? How might the current cropping systems be improved to increase crop yield and quality and improve resource use efficiencies while minimizing input costs and decreasing negative impact on the environment? Canada is one of the major durum wheat producers in the world, as Canada contributes about 50% to global trade of durum grain. Canada’s research achievements in durum wheat might serve as a guide for advancing the cultivation of the crop in other regions/countries on the planet. This review summarizes the major Canadian research findings in the aspects of durum wheat agronomics during the period 2001 to 2017 years. It highlights the main advancements in seeding and tillage, crop rotation and diversification, and use of pulse-induced microbiomes to improve soil health and feedback mechanism. The genetic gain and breeding for resistance against abiotic and biotic stresses are discussed. Finally, we identified main constraints and suggested some near-term research priorities. The research findings highlighted in this review will be of use for other areas on the planet to increase durum wheat productivity, improve soil fertility and health, and enhance long-term sustainability.
ARTICLE | doi:10.20944/preprints201803.0120.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Oryza sativa; genetic diversity; tidal swamp; breeding and conservation programs
Online: 15 March 2018 (06:50:32 CET)
Tidal swamp rice has long been cultivated by the local people of the South Kalimantan, Indonesia. This germplasm possess some important traits for adapted to a wide range of abiotic and biotic stresses. In this study, a total of sixteen cultivars of this germplasm, consisting of fifteen of the South Kalimantan Province and one of Sumatera Island, Indonesia (an outgroup) were analyzed, phylogenetically based on the chloroplast trnL-F and nuclear intergenic spacer region (IGS). The results showed that this germplasm has a relatively more extraordinary genetic diversity than other local rice germplasm. In a nucleotide level, this germplasm showed a genetic diversity of 0.61 for nuclear IGS and 0.58 for trnL-F. The phylogenetic reconstruction also exhibited that this germplasm has the unique illustration of phylogenetic trees, particularly for the combined sequence datasets. Thus, the results of our study would provide useful information for further understanding of evolutionary relationships of this germplasm and facilitate the efficient utilization of valuable genes for genetic improvement, particularly in the tidal swamp areas.
REVIEW | doi:10.20944/preprints201705.0200.v1
Subject: Chemistry And Materials Science, Food Chemistry Keywords: Diet: Functional foods: Western foods: Mediterranean foods: Feeding, Plant breeding
Online: 29 May 2017 (17:38:59 CEST)
There is evidence that optimal nutrition is fundamental to human health and in the prevention of non-communicable diseases (NCDs) later in adult life. The identification, production and consumption of functional foods worldwide can increase health benefits for all who can access and afford such foods subject to advice from nutritionists. Recent meetings organized by the health agencies, give a crucial opportunity to make nutrition, a central part of the post-2015 sustainable human and agricultural development agenda. The aim of discussions in these meetings was to provide functional crops and foods to achieve optimal health by prevention of NCDs. It is possible that these efforts might ensure that the goals and targets set in the agenda are adequate to address the many challenges of global undernutrition as well as obesity which are major risk factors of NCDs. In many developing and middle income countries, food security provided by the governments, in one sense understandably, gave least consideration to functional foods supply and the prevention of obesity and metabolic syndrome, resulting in to emergence of NCDs. The Thailand Declaration reiterates that commitments to eradicate hunger and undernutrition as well as over-nutrition, and to increase investments in effective interventions; designers foods and designers crops. However, in planning coherent policies, our past experience on rapidly absorbed, energy-rich processed foods should be taken in to account while developing sustainable food systems. The food industry should be educated to exploit the expertise of food scientists and health professionals in designing functional foods taking cognizance of manufacturing and processing. Similarly, agriculture scientists may be actively involved in educating farmers so as to grow cash crops providing functional foods. The aim should be to achieve an increase in the availability of functional foods to an extent, or by a policy, by which such foods are available to poors, at affordable cost to prevent hunger and undernutrition and related diseases as well as NCDs. In addition our efforts might help in developing an international consensus on how to approach the development of new designer foods by farmers and food industry to produce low glycemic index foods. Such efforts may establish an international framework for the prevention of NCDs, so that human susceptibility to these diseases is substantially diminished.
ARTICLE | doi:10.20944/preprints202003.0442.v1
Subject: Engineering, Automotive Engineering Keywords: Terrain Referenced Navigation (TRN); Federated Filter; Interferometric Radar Altimeter (IRA); Batch Processing; Auxiliary Particle Filter; Digital Elevation Model (DEM); Captive Flight Test
Online: 31 March 2020 (04:29:41 CEST)
Autonomous unmanned aerial vehicles (UAVs) require highly reliable navigation information. Generally, navigation systems with the inertial navigation system (INS) and global navigation satellite system (GNSS) have been widely used. However, the GNSS is vulnerable to jamming and spoofing. The terrain referenced navigation (TRN) technique can be used to solve this problem. In this study, to obtain reliable navigation information even if a GNSS is not available or the degree of terrain roughness is not determined, we propose a federated filter based INS/GNSS/TRN integrated navigation system. we also introduce a TRN system that combines batch processing and an auxiliary particle filter to ensure stable flight of UAVs even in a long-term GNSS-denied environment. As an altimeter sensor for the TRN system, we use an interferometric radar altimeter (IRA) to obtain reliable navigation accuracy in high altitude flight. In addition, a parallel computing technique with general-purpose computing on graphics processing units (GPGPU) is applied to process a high resolution terrain database and a nonlinear filter in real time on board. Finally, we verify the performance of the proposed system through software-in-the-loop (SIL) tests and captive flight tests in a GNSS unavailable environment.
ARTICLE | doi:10.20944/preprints202312.0627.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Pollen viability; in vitro pollen germination; preservation; wheat breeding; heat tolerance
Online: 8 December 2023 (12:36:19 CET)
Wheat pollen, characterized by its short lifespan, exhibits rapid germination after anthesis. The preservation of wheat pollen is contingent upon environmental factors, including temperature, relative humidity, light, and wind. The objective is to develop a method for preserving wheat pollen effectively, specifically for the purpose of breeding. The short longevity of wheat pollen grains renders it impractical to conduct tests for pollen viability and in vitro germination on a large scale. Herein, the impact of storage temperatures and duration was assessed on pollen viability and in vitro germination to optimize storage conditions for preserving pollen viability. Pollen grains from 50 diverse spring wheat genotypes, each with three replicates, were harvested and stored at temperatures of 22°C, -20°C, and 4°C. Subsequently, pollen viability and in vitro germination rates were determined after storage of 1, 3, and 6 days. The results revealed that storage temperatures, durations, genotypes, and their interactions had a statistically significant impact on both pollen viability and in vitro germination. Notably, when pollen was kept at 22°C, almost all genotypes exhibited a loss of pollen viability and in vitro germination after 1, 3, and 6 days of storage. Likewise, storage at -20°C failed to extend pollen germination. However, at a storage temperature of 4°C, the pollen of 36 wheat genotypes exhibited a range of 6-14% in vitro pollen germination and remained viable even for 6 days. Simple linear regression analysis further revealed a significant negative correlation between pollen viability, in vitro germination, and storage time and temperature. In conclusion, our findings underscore 4°C as the optimal temperature for preserving pollen viability and in vitro pollen germination in spring wheat for up to 6 days. The results of the present study suggests that pollen viability of wheat is genotype de-pendent, storage temperature and storage duration. Thus, the 36 wheat genotypes identified during the present work could be efficiently maintained at 4◦C for short-term storage (6 days) and could be further used for genetics and breeding purposes.
REVIEW | doi:10.20944/preprints202309.0392.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: wheat dwarf virus; WDV; resistance; mastrevirus; resistance genes; geminiviridae; resistance breeding
Online: 6 September 2023 (10:15:48 CEST)
Wheat dwarf disease (WDD) is an important disease of monocotyledonous species, including economically important cereals. The causative pathogen, the wheat dwarf virus (WDV), is a monopartite Mastrevirus that has a circular single-stranded (ss)DNA genome and is transmitted persistently and propagatively mainly by the leafhopper Psammotettix alienus. The disease can induce high yield losses in many European countries in a range of 20-100%. Due to climate change the periods of vector activity increased and the vectors spread to new habitats, leading to an increased importance of WDV in large parts of Europe. In the light of integrated pest management approaches cultivation practices and the use of resistant/tolerant host plants are currently the only effective methods for controlling WDV. To date, there is limited knowledge of the pathosystem and epidemiology of the disease. The few sources of genetic tolerance, indicate the need for further research. Considering the economic importance of the disease, and its likely increasing relevance in the coming decades, this review was prepared to compile and update knowledge on aspects of WDV.
