REVIEW | doi:10.20944/preprints202010.0051.v1
Subject: Biology, Anatomy & Morphology Keywords: melatonin; ROS; NO; posttranslational modifications (PMTs); abiotic stress; drought; salinity; high temperature; high light; waterlogging; abiotic stress combination
Online: 5 October 2020 (07:48:29 CEST)
Abiotic stress in plants is an increasingly common problem in agriculture, and thus, studies on plant treatments with specific certain compounds that may help to mitigate these effects have increased in recent years Melatonin (MET) application and its role in mitigating the negative effects of abiotic stress in plants have become important in the last few years. MET, a derivative of tryptophan, is an important plant-related response molecule involved in the growth, development, and reproduction of plants, and the induction of different stress factors. In addition, MET plays a protective role against different abiotic stresses such as salinity, high/low temperature, high light, waterlogging, nutrient deficiency and stress combination by regulating both the enzymatic and non-enzymatic antioxidant defense systems. Also, MET interacts with many signaling molecules, among these, reactive oxygen species (ROS) and nitric oxide (NO), and participates in a wide variety of physiological reactions. It is well known that NO produces S-nitrosylation and NO2-Tyr of important antioxidant-related proteins, being this an important mechanism for maintaining the antioxidant capacity of the AsA/GSH cycle under nitro-oxidative conditions, being extensively reviewed here under different abiotic stress conditions. Lastly, in this review, we show the coordination between NO and MET as a long-range signaling molecule, regulating many responses in plants, including plant growth and abiotic stress tolerance. Despite all the knowledge acquired over the years, there is still more to know about how MET and NO act on tolerance to abiotic stresses.
ARTICLE | doi:10.20944/preprints201911.0358.v1
Subject: Biology, Plant Sciences Keywords: abiotic stress; oxidative stress; salinity; nutrient deficiency; osmolytes; methylglyoxal
Online: 28 November 2019 (09:49:35 CET)
This study was undertaken to elucidate the role of trehalose (Tre) in mitigating oxidative stress under salinity and low P in maize. Eight-day-old maize seedlings of two maize varieties, BARI Hybrid Maize-7 and BARI Hybrid Maize-9 were subjected to salinity (150 mM NaCl), low P (5 µM KH2PO4) and their combined stress with or without 10 mM Tre for 15-d.Salinity and combined stress significantly inhibited the shoot length, root length, and root volume, whereas, low P increased the root length and volume in both genotypes. Exogenous Tre in the stress treatments increased all of the growth parameters as well as decreased the salinity, low P and combined stress-mediated Na+/K+, ROS, MDA, LOX activity and MG in both genotypes. Under salinity and low P stress, the SOD activity increased in both genotypes, but the activity decreased in combined stress. POD activity increased in all stress treatments. Interestingly, Tre application enhanced the SOD activity in all the stress treatments but inhibited the POD activity. Both CAT and GPX activity were increased by saline and low P stress while the activities inhibited in combined stress. Similar results were found for APX, GR, and DHAR activities in both genotypes. However, MDHAR activity was inhibited in all the stresses. Interestingly, Tre enhanced CAT APX, GPX, GR, MDHAR and DHAR activities suggesting the amelioration of ROS scavenging in maize under all the stresses. Increased GST activity in presence or absence of Tre might involve in detoxification of hydroperoxides as well as leaf senescence. On the other hand, increased glyoxalase activities in saline and low P stress in BHM-9 suggested better MG detoxification system because of down-regulation of Gly-I activity in BHM-7 in those stresses. Tre also increased the glyoxalase activities in both genotypes under all the stresses. Tre improved the growth in maize seedlings by decreasing Na+/K+, ROS, MDA, and MG through regulating antioxidant and glyoxalase systems.
REVIEW | doi:10.20944/preprints202008.0359.v1
Subject: Biology, Plant Sciences Keywords: Abiotic stress; Melatonin; Water stress; Drought; Waterlogging; Antioxidants; Stress signalling, phytohormones
Online: 17 August 2020 (10:19:52 CEST)
Water stress (drought and waterlogging) is drastic abiotic stress to plant growth and development. Melatonin, bioactive plant hormone, has been widely tested in drought situations in diverse plant species, while a few studies on the role of melatonin in waterlogging stress conditions have been published. In the current review, we analyze the bio-stimulatory functions of melatonin on plants under both drought and waterlogging stress. Melatonin controls the levels of reactive oxygen and nitrogen species and positively changes the molecular defense to improve plant tolerance against drought and waterlogging stress. Moreover, the crosstalk of melatonin and other phytohormones is a key element on plant survival under drought stress, while this relationship needs further investigation under waterlogging stress. In this review, we draw the complete story of water stress on both sides: drought and waterlogging through discussing the previous critical studies under both conditions. Moreover, we suggest several research directions, especially for waterlogging, which remains a big vague piece of melatonin and water stress puzzle.
REVIEW | doi:10.20944/preprints202101.0616.v1
Subject: Biology, Plant Sciences Keywords: abiotic stress; crop improvement; drought; nitric oxide; S-nitrosylation; signaling molecule; water deficit
Online: 29 January 2021 (12:14:53 CET)
Water deficit caused by drought is a significant threat to crop growth and production. Nitric oxide (NO), a water- and lipid-soluble free radical, plays an important role in cytoprotection. Apart from a few studies supporting the role of NO in drought responses, little is known about this pivotal molecular amendment in the regulation of abiotic stress signaling. In this review, we highlight the knowledge gaps in NO roles under drought stress and the technical challenges underlying NO detection and measurements, and we provide recommendations regarding potential avenues for future investigation. The modulation of NO production to alleviate abiotic stress disturbances in higher plants highlights the potential of genetic manipulation to influence NO metabolism as a tool with which plant fitness can be improved under adverse growth conditions.
ARTICLE | doi:10.20944/preprints202102.0290.v1
Subject: Biology, Anatomy & Morphology Keywords: abiotic stress; strawberry; companion plants; phytoremediation
Online: 11 February 2021 (19:00:26 CET)
Strawberry is a saline sensitive plant adversely affected under slightly or moderately saline conditions. Growth and biochemical parameters of strawberry plants grown under NaCl (0-, 30-, 60-, and 90 mmol L-1) conditions with or without a halophytic companion plant (Portulaca oleracea L.) were investigated in a pot experiment. Salt stress negatively affected the growth, physiological (stomatal conductance, electrolyte leakage, total soluble solids) and biochemical parameters such as chlorophyll contents (chl-a and chl-b), proline, hydrogen peroxide, malondialdehyde, catalase, and peroxidase enzyme activities, lycopene, vitamin C contents along with the mineral uptake of strawberry plants. The companionship of P. oleacea increased fresh weight, dry weight, and fruit average weight and total fruit yield of strawberry plants along with the improvement of physiological and biochemical parameters. This study showed that cultivating of P. oleracea with strawberry plants under salt stress conditions effectively increased strawberry fruit yield and quality. We, therefore, that approaches towards the use of P. oleracea could be an environmentally friendly method that should be commonly practised where salinity is of great concern.
ARTICLE | doi:10.20944/preprints202107.0311.v1
Online: 13 July 2021 (15:11:54 CEST)
The SnRK gene family is a key regulator playing an important role in plant stress response by phosphorylating the target protein to regulate the signalling pathways. The function of SnRK gene family has been reported in many species but is limited to Triticum asetivum. In this study, SnRK gene family in the wheat genome was identified and its structural characteristics were described. One hundred forty-seven SnRK genes distributed across 21 chromosomes were identified in the Triticum aestivum genome and categorised into three subgroups (SnRK1/2/3) based on phylogenetic analyses and domain types. The gene intron-exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication between the wheat, Arabidopsis, rice and barley genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. SnRK genes showed differential expression patterns in leaves, roots, spike, and grains. Redundant stress-related cis-elements were also found in the promoters of 129 SnRK genes and their expression levels varied widely following drought, ABA and light regulated elements. In particular, TaSnRK2.11 had higher and increased expression under the abiotic stresses and can be a candidate gene for the abiotc stress tolerance. The findings will aid in the functional characterization of TaSnRK genes for further research.