ARTICLE | doi:10.20944/preprints202306.1567.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: Kentish plover; life-history; reproductive output; breeding behavior; inland arid area
Online: 21 June 2023 (14:48:00 CEST)
Due to the influence of bio-geographical and environmental factors, as well as anthropogenic landscape features, organism shows different reproductive strategies among different populations. There is lack of detailed information on the reproductive biology of Kentish plover Charadrius al-exandrinus in arid lands in Central Asia. In this study, we summarized the characteristics of the reproductive biology of three geographically distinct plover populations in Aibi Lake in the Northwestern Xinjiang, Taitema Lake in the Southern Xinjiang and artificial reservoirs around Urumqi City in Northern Xinjiang respectively, based on 440 eggs of 158 nests observed and ana-lyzed from April to July of 2019 and 2020. We find that there is no significant difference in clutch size among the three populations. However, the egg size of Taitema Lake population is signifi-cantly larger than those of the other two populations, whilst egg volume and clutch volume of ar-tificial reservoirs population are significantly larger than that of Aibi Lake. With the postpone-ment of laying date, the northern and northwestern populations respectively show the character-istics of small clutch size and relatively small egg size, and decrease of reproductive outputs. The heavier female plovers in Taitema Lake lays eggs earlier, and there was significantly positive cor-relation between the female body mass and the clutch size and egg size. The tarsometatarsus length of the female plovers was significantly positively correlated with the reproductive output in all three populations. The model selection results show that female body size and ambient tem-perature restrict the egg size and reproductive output of Kentish plovers, which is consistent with the upper limit hypothesis of the maternal condition and the maternal constraint. Our data sup-port that Kentish plover show distinct flexibility in breeding strategies to cope with the harsh nat-ural environment in arid lands of Xinjiang, China. The results of relatively high average clutch size and average egg size imply that saline wetlands in Western China are important breeding habitats for Kentish plover.
ARTICLE | doi:10.20944/preprints202305.0809.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Camelina sativa; oilseed crop; cover crop; plant breeding; synthetic population; agrobiodiversity
Online: 11 May 2023 (06:01:42 CEST)
In recent years, the interest in increasingly sustainable agriculture has also turned attention towards new crops which could enter the food chain as new protein and oil sources or that can be used as new cover crops. In this scenario, Camelina sativa is a perfect crop to study. Camelina is an annual herbaceous plant belonging to the Brassicaceae which is interesting for its oil content, since the seeds contain about 40% of oils, with a high level of polyunsaturated fatty acids (30-40% alpha linolenic acid, 15-25 % linoleic acid, 15% oleic acid and about 15% eicosenoic acid). It is a hexaploid species (2n = 40, genome size ~782 Mb) characterized by rapid growth, short life cycle (85-100 days for spring varieties, 190-210 for autumn varieties) and low input cultivation needs. All these traits make it suitable for use in marginal areas. However, its use in feed and food is limited by the presence of glucosinolates (GLS). GLS are sulfur molecules involved in plant defense. In recent years, they have been studied not only as anti-nutritionals, but also for their anti-carcinogenic effects against chronic inflammatory and heart diseases and for their use as natural pesticides. Given the recent interest in camelina and its highly nutritious oil, eight pure lines and a synthetic population were compared in two different growing periods, spring and winter. In this work, the genetic materials were characterized for different phenotypic traits, yields and yield components, bromatological and glucosinolate content. The results confirmed that in North Italy camelina has higher yields if cultivated in the autumn-winter period (about 2 t/ha vs 0.6 t/ha), furthermore, a negative correlation was found between spring and winter yields, indicating that varieties that produce more in winter cultivation produce less in spring cultivation. Moreover, to our knowledge, it is the first work in which a synthetic population of Camelina sativa has been tested and proved to be a valid solution for use in various environments both for its adaptability and for the low content of glucosinolates (about 17 mmol/ kg).
ARTICLE | doi:10.20944/preprints202109.0102.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: abiotic stress; HSFs; genomics; gene ontology; maize breeding; protein 3D structures
Online: 6 September 2021 (13:57:37 CEST)
Heat shock transcription factors (HSFs) participate in regulating many environmental stress responses and biological processes in plants. Maize (Zea mays L.) is a major cash crop that is grown worldwide. However, the growth and yield of maize are affected by several adverse environmental inputs. Therefore, investigating the factors that regulate maize growth and development and resistance to abiotic stress is an essential task for developing stress-resilient maize varieties. Thus, a comprehensive genome-wide identification analysis was performed to identify HSFs in the maize genome. The current study identified 25 ZmHSFs, randomly distributed throughout the maize genome. Phylogenetic analysis revealed that ZmHSFs are divided into three classes and 13 sub-classes. Gene structure and protein motif analysis supported the results obtained through the phylogenetic analysis. Domain analysis showed the DNA-binding domain to be the most conserved region of ZmHSFs. Segmental duplication is shown to be responsible for the expansion of ZmHSFs. Most of the ZmHSFs are localized inside the nucleus, and the ZmHSFs which belong to the same group show similar physio-chemical properties. The 3D structures revealed comparable conserved ZmHSFs protein structures. RNA-seq analysis revealed a major role of class A HSFs including, ZmHSFA-1a and ZmHSFA-2a in all the maize growth stages, i.e., seed, vegetative, and reproductive development. Furthermore, ZmHSFs displayed an obvious spatiotemporal expression. Under abiotic stress conditions (heat, drought, cold, UV, and salinity), members of class A and B ZmHSFs are induced. Gene ontology (GO) annotation analysis indicated a major role of ZmHSFs in resistance to environmental stress and regulation of primary metabolism. Further, the protein-protein interaction analysis showed that ZmHSFs interact with several molecular chaperons and major stress-responsive proteins. To summarize, this study provides novel insights for functional studies on the ZmHSFs in maize breeding programs.
ARTICLE | doi:10.20944/preprints202010.0022.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: unmanned aerial vehicle; grain sorghum; herbicide injury; remote sensing; sorghum breeding
Online: 1 October 2020 (15:47:27 CEST)
Manual evaluation of crop injury to herbicides is time-consuming. Unmanned aircraft systems (UAS) and high-resolution multispectral sensors and machine learning classification techniques have the potential to save time and improve precision in the evaluation of herbicide injury in crops, including grain sorghum (Sorghum bicolor L. Moench). The objectives of this research were to (1) evaluate three supervised classification algorithms (support vector machine, maximum likelihood, and random forest) for categorizing high-resolution UAS imagery to aid in data extraction and (2) evaluate the use of vegetative indices (VIs) collected from UAV imagery as an alternative to traditional methods of visual herbicide injury assessment in mesotrione-tolerant grain sorghum breeding trials. An experiment was conducted in a randomized complete block design using a factorial treatment arrangement of three genotypes by four mesotrione doses. Herbicide injury was rated visually on a scale of 0 (no injury) to 100 (complete plant mortality). The UAS flights were flown at 9, 15, 21, 27, and 35 days after treatment. Results show the SVM algorithm to be the most consistently accurate, and high correlations (r = -0.83 to -0.94; p < 0.0001) were observed between the normalized difference vegetative index (NDVI) and ground-measured herbicide injury. Therefore we conclude that VIs collected with UAS coupled with machine learning image classification, has the potential to be an effective method of evaluating mesotrione injury in grain sorghum.