ARTICLE | doi:10.20944/preprints202208.0315.v1
Subject: Life Sciences, Other Keywords: Transcription Factors; Evolutionary progression; Pearl millet; Phytohormones; Abiotic stress
Online: 17 August 2022 (09:50:48 CEST)
Transcription factors (TFs) are the regulatory proteins that act as molecular switches in controlling stress responsive gene expression. Among them MYB transcription factor family is one of the largest TF family in plants, playing a significant role in plant growth, development, phytohormone signaling and stress-responsive processes. Pearl millet (Pennisetum glaucum L.) is one of the most important C4 crop plant of the arid and semi-arid regions of Africa and South-east Asia for sustaining food and fodder productions. To explore the evolutionary mechanism and functional diversity of the MYB family in pearl millet, we conducted a comprehensive genome-wide survey and identified 279 MYB TFs (PgMYB) in pearl millet and distributed unevenly across seven chromosomes of pearl millet. Phylogenetic analysis of identified PgMYBs classified them into 18 subgroups and members of the same group showed a similar gene structure and conserved motif/s pattern. Further, duplication events were identified in pearl millet that indicated towards evolutionary progression and expansion of the MYB family. Transcriptome data and relative expression analysis by qRT-PCR identified differentially expressed candidate PgMYBs (PgMYB2, PgMYB9, PgMYB88 and PgMYB151) under dehydration, salinity, heat and phytohormones (ABA, SA and MeJA) treatment. Taken together, this study provides valuable information for a prospective functional characterization of MYB family members of pearl millet and genetic improvement of crop plants.
REVIEW | doi:10.20944/preprints202103.0041.v1
Subject: Life Sciences, Biochemistry Keywords: PGPR; salt stress; salinity; abiotic stress; ACC deaminase; seed priming; IAA
Online: 1 March 2021 (18:27:16 CET)
To date, soil salinity becomes a huge obstacle for food production worldwide since salt stress in plants is one of the major factors limiting agricultural productivity. It is estimated that a significant loss of crops (20%–50%) would be due to drought and salinity. To embark upon this harsh situation, numerous strategies such as plant breeding, plant genetic engineering, and a large variety of agricultural practices including the applications of plant growth-promoting rhizobacteria (PGPR) and seed biopriming technique have been developed to improve plant defense system against salt stress, resulting in higher crop yields to meet human’s increasing food demand in the future. In the present review, we update and discuss the advantageous roles of beneficial PGPR as green bioinoculants in mitigating the burden of high saline conditions on morphological parameters and on physio-biochemical attributes of plant crops via diverse mechanisms. In addition, the applications of PGPR as a useful tool in seed biopriming technique are also updated and discussed since this approach exhibits promising potentials in improving seed vigor, rapid seed germination, and seedling growth uniformity, Furthermore, the controversial findings regarding the fluctuation of antioxidants and osmolytes in PGPR-treated plants are also pointed out and discussed.
ARTICLE | doi:10.20944/preprints202202.0295.v1
Subject: Biology, Plant Sciences Keywords: Alfalfa; bZIP transcription factor; phylogenetic analysis; expression pattern; abiotic stress
Online: 23 February 2022 (13:40:34 CET)
Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies such as differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa. In the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in Arabidopsis thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that particular bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. However, further functional characterization of bZIP transcription factors in alfalfa will help illuminate the role they play in stress tolerance mechanisms in legumes and facilitate the molecular breeding of stress tolerance in alfalfa.
REVIEW | doi:10.20944/preprints202209.0117.v1
Subject: Life Sciences, Biotechnology Keywords: abiotic stress tolerance; base editing; CRISPR/Cas9; crop production; gene editing; prime editing
Online: 8 September 2022 (03:31:39 CEST)
Abiotic stresses, including drought, salinity, cold, heat, and heavy metals, extensively reduce global agricultural production. Approaches such as conventional breeding and transgenic breeding have been widely used to cope with these environmental stresses. The clustered regularly interspaced short palindromic repeat- Cas (CRISPR/Cas) based gene-editing tool has revolutionized due to its simplicity, accessibility, adaptability, flexibility, and wide applicability. This system has a great potential to build up crop varieties with enhanced tolerance against abiotic stresses. In this review, we summarize the most recent findings on understanding the mechanism of abiotic stress response in plants and the application of CRISPR/Cas mediated gene-editing system towards enhanced tolerance to drought, salinity, cold, heat, and heavy metals stresses. Furthermore, in this review, we highlighted the recent advancements in prime editing and base editing tools for crop improvement.
ARTICLE | doi:10.20944/preprints202010.0110.v1
Subject: Biology, Anatomy & Morphology Keywords: Abiotic stress; Linum album Ky. ex Boiss.; Morphological properties; Phenology; Pigments; Seed yield
Online: 6 October 2020 (09:02:20 CEST)
Linum album is an important medicinal plant contains important lignan compounds such as podophyllotoxin as well as fatty acids. Despite the high medicinal value, it has not been studied in agricultural conditions so far. This study was conducted to evaluate the morphological, phenological, and physiological responses of six L. album accessions under water deficit treatments (100% available water, 75%, 50%, and 25%) in pot conditions. Based on the results the morphological properties of accessions reduced due to water deficit. Accessions of UTLA7 and UTLA9 showed higher seed yield and dry weight of the vegetative part. The occurrence of phenological stages in the accessions showed a significant difference. Maturity was accelerated in plants under stress conditions, and accession of UTLA9 completed its growth earlier than others. Physiological responses of the accessions did not have the same trend based on the measured traits, and significant differences were observed depending on the trait and accession. The most important result of this study was the diversity of responses in different accessions. The results showed that the effect of water stress on the measured traits depends on the level of stress and accession, which suggests that it is possible to select the tolerable accessions for the production of the desired product. Based on the results, plant breeders may be able to use the chlorophyll content as a marker to identify tolerate L. album accessions.
REVIEW | doi:10.20944/preprints201911.0382.v1
Subject: Biology, Plant Sciences Keywords: abscisic acid; abiotic-stresses signaling; ubiquitination; seed-germination; e3 ubiquitin ligase; stomatal-regulation
Online: 30 November 2019 (09:20:52 CET)
Plants are immobile, and, to overcome harsh environmental conditions, such as drought, salt, and cold, they have evolved complex signaling pathways. Abscisic acid (ABA), an isoprenoid phytohormone, is a critical signaling mediator that regulates diverse biological processes in various organisms. Significant progress has been made in the determination and characterization of key ABA-mediated molecular factors involved in different stress responses, including stomatal closure and developmental processes, such as seed germination and bud dormancy. Since ABA-signaling is a complex signaling network that integrates with other signaling pathways, the dissection of its intricate regulatory network is necessary to understand the function of essential regulatory genes involved in ABA signaling. In the present review, we focus on two aspects of ABA signaling. First, the perception of the stress signal (abiotic and biotic) and the response network of ABA-signaling components that transduce the signal to the downstream pathway to respond to stress tolerance, regulation of stomata, and ABA signaling component ubiquitination. Second, ABA-signaling in plant development processes, such as lateral root growth regulation, seed germination, and flowering time regulation. Examining such diverse signal integration dynamics could enhance our understanding of the underlying genetic, biochemical, and molecular mechanisms of ABA signaling networks in plants.