ARTICLE | doi:10.20944/preprints202008.0423.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: gene editing; mutagenesis; genetically modified; GMO; crop breeding; RNP; genetic screening
Online: 20 August 2020 (04:34:55 CEST)
CRISPR-Cas9 technology allows the modification of DNA sequences in vivo at the location of interest. Although CRISPR-Cas9 can produce genomic changes that do not require DNA vector carriers, the use of transgenesis for stable integration of DNA coding for gene-editing tools into plant genomes is still the most used approach and it can generate unintended transgenic integrations, while Cas9 prolonged expression can increase cleavage at off-target sites. In addition, the selection of genetically modified cells from millions of treated cells, especially plant cells, is still challenging. These downfalls can be avoided with the delivery of preassembled ribonucleoprotein complexes (RNPs) composed of purified recombinant enzyme Cas9 and in vitro- transcribed guide RNA (gRNA) molecules in a protoplast system. We therefore aimed to develop the first DNA-free protocol for gene-editing in maize and introduced RNPs into their protoplasts with PEG 4000. We performed effective transformation of maize protoplasts using different gRNAs sequences targeting the inositol phosphate kinase gene and applying two different exposure times to RNPs. Using low-cost Sanger sequencing protocol, we observed an efficiency rate of 0.85 up to 5.85%, which is equivalent to DNA-free protocols used in other plant species. A positive correlation was displayed between exposure time and mutation frequency. Mutation frequency was gRNA sequence- and exposure time-dependent. In summary, we demonstrated the suitability of RNP transfection as an effective screening platform for gene-editing in maize. This efficient and relatively easy assay method for selection of gRNA suitable for editing of gene of interest will be highly useful for genome editing in maize, since genome size and GC-content are large and high in maize genome, respectively. Nevertheless, the large amplitude of mutations at target site requires scrutiny when checking mutations at off-target sites and potential safety concerns.
Subject: Biology And Life Sciences, Plant Sciences Keywords: drought stress; osmotic stress; rice; transcription factors; stress signaling; qtl; breeding
Online: 24 December 2019 (11:39:50 CET)
Many studies were done in the development of drought stress-tolerant transgenic plants, including crop plants. Rice is considered to be a vital crop target for improving drought stress tolerance. Much transgenic rice showed improved drought stress tolerance was reported to date. They are genetically engineered plants that are developed by using genes that encode proteins involved in drought stress regulatory networks. These proteins include protein kinases, transcription factors, enzymes related to osmoprotectant or plant hormone synthesis, receptor-like kinase. Of the drought stress-tolerant transgenic rice plants described in this review, most of them display retarded plant growth. In crop crops, plant health is a fundamental agronomic trait that can directly affect yield. By understanding the regulatory mechanisms of retarded plant growth under drought stress, conditions are necessary precursors to developing genetically modified plants that result in high yields.
REVIEW | doi:10.20944/preprints201912.0316.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Peanut; plant breeding; research; funding; genomics; INERA; cultivar; selection; Arachis hypogaea
Online: 24 December 2019 (11:07:38 CET)
Groundnut (Arachis hypogaea L.) is a major food and cash crop in Burkina Faso. Due to growing demand for raw oilseeds, there is an increasing interest in groundnut production from traditional rain-fed areas to irrigated environments. However, despite implementation of many initiatives in the past to increase groundnut productivity and production, the groundnut industry still struggles to prosper, due to several constraints including minimal development research and fluctuating markets. Yield penalty due to drought and biotic stresses continue to be a major drawback for groundnut production. This review traces progress in the groundnut breeding that started in Burkina Faso before the country’s political independence in 1960 through to present times. Up to the 1980s, groundnut improvement was led by international research institutions such as IRHO (Institute of Oils and Oleaginous Research) and ICRISAT (International Crops Research Institute for the Semi-Arid Tropics). However, international breeding initiatives were not sufficient to establish a robust domestic groundnut breeding programme. This review also provides essential information about opportunities and challenges of groundnut research in Burkina Faso, emphasising the need for institutional attention to genetic improvement of the crop.
Subject: Biology And Life Sciences, Plant Sciences Keywords: solanum tuberosum; potato breeding; potato genebank; biotechnology; wild potato species; Solanaceae
Online: 28 July 2019 (14:25:23 CEST)
The goal of germplasm enhancement is to introgress traits from wild crop relatives into cultivated material and eventually cultivars. It seeks to restore genetic diversity that has been lost over time or to augment cultivated material with novel alleles that improve parents in breeding programs. This paper discusses potato germplasm enhancement efforts in the past, focusing on effective examples such as disease resistance and processing quality. In addition, it outlines new strategies for enhancement efforts, shifting the focus from evaluating phenotypes to tracking and manipulating specific DNA sequences. In the genomics era, germplasm enhancement will increasingly be focused on identifying and introgressing alleles rather than traits. Alleles will come from a broad pool of genetic resources that includes wild species relatives of potato, landraces, cultivated potato itself, and distantly related species. Genomics tools will greatly increase the efficiency of introgressing multigenic traits, and will make it possible to identify rare alleles and utilize recessive alleles.
ARTICLE | doi:10.20944/preprints201808.0536.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Breeding population, internal standards, matrix effects, plant volatiles, SPME, odorant analysis
Online: 30 August 2018 (21:22:47 CEST)
Headspace solid phase microextraction (HS-SPME) coupled to gas chromatography-mass spectrometry is widely employed for volatile analyses of plants, including mapping populations used in plant breeding research. Studies often employ a single internal surrogate standard, even when multiple analytes are measured, with the assumption that any relative changes in matrix effects among individuals would be similar for all compounds, i.e. matrix effects do not show Compound × Individual interactions. We tested this assumption using individuals from two plant populations, an interspecific grape (Vitis spp.) mapping population (n = 140) and a tomato (Solanum spp.) recombinant inbred line (RIL) population (n = 148). Individual plants from the two populations were spiked with a cocktail of internal standards (n = 6, 9, respectively) prior to HS-SPME-GC-MS. Variation in the relative responses of internal standards indicated that Compound × Individual interactions exist but were different between the two populations. For the grape population, relative responses among pairs of internal standards varied considerably among individuals, with a maximum of 249% relative standard deviation (RSD) for the pair of [U13C]hexanal and [U13C]hexanol. However, in the tomato population, relative responses of internal standard pairs varied much less, with pairwise RSDs ranged from 8% to 56%. The approach described in this paper could be used to evaluate the suitability of using surrogate standards for HS-SPME-GC-MS studies in other plant populations.
ARTICLE | doi:10.20944/preprints202306.2197.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: climate change; global warming; indigenous cultivars; berry composition; clonal selection; grape breeding
Online: 30 June 2023 (09:43:29 CEST)
In the case of indigenous grapevine varieties, the aim of clonal selection is twofold: to improve their technological cultivation problem while preserving the varietal character. As the sensitivity of perennial crops to climate change becomes more pronounced, clonal selection, which is already very time-consuming for perennial woody crops, may take even longer. In Badacsony, clonal selection breeding of the ‘Kéknyelű’ and ‘Juhfark’ varieties was started in the early 2000s. The problem mentioned above in cultivation technology is the poor fertility of ‘Kéknyelű’ (functionally female-flowered variety), while in the case of ‘Juhfark’ the high susceptibility to grey rot (Botrytis). Based on 11 years of data significant difference in yield between clone B.2. and the base variety was found. In this comparison the year clusters also gave different values, as in years belonging to cluster 1 the ’Kéknyelű’ yielded more than in another year. Both clones of ‘Kéknyelű’ matured with significantly lower pH compared to the base variety. ‘Kéknyelű' is renowned for the distinctive variety character of its wine, which is said to be acidic. Given the acidic nature of ‘Kéknyelű’ wine and the expected increase in must degrees and pH due to climate change, these distinctions may be beneficial in the future. Daily meteorological parameters were also recorded in the years under study, and different indexes were calculated for both of varieties for different phenological periods. The years were classified into 3 clusters and the harvest data were analyzed within each cluster. In the case of 'Kéknyelű' our results revealed significant differences in yield between vintage clusters for clone B.2. However, clone B.1 demonstrated distinct KMW and pH values. Both 'Kéknyelű’ clones have produced a substantially higher incidence of Botrytis infection in cluster 2 years than in cluster 3 years. Botrytis infection only showed statistically significant differences between year clusters for ‘Juhfark’. It is intriguing that in most years, the rotting rate was lower in both clones, especially in year clusters 1 and 3 when the overall rate of Botrytis infection was quite low. Our results highlighted the year-round sensitivity of the two varieties studied and the difficulties of clonal selection.