ARTICLE | doi:10.20944/preprints202209.0345.v1
Subject: Biology, Ecology Keywords: Abiotic Stress; Amazon; Canga; Iron mining; Mineland Rehabilitation; Proteomics; Symbiosis
Online: 22 September 2022 (13:34:43 CEST)
Mimosa acutistipula is endemic to Brazil and grows in ferruginous outcrops (canga) in Serra dos Carajás, eastern Amazon, where one of the largest iron ore deposits in the world is located. Plants that develop in these ecosystems are subject to severe environmental conditions and must have adaptive mechanisms to grow and thrive in cangas. Mimosa acutistipula is a native species used to restore biodiversity in post-mining areas in canga. Understanding the molecular mechanisms involved in the adaptation of M. acutistipula in canga is essential to deduce the ability of native species to adapt to possible stressors in rehabilitating minelands over time. In this study, the root proteomic profiles of M. acutistipula grown in a native canga ecosystem and rehabilitating minelands were compared to identify essential proteins involved in the adaptation of this species in its native environment and that should enable its establishment in rehabilitating minelands. The results showed differentially abundant proteins, where 436 proteins with significant values (p < 0.05) and fold change ≥ 2 were more abundant in canga and 145 in roots from the rehabilitating minelands. Among them, a representative amount and diversity of proteins were related to responses to water deficit, heat, and responses to metal ions. Other identified proteins are involved in biocontrol activity against phytopathogens and symbiosis. This research provides insights into proteins involved in M. acutistipula responses to environmental stimuli, suggesting critical mechanisms to support the establishment of native canga plants in rehabilitating minelands over time.
REVIEW | doi:10.20944/preprints202108.0411.v1
Subject: Life Sciences, Biotechnology Keywords: abiotic stresses; gene-expression; genomics; ion homeostasis; plant growth and development; plasma membrane; sugar translocation
Online: 20 August 2021 (11:43:31 CEST)
Membrane transporters (MTs) are mainly localized at the plasma membrane (PM), tonoplast and vacuolar membrane (VM) of cells in all plant organs. Their work is to maintain the cellular homeostasis by controlling ionic movements across PM channels from roots to upper plant parts, xylem loading and remobilization of sugar molecules from photosynthesis tissues in the leaf (source) to roots, stem and seeds (sink) via phloem loading. The plant’s whole source-to-sink relationship is regulated by multiple transporting proteins in a highly sophisticated manner and driven based on different stages of plant growth and development (PG&D), and environmental changes. The MTs play a pivotal role in PG&D in terms of increased plant height, branches/tiller numbers, enhanced numbers, length and filled panicles per plant, seed yield and grain quality. Dynamic climatic changes disturbed the ionic balance (salt, drought and heavy metals) and sugar supply (cold and heat stress). Due to poor selectivity, some of the MTs also uptake toxic elements in the roots that negatively impact on PG&D, later on also exported to upper parts and then deteriorate the grain quality. As an adaptive strategy, in response to salt and HMs plants activated PM and VM localized MTs that export toxic elements into vacuole, and also translocate in the root’s tips and shoot. However, in case of drought, cold and heat stresses, MTs increased the water and sugar supply to all organs. In this review, we mainly reviewed recent literature from Arabidopsis, halophytes, and major field crops such as rice, wheat, maize and oilseed rape to argue on the global role of MTs in PG&D and abiotic stress tolerance. We also discussed the gene expression level changes and genomic variations within a species as well as within a family in response to developmental and environmental cues.
ARTICLE | doi:10.20944/preprints202001.0185.v1
Subject: Biology, Plant Sciences Keywords: Abiotic stress; Antioxidant defense; Glyoxalase; Ion homeostasis; Organic acid; Osmotic stress
Online: 17 January 2020 (10:02:34 CET)
Salinity is a serious environmental hazard which limits world agricultural production by adversely affects plant physiology and biochemistry. Hence increase tolerance against salt stress is very important. In this study, we explored the function of β-aminobutyric acid (BABA) in enhancing salt stress tolerance in rapeseed (Brassica napus L.). After pretreatment with BABA, seedlings were exposed to NaCl (100 mM and 150 mM) for 2 days. Salt stress increased Na content and decreased K content in shoot and root. It disrupted the antioxidant defense system by producing reactive oxygen species (ROS; H2O2 and O2•−), methylglyoxal (MG) content and causing oxidative stress. It also reduced the growth and photosynthetic pigments of seedlings but increased proline (Pro) content. However, BABA pretreatment in salt-stressed seedlings increased ascorbate (AsA) and glutathione (GSH) contents; GSH/GSSG ratio; and the activities of ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), glutathione reductase (GR), glutathione peroxidase (GPX), superoxide dismutase (SOD), catalase (CAT), glyoxalase I (Gly I), and glyoxalase II (Gly II) as well as growth and photosynthetic pigments of plants. In addition, compared to salt stress alone BABA increased Pro content, reduced the H2O2, MDA and MG contents and decreased Na content in root and increased K content in shoot and root of rapeseed seedlings.
ARTICLE | doi:10.20944/preprints202103.0223.v1
Subject: Biology, Anatomy & Morphology Keywords: Abiotic Stress; Forestry; Tree Physiology; Plant Selection; Urban Forestry
Online: 8 March 2021 (13:42:34 CET)
Responses to water stress were measured for sugar maple (Acer saccharum subsp. saccharum Marshall) sources from Oklahoma (Caddo sugar maple), Missouri, Tennessee, Ontario and a black maple (Acer saccharum subsp. nigrum F. Michx.) source from Iowa. Seedling sources were selected for differences in temperature and precipitation of their geographic origins. Seedlings were preconditioned through moist (watered daily) or dry (watered every 4-7 days) cycles and then exposed to prolonged water stress. Dry preconditioned sugar maple seedlings from Oklahoma, Missouri, and Tennessee, sources from warmer and/or drier climates with greater relative evapotranspiration potentials, declined less rapidly in net photosynthesis, stomatal conductance, and water use efficiency (WUE) as water stress increased than dry preconditioned seedlings from Ontario and Iowa having origins in cooler, moister climates. Under imposed water stress the Ontario and Iowa sourced seedlings increased their root to shoot ratios and decreased their specific leaf area, mechanisms for drought avoidance. However, no corresponding changes in these values occurred for Oklahoma, Missouri, and Tennessee sources. Results from this study suggest greater tolerance of water stress in the Oklahoma, Missouri and Tennessee ecotypes from the western and southern range of sugar maple resulted primarily with WUE rather than other water stress coping mechanisms.
ARTICLE | doi:10.20944/preprints202206.0197.v1
Subject: Life Sciences, Other Keywords: sodium chloride; photosystem II; Green Forest; carbon assimilation; salt-sensitive; C3 plant; climate change; abiotic stress
Online: 14 June 2022 (08:04:31 CEST)
Lettuce is a salt-sensitive crop and has a threshold electrical conductivity of 1.3–2.0 mS cm-1 and above that is considered detrimental. As there has been very little information on the physio-logical response of different critical stages of lettuce under different salt stress (SS), the current study is focused on investigating the effects of SS on the critical physiological traits influencing the carbon assimilation in different growth stages of lettuce. The experiment was conducted in deep-water culture hydroponic system in a greenhouse condition. Four levels of sodium chloride salt treatments (EC: 20, 16, 8, and 1.8 mS cm-1) were applied. During both growth stages (day 11 (GS1) and day 19 (GS2) after salt treatment), the leaf transpiration rate, stomatal conductance, and intercellular CO2 were severely decreased. However, the carbon assimilation rate remained unchanged under SS. Similarly, the water use efficiency increased under the SS. It is concluded that the increasing SS increased stomatal and non-stomatal limiting factors during GS1 suggesting the enhanced limitation in photosynthetic activity while no such trend was observed during GS2. The decreased gm with increased SS at GS1 and GS2 suggested that SS induced the irreversible decrease of gm, which in turn can be responsible for the transient reduction in the Vcmax and Jmax during GS2. Taken together, the evidence from this research recommends that varying the SS levels can significantly affect the physiological performance of lettuce at both growth stages.