ARTICLE | doi:10.20944/preprints202305.0758.v1
Subject: Biology And Life Sciences, Behavioral Sciences Keywords: Honeybee bred lines; Apis mellifera L.; Controlled breeding; Defensive behavior; Chemical pheromone
Online: 10 May 2023 (14:03:49 CEST)
Honey bees (Apis mellifera L.) express complex behavioral patterns (aggressiveness) to exhibit defensive mechanisms for their survival. Their phenotypic expression of aggressive behavior is influenced by internal and external stimuli. Knowledge of this behavior is recently important though beekeepers are still faced with the challenges of selecting aggressive and less-aggressive bred lines. Field evaluation of aggressiveness among bred lines of honey bees is required to overcome the challenges. Chemical cues (alarm pheromone and isopentyl acetate mixed with paraffin oil), physical and visual stimuli (dark leather suede, colony marbling and suede jiggling) were used to evaluate aggressiveness and orientation among five bred lines of honeybee colonies. Our results showed that both chemical assays recruited bees but the time of recruitment was significantly lower for alarm pheromone. Honeybees’ response to both assays culminated to stings which differed among bred lines for alarm pheromone and paraffin when colonies were marbled. Honeybee aggression varied among bred lines and was higher in more aggressive bred lines compared to less-aggressive bred lines. Our findings suggest that it is crucial to repeatedly evaluate orientation aggressiveness at the colony level and among bred lines when selecting breeding colonies.
REVIEW | doi:10.20944/preprints202304.0549.v1
Subject: Biology And Life Sciences, Forestry Keywords: forest plants; genetic breeding; omics technologies; multi-omics integration; gene regulatory networks
Online: 19 April 2023 (05:31:46 CEST)
In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, the growing global demand for new forest plant varieties with higher wood production capacity and better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted selection, and genomic selection. In the recent past, diverse omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and metabolomics, have been developed rapidly, providing powerful tools for the precision genetic breeding of forest plants. Genomics lays a solid foundation for understanding complex biological regulatory networks, while other omics technologies provide different perspectives at different levels. Multi-omics integration has combined the different omics technologies, becoming a powerful tool for genome-wide functional element identification in forest plant breeding. This review summarizes the recent progress of omics technologies and their applications in the genetic studies of forest plants. It will provide forest plant breeders with an elementary knowledge of multi-omics techniques for future breeding programs.
ARTICLE | doi:10.20944/preprints202103.0132.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Wine yeast; malic acid; pH; breeding; Malo Lactic Fermentation; Marker Assisted Selection
Online: 3 March 2021 (12:43:08 CET)
Background Natural Saccharomyces cerevisiae yeast strains exhibit very large genotypic and phe-notypic diversity. Breeding programs taking advantage of this characteristic, are widely used for yeast selection in the wine industry, especially in the recent years when winemakers need to adapt their production to climate change. The aim of this work was to evaluate a Marker Assisted Se-lection (MAS) program to improve malic acid consumption capacity of Saccharomyces cerevisiae in grape juice. Methods Optimal individuals of two unrelated F1-hybrids were crossed to get a new genetic background carrying many “malic consumer” loci. Then, eleven QTLs already identified were used for implementing the MAS breeding program. Results By this way, extreme individuals able to consume more than 70% of malic acid in grape juice were selected. These individuals were tested in different enological matrixes and compared to their original parental strains. They greatly reduced the malic acid content at the end of alcoholic fermentations, they appeared to be robust to the environment and accelerate the ongoing of malo-lactic fermentations by Oenococcus oeni. Conclusions This study illustrates how MAS can be efficiently used for selecting industrial Saccharomyces cerevisiae strains with outlier properties for winemaking.
ARTICLE | doi:10.20944/preprints202101.0164.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Arbutus unedo L. Artificial Pollination, Breeding, Drought stress, Microscopy, Pollen, Physiological performance
Online: 8 January 2021 (14:08:49 CET)
Arbutus unedo L. is a small Ericaceae tree with a circum-Mediterranean distribution. It has a huge ecological impact on southern Europe forests and a great economic importance, as a source of phytochemicals with bioactive properties and for fruit production. On the foreseen climate change context, breeding towards drought tolerance is necessary in order to ameliorate plant performance. The aim of this work was therefore to study the reproduction mechanisms of strawberry tree, obtain new genetic combinations by hybridization and select genotypes more tolerant to drought stress. A morphological analysis of flowers and pollen was carried out, and controlled pollinations performed both in vitro and ex vitro. The very first approach on strawberry tree breeding by means of hybridization is also presented. Several physiological parameters were evaluated on 26 genotypes submitted to a water deficit regime. Plant behavior under drought greatly varied among genotypes, which showed a high phenotype plasticity. Three genotypes that were able to cope with water restriction without compromising net CO2 assimilation were identified as highly tolerant to drought stress. The results obtained elucidate the reproduction mechanisms of strawberry tree and open the way for a long-term breeding program based on the selection of drought tolerant plants.
BRIEF REPORT | doi:10.20944/preprints202012.0640.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: breeding; nursery gound; Eubalaena australis; Chile; Humboldt Current System; mark-recapture; drone
Online: 25 December 2020 (07:07:22 CET)
The Chile-Peru subpopulation (CPe) of the southern right whale (Eubalaena australis) is classified as critically endangered following intense whaling in past centuries. Due to their very low abundance, information on breeding and feeding grounds is also scarce. Unmanned aerial vehicles (UAVs) are increasingly applied in marine mammal research thanks to their low cost and relative ease of use. This case study documents a southern right whale nursing in Bahía Moreno (23ºS), Antofagasta, northern Chile, through high-resolution images taken by UAV of a lone adult in July 2019 and the same (photo-identified) whale with a neonate in August, confirming local parturition. Combined with earlier data we hypothesize that the Antofagasta Region may be a calving and nursing ground for the CPe subpopulation. Given the intense shipping traffic and fishing activities around the Mejillones Peninsula and Antofagasta port, priorly recommended marine spatial planning to help avoid net entanglements and vessel collisions of fin and humpback whales would also contribute to the conservation of the CPe stock of southern right whale.
REVIEW | doi:10.20944/preprints202009.0308.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Tomato; genetic breeding value; training population; genotyping; marker effect; phenotyping; selection schemes
Online: 14 September 2020 (00:08:23 CEST)
Genomic selection (GS) is a predictive approach that was build up to increase the rate of genetic gain per unit of time in breeding programs. It has emerged as a valuable method for improving complex traits that are controlled by many genes with small effect. GS enables the prediction of breeding value of candidate genotypes for selection. In this work we address important issues related to GS and its implementation in tomato breeding context. Genomic constrains and critical parameters affecting the accuracy of prediction in such crop such as phenotyping, genotyping training population composition and size and statistical method should be carefully evaluated. Comparison of GS approaches for facilitating the selection of tomato superior genotypes during breeding program are also discussed. GS applied to tomato breeding has already shown to be feasible. We illustrated how GS can improve the rate of gain in elite lines selection, descendent and in backcross schemes. The GS schemes begin to be delineated and computer science can provide support for future selection strategies. A new breeding framework is beginning to emerge for optimizing tomato improvement procedures.
REVIEW | doi:10.20944/preprints202003.0044.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Apis mellifera; host–parasite relationship; natural selection; resistance; selective breeding; Varroa destructor
Online: 3 March 2020 (11:53:56 CET)
Despite the implementation of control strategies, the invasive parasitic mite Varroa destructor remains one of the principal causes of honey bee (Apis mellifera) colony losses in numerous countries. For this reason, the parasite represents a serious threat to beekeeping and to agro-ecosystems that benefit from the pollination services provided by honey bees. Numerous selection programmes have been initiated over the last three decades with the aim of promoting the establishment of balance in the host–parasite relationship and, thus, helping European honey bees to survive in the presence of the parasite without the need for acaricide treatments. Such programmes have focused on either selective breeding for putative resistance traits or natural selection. To date, no clear overview of these attempts has been available, which has prevented building on past successes or failures and, therefore, hindered the development of a sustainable strategy for solving the V. destructor problem. In the present study, we review past and current selection strategies, report on their outcomes and discuss their limitations. Based on this state-of-the-art knowledge, we propose a strategy for increasing response to selection and colony survival against V. destructor infestations. Developing in-depth knowledge regarding the selected traits, optimising selection programmes and communicating their outcomes are all crucial to our efforts to establish a balanced relationship between the invasive parasite and its new host.
REVIEW | doi:10.20944/preprints201911.0300.v1
Subject: Biology And Life Sciences, Insect Science Keywords: artificial selection; biological control; genetics; genome assembly; genomics; insect breeding; microbiome; modelling
Online: 24 November 2019 (17:10:31 CET)
Biological control is widely successful for controlling pests, but effective biocontrol agents are now more difficult to obtain due to more restrictive international trade laws. Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, applying genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them, incorporating evolutionary and ecological principles. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined to better target their selection, followed by how to implement this information into a breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depends on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci (QTL) analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices include marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.
ARTICLE | doi:10.20944/preprints202106.0389.v2
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Tomatoes; Night low temperature; Physiological traits; Fruit yield; Tomato breeding; 28 correlation coefficients
Online: 19 July 2021 (10:01:59 CEST)
Tomato is exposure to diverse abiotic stresses. Cold stress is one of harsh environmental stresses and abnormal low temperature affects tomato growth and development including physio- logical disorders, flower drops, and abnormal fruit morphology, causing the decrease of tomato yield and a fruit quality. It is important to identify low temperature-(LT) tolerant tomato (Solanum lycopersicum L.) cultivars relying on different fruit types. This study focused on analyzing physiological traits of 35 tomato accessions with three different fruit types (cherry, medium, and large sizes) under night temperature set-points of 15°C for normal temperature (NT) and 10°C for LT, respectively. Plant heights (PH) of most tomato accessions in LT were remarkably decreased compared to those in NT. The growth of leaf length (LL) and leaf width (LW) was reduced depending on the genotypes under LT. In addition, the number of fruits (NFR), fruit set (FS), fruit yield (FY), and marketable yield (MY) were negatively affected in LT. The variation was further investigated by the correlation analysis, the principal component (PCA), and the cluster analysis. Interestingly, positive correlations between different vegetative and reproductive traits were uncovered. Multivariate analysis including the PCA and hierarchical clustering classified LT-treated 35 tomato accessions into four major groups. The identified accessions were associated with vegetative and reproductive parameters on positive directions and might be utilized for breeding programs on selecting LT-tolerant cultivars.
REVIEW | doi:10.20944/preprints201808.0089.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: firmness; Vaccinium; ripening; cell wall; crispy; quantitative genetics; breeding; molecular markers; genome editing
Online: 5 August 2018 (10:11:33 CEST)
Blueberry (Vaccinium spp.) has been recognized worldwide as a valuable source of health-promoting compounds, becoming a crop with some of the fastest rising consumer demand trends. Fruit firmness is a key target for blueberry breeding as it directly affects fruit quality, consumer preference, transportability, shelf life, and the ability of cultivars to be machine harvested. Fruit softening naturally occurs during berry development, maturation, and postharvest ripening. However, some genotypes are better at retaining firmness than others, and some are crispy, which is a putatively extra-firmness phenotype that provides a distinct eating experience. In this review, we summarized important studies addressing the firmness trait in blueberry, focusing on physiological and molecular changes affecting this trait at the onset of ripening and also the genetic basis of firmness variation across individuals. New insights into these topics were also achieved by using previously available data and historical records from the blueberry breeding program at the University of Florida. The complex quantitative nature of firmness in an autopolyploid species such as blueberry imposes additional challenges for the implementation of molecular techniques in breeding. However, we highlighted some recent genomics-based studies and the potential of a QTL mapping analysis and genome editing protocols such as CRISPR to further assist and accelerate the breeding process for this important trait.
ARTICLE | doi:10.20944/preprints201807.0216.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: nutrient use efficiency; grain yield; nitrogen, phosphorus; potassium; green super rice; BC breeding
Online: 12 July 2018 (11:05:46 CEST)
To develop green super rice varieties with high and stable yields under the rainfed conditions and improved nutrient use efficiency (NuUE), a modified backcross (BC) breeding approach was adopted using a high yielding and widely adaptable Xian variety, WTR1, as the recipient and a Geng variety, HAN, as the donor. Starting from the BC1F2 generation, the BC population had gone through one generation of selection under the IG, LI and RF conditions, followed by consecutive four generations of screening and selection for high GY under six different nutrient conditions, leading to the development of 230 BC1F6 introgression lines (ILs). The final evaluation of the 230 ILs under the six nutrient conditions identified many ILs with improved yields under various combinations of nutrient deficient conditions, including 12 promising lines that had significantly improved NuUE under two or more nutrient deficiency conditions. Our results demonstrated an efficient inter-subspecific BC breeding procedure with first round selection under the rainfed-drought condition followed by four generations of progeny testing for yield performances under six different nutrient conditions. The promising ILs were studied under replicated yield trials under 75N and -NPK conditions for developing high yield rice varieties with improved NuUE. Our results indicated that NuUE in rice was controlled by complex genetic and physiological mechanisms and the developed ILs provided useful materials for genetic and molecular dissection of NuUE in rice.
ARTICLE | doi:10.20944/preprints202305.1960.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: C. dactylon; C. transvaalensis; interspecific hybrids; cluster analysis; genetic similarity; genetic diversity; directional breeding
Online: 29 May 2023 (08:55:06 CEST)
Bermudagrass (Cynodon spp.) is one of the drought-resistant warm-season turfgrasses adapted to the southern and transitional zones in the United States. Multiple hybrid varieties have been developed and released for use as a turfgrass and others are in pipeline. Increasing genetic di-versity of commercial varieties is vital to tackle stress tolerance. A DNA profiling study of 21 experimental selections from the Oklahoma State University (OSU) turfgrass breeding program and 11 cultivars was conducted using 51 simple sequence repeat (SSR) primer pairs that spread across the bermudagrass genome. Pairwise genetic relationship analysis among the genotypes using 352 polymorphic bands showed genetic similarity coefficients ranging from 0.59 to 0.89. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method grouped the entries into six clusters. Correlation analysis identified different levels of pairwise genetic relationship among the entries that largely reflected parental relationship. Di-rectional breeding and selection for cold hardiness or drought resistance created progeny that had distinct genetic diversity in the tested bermudagrasses. It is evident that an increase in genetic diversity of the existing cultivar pool with the release of one or more of the experimental selec-tions for commercial use will strengthen and improve bermudagrass systems.
ARTICLE | doi:10.20944/preprints202304.0932.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Acoustic biomass; breeding success; chicks raised per nest; catch limit; Euphausia superba; fishery management
Online: 26 April 2023 (03:01:21 CEST)
Pygoscelis penguin populations in the Antarctic Peninsula have dropped dramatically in the last 50 years. The main probable cause is the reduction in Krill (Euphausia superba), the most important feeding item for Pygoscelis penguins during breeding. The scientific community has expressed concerns on the potential that competition with the fishery during periods of low krill availability might be exacerbating the effects of climate change. By bringing together data on breeding success of penguin colonies throughout the Antarctic Peninsula with information of krill availability from acoustic survey and krill fishery monitoring data, we were able to show that fishery has had in the past an effect over breeding success. That is a consequence of a management strategy based on a constant catch level enabling the fishery to maintain the same levels of production even when krill availability is low. The total catch limit may have represented a substantial amount of the available krill biomass in some years, and we detected that when the catch goes over 5% of the available biomass during summer, breeding success of penguins decreased by one third. We discuss the implications of our findings to the revised ecosystem-based management strategy of the krill fishery in Antarctica.
REVIEW | doi:10.20944/preprints202102.0168.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: aquaculture; shellfish; future food; nursery stage; mud crab; juvenile; seed production; hatchery; crablet; breeding
Online: 5 February 2021 (16:18:19 CET)
This study attempted to explain the definition, objectives, and key stages in mud crab nursery activities. The nursery stages of Scylla spp was started from megalopa stage to several crablet instar stages or started from earlier crablet stage to several crablet stages. Direct stocking of megalopa into ponds is not recommended due to their sensitivity. Instead, nursery rearing is needed to produce mud crab of larger size before stocking. Individual nursery rearing results in higher survival rate (up to 100%), but with reduced growth rate, and a more complicated maintenance process compared with communal rearing. Nursery of mud crab can be done indoors, or outdoors, with adequate shelter and feed required to obtain good survival and growth performance. Artemia nauplii are the main, established nursery feed, particularly at megalopa stage, while survival rate may be improved if combined with artificial feed, such as micro bound diet formulations. Water quality parameters, identical to those proposed in tiger shrimp culture, can followed. Crablets may be transported to the pond location with, or without water. The provision of monosex seeds from mud crab hatcheries is expected to become more common, increasing seed price, and thus improving income of farmers. Numerous aspects of mud crab nursery, including nutrition, feeding strategies, understanding of their behaviour, i.e., cannibalism, control of environmental factors, and practical rearing techniques, still need further improvement.
ARTICLE | doi:10.20944/preprints202009.0097.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: orphan crop; genotyping-by-sequencing; inbreeding; pre-breeding; population genetics; DArTseq; isolation by distance
Online: 4 September 2020 (11:11:37 CEST)
Kersting’s groundnut is an important source of protein and essential nutrients that contribute to food security in West Africa. However, the crop is still underexploited by the populations and under-researched by the scientific community. This study aimed to investigate the genetic diversity and population structure of 217 Kersting’s groundnut accessions from five origins using 886 DArTseq markers. Gene diversity was low and ranged from 0.049 to 0.064. The number of private alleles greatly varied among populations (42–192) and morphotypes (40–339). Moderate to very high levels of selfing and inbreeding were observed among populations (s=56–85%, FIS=0.389–0.736) and morphotypes (s=57–82%, FIS=0.400–0.691). Moreover, little to very high genetic differentiations were observed among populations (0.006≤FIS≤0.371) and morphotypes (0.029≤FIS≤0.307). Analysis of molecular variance partitioned 38.5% of the genetic variation among and 48.7% within populations (P<0.001). Significant isolations by distance were detected between populations (R2=0.612, P=0.011) and accessions (R2=0.499, P<0.001). Discriminant analysis of principal components and neighbour joining consistently distinguished eight distinct clusters. These data provide a global picture of the existing genetic diversity for Kersting’s groundnut and will guide the choice of breeding strategies to increase production.
ARTICLE | doi:10.20944/preprints202311.1031.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: plant-microbe symbiosis; legumes; Pisum sativum; symbiotic responsivity; genomics; transcriptomics; differential gene expression; molecular breeding
Online: 15 November 2023 (15:49:19 CET)
Pea (Pisum sativum L.), like most legumes, forms mutualistic symbioses with nodule bacteria and arbuscular mycorrhizal (AM) fungi. The positive effect of inoculation is partially determined by the plant genotype, thus, pea varieties with high and low symbiotic responsivity have been described, but the molecular genetic basis of this trait remains unknown. Here, we compare the symbiotically responsive breeding line ‘Triumph’ of grain pea with its parental cultivars ‘Vendevil’ (a donor of high symbiotic responsivity) and ‘Classic’ (a donor of agriculturally valuable traits) using genome and transcriptome sequencing. We show that ‘Triumph’ inherited one-fourth of its genome from ‘Vendevil’, including the genes related to AM and nodule formation, and reveal that under combined inoculation with nodule bacteria and AM fungi, ‘Triumph’ and ‘Vendevil’, in contrast to ‘Classic’, demonstrate similar up-regulation of the genes related to solute transport, hormonal regulation and flavonoid biosynthesis in their roots. We also identify the gene PsGLP2, whose expression pattern distinguishing ‘Triumph’ and ‘Vendevil’ from ‘Classic’ correlates with difference within the promoter region sequence, making it a promising marker for the symbiotic responsivity trait. The results of the study may be helpful for future molecular breeding programs aimed at creation of symbiotically responsive cultivars of pea.
ARTICLE | doi:10.20944/preprints202212.0337.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: diet; breeding performance; population trends; Aegolius funereus; Asio otus; Strix aluco; Strix uralensis; Bubo bubo
Online: 19 December 2022 (10:06:50 CET)
Strong numerical and functional response of owls to voles in cyclic environments is well known, but there is insufficient knowledge from boreonemoral region, in particular, with depleted populations of the small mammals. In this study we describe the dynamics of the small mammal population in Latvia from 1991 to 2016 and link them to owl population characteristics. We used food niche breadth, number of fledglings and population trends to describe the numerical response of six owl species to dampened small mammal population cycles. We found temporarily in-creasing food niche breadth in tawny and Ural owls. There were no other responses in tawny owl, whereas the breeding performance of three forest specialist species – pygmy, Tengmalm`s and Ural owls – were similar to vole crash years in Fennoscandia. Moreover, the populations of forest specialist owls are decreasing and the change in Ural owl can be attributed to the depletion of small mammal populations. We found evidence of carry-over effect in eagle owl arising from strong correlation of declining breeding performance with the small mammal abundance indices in previous autumn. We conclude that dampening of the small mammal population cycles is an important covariate to overwhelming impacts of habitat destruction with stronger response in more specialized (to prey or habitat) species.
REVIEW | doi:10.20944/preprints202208.0154.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Genome selection; Rice breeding; Genetic analysis; Omics assisted markers; Nutritional quality; Genomics and pangenomics; Biofortification
Online: 8 August 2022 (10:53:16 CEST)
The primary considerations while producing rice (Oryza sativa L.) include improving its nutritional quality and production. To tackle widespread hunger globally, better nutritional, high-yielding rice cultivars need to be developed. The conventional ways are to increase the production of rice and add balanced nutrients in the daily diet to fulfill the need of yield and nutrient quality. This article focuses on nutritional strategies for rice and illustrates the availability of omics technologies. Current advancements providing many methodologies and approaches for exploring genetic resources and for understanding the molecular mechanisms involved in trait formation have been highlighted. Studying the genetic influences of various characteristics has been proven to expedite crop breeding processes. In this perspective, genome-wide association research, genome selection (GS), and QTL mapping are all genetic analysis that helps in increasing the nutritional content of rice. Implementation of several omic techniques are effective approaches to enhance and regulate the nutritional quality of rice cultivars. Advancements in different types of omics including genomics and pangenomics, transcriptomics, metabolomics, nutrigenomics, and proteomics are also relevant to rice development initiatives. This review article compiles genes, locus, mutants and all omic approaches for rice enhancement. This knowledge will be very useful for now and for the future regarding rice studies.
ARTICLE | doi:10.20944/preprints202009.0458.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: machine learning; deep leaning; physiological maturity; computer vision; plant breeding; Phenology; Glycine max (L.) Merr.
Online: 19 September 2020 (10:08:43 CEST)
Soybean maturity is a trait of critical importance for the development of new soybean cultivars, nevertheless, its characterization based on visual ratings has many challenges. Unmanned aerial vehicles (UAVs) imagery-based high-throughput phenotyping methodologies have been proposed as an alternative to the traditional visual ratings of pod senescence. However, the lack of scalable and accurate methods to extract the desired information from the images remains a significant bottleneck in breeding programs. The objective of this study was to develop an image-based high-throughput phenotyping system for evaluating soybean maturity in breeding programs. Images were acquired twice a week, starting when the earlier lines began maturation until the latest ones were mature. Two complementary convolutional neural networks (CNN) were developed to predict the maturity date. The first using a single date and the second using the five best image dates identified by the first model. The proposed CNN architecture was validated using more than 15,000 ground truth observations from five trials, including data from three growing seasons and two countries. The trained model showed good generalization capability with a root mean squared error lower than two days in four out of five trials. Four methods of estimating prediction uncertainty showed potential at identifying different sources of errors in the maturity date predictions. The architecture used solves limitations of previous research and can be used at scale in commercial breeding programs.
REVIEW | doi:10.20944/preprints202202.0042.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: plant breeding; two-part strategy; recurrent selection; population improvement; product development; optimization; genetic gain; cross-prediction
Online: 2 February 2022 (18:07:58 CET)
Wheat (Triticum aestivum L.) breeding programs can take over a decade to release a new variety. However, new methods of selection such as genomic selection (GS) must be integrated to decrease the time it takes to release new varieties to meet the demand of a growing population. The implementation of GS into breeding programs is still being explored, with many studies showing its potential to change wheat breeding through achieving higher genetic gain. In this review, we explore the integration of GS for a wheat breeding program by redesigning the traditional breeding pipeline to implement GS. We propose implementing a two-part breeding strategy by differentiating between population improvement and product development. The implementation of GS in the product development pipeline can be integrated into most stages and can predict within and across breeding cycles. Additionally, we explore optimizing the population improvement strategy through GS recurrent selection schemes to reduce crossing cycle time and significantly increase genetic gain. The recurrent selection schemes can be optimized for parental selection, maintenance of genetic variation, and optimal cross-prediction. Overall, we outline the ability to increase the genetic gain of a breeding program by implementing GS and a two-part breeding strategy.
REVIEW | doi:10.20944/preprints202004.0083.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: drought-tolerance characteristics; maize breeding; maize drought tolerance; molecular markers; phenotype; screening of drought-tolerant plants
Online: 7 April 2020 (10:28:30 CEST)
Drought is among the most important abiotic stressors influencing food-crop production worldwide. Currently, drought-tolerant maize materials are rarely used for actual breeding because corn production primarily focuses on heterosis to generate desired varieties. In this article, we reviewed current work on assessing maize drought tolerance. We suggested that the development of enhanced screening techniques must clearly consider the connection between theory and application. We strongly recommend that agricultural scientists focus on translating the results of laboratory experiments into practical methods for improving crop productivity.
ARTICLE | doi:10.20944/preprints202310.1123.v1
Subject: Biology And Life Sciences, Forestry Keywords: list of breeding forest birds; distribution over 150 years; distribution limits; peninsulas; islands; influence of man; fires
Online: 18 October 2023 (05:20:30 CEST)
The author attempts to reconstruct the climatic vicissitudes of the Mediterranean to explain why only broadly distributed Eurasian forest species have penetrated the Mediterranean peninsulas. He has carried out a bibliographic survey of the status of breeding forest birds in Italy over 15 decades (1872-2022) in order to establish an objective long-term trend (stable, increasing, decreasing, etc.). The number of breeding forest birds in Italy amounts to 61; their distribution, with a few exceptions, indicates that they are widespread in Eurasia, but only a small percentage of Eurasian forest species have colonized Italy and the other Mediterranean peninsulas, namely 49 in Iberian, 61 in Italian and 64 in Balkan peninsulas; a small percentage of them (between 10.9 and 14.3%) belongs to trans-Saharan migrants. The similarity between the forest species on the three peninsulas (Iberian, Italian and Balkan) results between 0.45 and 0.48, indicating a certain differ-ence in the overall fauna on the three territories. Not all species have penetrated southwards into the three peninsulas; for example, some that stopped in the Italian Alps have instead arrived to the forests of Greece, at a latitude corresponding to southern Italy, or species that in Italy stopped in the northern Apennines in the other two peninsulas have instead arrived far south. Iberian peninsula and the island of Corsica hold three endemic species among breeding forest birds, Italian and Balkan peninsulas have not endemic species. Overall, the Mediterranean presently hosts mainly neo-endemic taxa among forest bird species; the only paleo-endemics can be considered the three species of nuthatches living in Corsica, Algeria, and Turkey (other than Caucasus and the islet of Lesvos) and Le Vaillant’s woodpecker in the Maghreb (North Africa). Italian forests cover ca. 40% of land surface and since 1980’ are increasing, but 22% of them do not have a natural origin. However, it is difficult to know the true increase of forests, because some of them are fired every year. The presence of some ecologically demanding forest birds depends on the age of the trees, permanent open spaces and other characteristics at the edge of woodland.
REVIEW | doi:10.20944/preprints202306.1268.v1
Subject: Biology And Life Sciences, Horticulture Keywords: Foliar fungal diseases; Integrated disease management; Marker-assisted selection; Quantitative trait loci; Resistance breeding; Solanum lycopersicum; Tomato
Online: 19 June 2023 (03:14:19 CEST)
Foliar fungal diseases in tomatoes include early blight (Alternaria linariae), Septoria leaf spot (Septoria lycopersici), and late blight (Phytophthora infestans) which is oomycetes. These are one of the significant production constraints in tomatoes. We describe the etiology, host range, distribution, symptoms, and disease cycle to understand the biology followed by management practices emphasizing the resistance breeding approach for these diseases. In crop improvement efforts, we provide an analytical review, including conventional and molecular methods for improving this disease resistance. Modern breeding tools, including genomics, genetic transformation, and genome editing, can be used to improve these traits. There is a good possibility of using these tools in the future to improve these traits.
ARTICLE | doi:10.20944/preprints202009.0303.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Breeding birds; bird diversity; birdsong; biophilic; mental wellbeing; Nature’s Fix; Strawberry Line; Vale of Winscombe; Mendip Hills
Online: 13 September 2020 (23:51:52 CEST)
The Strawberry Line is a linear Local Nature Reserve extending along a dismantled railway corridor in North Somerset, England. The Reserve is cherished as a recreational resource by local communities and I am very fortunate to live beside it. During the COVID-19 lockdown of spring 2020, I decided to make use of my permissible daily exercise to record the distribution of breeding birds along my particular ‘patch’ of the Strawberry Line - the Vale of Winscombe section in the Mendip Hills. In describing the Reserve’s birdlife, I hope that I can provide an added layer of interest for locals and visitors, which might help in these difficult times deliver an enhanced dose of ‘Nature’s Fix’ and perhaps also shine a light towards a greater appreciation and connection with the natural world.
ARTICLE | doi:10.20944/preprints202002.0402.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: chromosome engineering; wheat breeding; Aegilops longissima; Thinopyrum ponticum; gluten quality; yield; leaf rust; stem rust; powdery mildew
Online: 27 February 2020 (11:29:25 CET)
If genetic gains in wheat yield are to be achieved in today’s breeding, increasing genetic variability of cultivated genotypes is an essential requisite to meet. To this aim, alien gene transfer through chromosome engineering (CE) is a validated and sound strategy. Attempts to incorporate more than one alien segment into cultivated wheat have been rare, particularly for tetraploid durum wheat. Here we present the agronomic and quality performance of the first successful CE-mediated multiple introgression into the latter species. By assembling into 7AL, 3BS and 1AS arms of a single genotype homoeologous segments of Thinopyrum ponticum 7el1L, Aegilops longissima 3SlS, and Triticum aestivum 1DS arms, respectively, we have stacked several valuable alien genes, comprising Lr19+Sr25+Yp (leaf and stem rust resistance and a gene increasing semolina yellowness), Pm13 (powdery mildew resistance) and Gli-D1/Glu-D3 (genes affecting gluten properties), respectively. Advanced progenies of single, double and triple recombinants were field-tested across three years in a typical durum wheat growing area of Central Italy. The results showed that not only all recombinants had normal phenotype and fertility, but also that one of the triple recombinants had the highest yield through all seasons compared with all other recombinants and control cultivars. Moreover, the multiple introgressions enhanced quality traits, including gluten characteristics and semolina yellow index. Presence of effective disease resistance genes confers additional breeding value to the novel and functional CE products, which can greatly contribute to crop security and safety.
ARTICLE | doi:10.20944/preprints202311.0022.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Apis mellifera; honey bee subspecies; cryopreservation; breeding stock; honey bee selection; tRNAleu-COII (COI-COII); microsatellite markers; morphometry
Online: 1 November 2023 (07:04:12 CET)
The cryopreservation of gametes and embryos is an important element of biodiversity conservation. One species in need of conservation is the honey bee Apis mellifera L. Changing environmental factors, especially the anthropogenic factor, have led to a reduction in the numbers of this insect species. In this study, we provide an example of the creation of a biobank of honey bee drone sperm. For sperm cryopreservation, drones of the most common subspecies of honey bees common in Russia were selected. These were the dark forest bee, Apis mellifera mellifera from the Republic of Bashkortostan, with three subspecies (A. m. carnica, A. m. carpatica, and A. m. caucasica) from the southern regions of Russia, as well as two breeding stocks, the Far Eastern bee and Prioksky bee. For subspecies identification, morphometric and genetic methods were used. The subspecies of the studied samples were confirmed by the analysis of the tRNAleu-COII locus of mitochondrial DNA and nine microsatellite markers of nuclear DNA. It was shown that bees of the Prioksky breeding stock belong to the subspecies A. m. caucasica based on phylogenetic analysis, and the Far Eastern breeding stock is a stable hybrid, descending on the maternal line from the evolutionary lineage C or O. The results of the morphometric analysis are consistent with the results of the genetic analysis. For the cryopreservation of sperm, we used a honey diluent. As a result, the viability of frozen–thawed sperm decreased by 20.3% compared to fresh sperm, and overall motility decreased by 25-fold. The measurement of the sperm concentration in the spermatheca of artificially inseminated queens showed that it varied from 0.22 to 4.4 million/μL. Therefore, the use of honey in sperm cryopreservation has great potential.
Subject: Business, Economics And Management, Economics Keywords: new plant engineering techniques (NPETs); new breeding techniques (NBTs); genome editing; gene editing; cisgenic; willingness to pay (WTP)
Online: 1 October 2021 (12:55:10 CEST)
We follow the PRISMA extension for scoping reviews to review the emerging international body of empirical evidence on consumers’ attitudes and willingness to pay (WTP) for novel foods produced with New Plant Engineering Techniques (NPETs). NPETs include genome/gene editing, cisgenesis, intragenesis, RNA interference and others. These novel foods are often beneficial for the environment and human health and more sustainable under increasingly prevalent climate extremes. These techniques can also improve animal welfare and disease resistance when applied to animals. Despite these promising attributes, evidence suggests that many, but not all, consumers discount these novel foods relative to conventional ones. Our review sorts out findings to identify conditioning factors that can increase the acceptance of and WTP for these novel foods in a significant segment of consumers. International patterns of acceptance are identified. We also analyze how information and knowledge interact with consumer acceptance of these novel foods and technologies. Heterogeneity of consumers—across cultures and borders and in attitudes towards science and innovation—emerges as a key determinant of acceptance and WTP. Acceptance and WTP tend to increase when socially beneficial attributes—as opposed to producer-oriented cost-saving attributes—are generated by NPETs. NPET-improved foods are systematically less discounted than transgenic foods. Most of the valuation estimates are based on hypothetical experiments and surveys and await validation through revealed preferences in actual purchases in food retailing environments.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: tomato; 7-epi-zingiberene; 9-hydroxy-zingiberene; 9-hydroxy-10,11-epoxy zingiberene; spectrophotometer; absorbance; introgression; breeding; wild relatives
Online: 29 September 2021 (16:24:30 CEST)
Tomato (Solanum lycopersicum), an important vegetable crop, is a host for numerous pests and pathogens. Consequently, tomato breeders are striving to improve pest resistance. Many acces-sions of the wild relative S. habrochaites display high resistance towards arthropod pests such as spider mites and whiteflies and the presence of the sesquiterpene hydrocarbon 7-epi zingiberene in its trichomes has been associated with arthropod resistance. Consequently, tomato breeders are attempting to introgress 7-epi zingiberene from wild to cultivated tomato, which requires the ability to quantify zingiberene. 7-Epi zingiberene has conjugated double bonds causing it to ab-sorb uv light. In fact, de Freitas, et al.  have claimed that measurement of absorbance at 270 nm of tomato leaflet washes can be used to quantify zingiberene. However, this claim has never been critically evaluated. We initially evaluated the use of uv absorbance to estimate zingiberene content of leaflet washes from an interspecific hybrid tomato BC4F2 generation that was segre-gating widely for presence and abundance of zingiberene. When absorbances at 270 nm were compared with zingiberene measured by gas chromatography the resulting relationship did not obey the Beer-Lambert law. Consequently, we examined in detail aspects of the uv-absorbance of zingiberenoids by: 1) obtaining uv absorbance spectra for three isolated zingiberenoids and de-termining the relationship between the abundance of each isolated compound and absorbance at single wavelengths; 2) obtaining uv absorbance spectra of leaflet washes of relevant wild acces-sions and parents; 3) obtaining average absorbance spectra for interspecific generations of tomato that were segregating for abundance of zingiberenoids and determining their λmax values in the 250-280 nm region; 4) evaluating by regression the relationship between absorbance at a single wavelength and the concentration of zingiberene and when present, its derivatives, as measured by gas chromatography in several interspecific hybrid generations; and 5) exploring the potential use of absorbances at multiple wavelengths to improve estimates of concentrations of zingi-berenoids. Results indicated that isolated zingiberenoids as well as leaflet washes of wild tomatoes that contain zingiberenoids have broad absorbance spectra in the uv region with a λmax of 264 nm. The relationship between abundance of isolated zingiberenoids and absorbance at a single wavelength of 264 nm did obey the Beer-Lambert Law. Average absorbance spectra for leaflet washes from BC3F5 generation plants sampled by two methods, as well as from a BC5F1 and a BC3F3 generation showed subtle shifts in the λmax away from 264 nm. Furthermore, the rela-tionship between absorbance at 264 nm and zingiberenoid content of these generations did not obey the Beer-Lambert Law in that in each case regression of absorbance on zingiberenoid content of the leaflet washes resulted in non-zero intercept estimates that varied considerably among generations and sampling methods. Use of multiple wavelengths for estimation zingiberenoids in these breeding generations was explored and inclusion of additional absorbances at one or two wavelengths identified by stepwise regression always improved estimates of zingiberenoid content from absorbance data. However, the identified wavelength(s) differed among generations. Taken together the results indicate that measurement of absorbance of tomato leaflet washes at a single wavelength is not a reliable quantitative estimate of zingiberenoids in the leaflet wash. These estimates can be improved by utilizing absorbance at multiple wavelengths, but the par-ticular wavelengths will likely vary among generations. Lastly, measurement of absorbance may be a useful tool in identifying those relatively rare individuals in a generation that is widely segregating for zingiberenoid content. However, even in this situation the determination of the actual zingiberene content e.g., for comparison with the donor parent, would need to be back-stopped by a valid quantitative method such as gas chromatography.
REVIEW | doi:10.20944/preprints202012.0129.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: oil palm; breeding; sustainability; certification; diseases; basal stem rot; phytophthora; climate change; modelling; supply chains; biodiesel; covid-19
Online: 7 December 2020 (08:50:30 CET)
Background Oil palm (OP), Elaeis guineensis , is by far the most important global oil crop, supplying about 40% of total traded vegetable oil. Palm oils are key dietary components consumed daily by over three billion people, mostly in Asia, and also have a wide range of important non-food uses including in cleansing and sanitising products. Main body Oil palm is a perennial crop with a >25-year life cycle and an exceptionally small land footprint compared to annual oilseed crops. Oil palm crops globally produce an annual 81 million tonnes (Mt) of oil from about 19 million hectares (Mha). In contrast, the second and third largest vegetable oil crops, soybean and rapeseed, yield a combined 84 Mt oil but occupy over 163 Mha of increasingly scarce arable land. Despite this advantage, oil palm has acquired a poor environmental reputation, especially in Europe and North America, although soybean planting is now responsible for more deforestation. Oil palm crops face other challenges in the 2020s. On the demand side, these include changing consumer purchasing habits, threats to global trade systems, and diminishing demand for liquid fuels as transport systems become increasingly electrified. On the supply side, major issues include stagnant yields in ageing plantations, sluggish replanting of improved varieties, labour shortages, diseases and climatic/ environmental threats. The latter include the increasing incidence of new and existing pests/diseases and a general lack of climatic resilience, especially relating to elevated temperatures and increasingly erratic rainfall patterns. This review surveys the oil palm sector in the 2020s and beyond, its major challenges and options for future progress. Conclusions Oil palm crops face many future challenges, including emerging threats from climate change and new pests and diseases, that require more effective international collaboration. Nevertheless, new breeding technologies are providing the promise of improvements, such as much higher yielding varieties, improved oil profiles, enhanced disease resistance and modified crop architecture to enable harvesting mechanisation. The industry also needs to redouble its efforts to engage with global consumers in a constructive dialogue aimed at addressing its image problem and explaining the many benefits of its products.
ARTICLE | doi:10.20944/preprints202305.0231.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: breeding strategy; dark-light cycles; dead co-twin; early fetal loss; selection index; spontaneous twin reduction; standardized transmitting ability
Online: 4 May 2023 (08:20:36 CEST)
Twin pregnancies are highly undesirable in dairy cattle; they compromise the health and wellbeing of a cow, and its incidence dramatically impairs the farm economy. Recently, a genomic prediction for twin pregnancies has been developed. The objective of this study was to assess cow, environmental and management risk factors affecting the incidence of twin pregnancies in high-producing dairy cows in their first lactation, with special emphasis placed on the genomic prediction values for twin pregnancy. Our study population of primiparous cows proved valuable in identifying factors other than genomic predictive values influencing the twin pregnancy rate. The odds ratio for twin pregnancy was 0.85 (p <0.0001) for each unit of a prediction value increase, 3.5 (p = 0.023) for cows becoming pregnant during the negative photoperiod, and 0.33 (p = 0.016) for cows producing ≥42 kg of milk at AI, compared to the remaining cows producing <42kg of milk. As a general conclusion, the practical implication of our findings is that genomic prediction values can identify the risk of twin pregnancy at herd level. Given the cumulative effect of genomic selection, selecting for animals with reduced genetic risk of twin pregnancies can contribute to reduce its incidence in dairy herds.