ARTICLE | doi:10.20944/preprints201811.0352.v1
Subject: Biology, Plant Sciences Keywords: gene network; network analysis; transcription regulation network; Cytoscape; gene family evolution; divergence; A. thaliana; abiotic stress
Online: 15 November 2018 (09:02:34 CET)
Phylostratigraphic analysis is a way to look anew on phylogenetic data in the evolutionary aspect. It allows counting the evolutionary age based on the analysis of genes, their orthologs and finding the last common ancestor. We performed phylostratigraphic analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) determined by the Gene Ontology annotation. Comparison of the distributions of ages of genes associated with stresses of different type has shown the heat stress to involve older genes while the light stress – younger genes. At the same time, all types of stress are characterized by a significantly higher proportion of old genes (common to all eukaryotes) compared to the whole set of A.thaliana genes. This can be explained by the involvement of basic molecular processes in plant cells into the stress response. Reconstruction and graphical analysis of the gene network of the heat stress educed several clusters associated with different response functions. Some of these clusters contain only ancient genes. The results obtained show that the phylostratigraphic analysis reveals the fundamental features of the organization of gene networks and their evolution.
ARTICLE | doi:10.20944/preprints202109.0102.v1
Subject: Life Sciences, 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/preprints201806.0426.v1
Subject: Keywords: rice, abiotic stress, high temperature, drought, physiological responses, molecular mechanisms, systems biology
Online: 26 June 2018 (15:30:20 CEST)
Rice production, owing to its high-water requirement for cultivation, is very vulnerable to the threat of changing climate, particularly prolonged drought and high temperature. Such threats heighten the need for abiotic stress-resilient rice varieties with better yield potential. This review examines the physiological and molecular mechanisms of rice varieties to cope with stress conditions of drought (DS), high temperature (HTS) and their combination (DS-HTS). It appraises research studies in rice about its various phenotypic traits, genetic loci and response mechanisms to stress conditions to help craft new breeding strategies for rice varieties with improved resilience to abiotic stresses. This review consolidates available information on promising rice cultivars with desirable traits as well as advocates synergistic and complementary approaches in molecular and systems biology to develop new rice breeds that favorably respond to climate-induced abiotic stresses. The development of new breeding and cultivation strategies for climate-resilient rice varieties is a challenging task. It requires a comprehensive understanding of the various morphological, biochemical, physiological, and molecular components governing yield under drought and high temperature, but possible by implementing cohesive approaches involving molecular and systems biology approaches in genomics and molecular breeding, including genetic engineering.
REVIEW | doi:10.20944/preprints201807.0052.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Plant stress, abiotic stress, biotic stress, metabolomics, phytometabolomics, sensomics, phytohormonics, LC-MS/MS, NMR, targeted metabolomics, untargeted metabolomics, functional food.
Online: 3 July 2018 (14:18:19 CEST)
The breeding of stress-tolerant cultivated plants that would allow for a reduction in harvest losses and undesirable decrease in quality attributes requires a new quality of knowledge on molecular markers associated with relevant agronomic traits, on quantitative metabolic responses of plants on stress challenges, and on the mechanisms controlling the biosynthesis of these molecules. By combining metabolomics with genomics, transcriptomics and proteomics datasets a more comprehensive knowledge of the composition of crop plants used for food or animal feed is possible. In order to optimize crop trait developments, to enhance crop yields and quality, as well as to guarantee nutritional and health factors, that provides the possibility to create functional food or feedstuffs, the knowledge about the plants’ metabolome is crucial. Next to classical metabolomics studies, this review focusses on several metabolomics based working techniques, such as sensomics, lipidomics, hormonomics and phytometabolomics, which were used to characterize metabolome alterations during abiotic and biotic stress, to find resistant food crops with a preferred quality or at least to produce functional food crops are highlighted.
Subject: Earth Sciences, Geochemistry & Petrology Keywords: abiotic; hydrothermal; methane; clumped isotope
Online: 27 April 2020 (03:44:32 CEST)
Abiogenic hydrocarbons are fundamentally important for understanding the deep microbial communities and the origin of life. The generation of abiogenic hydrocarbons was proposed to be limited to ultramafic-hosted hydrothermal systems, fueled by the serpentinization product H2. Here, we present the discharge of short-chain alkanes from an andesitic rock-hosted Lutao geothermal field in the north Luzon arc, carrying abiotic chemical and isotopic signals. These abiogenic hydrocarbons were generated from CO2-H2O-rich fluid inclusions, where the long-term storage since Lutao volcanism (~ 1.3 Ma) allowed overcoming the sluggish kinetics of CO2 to CH4 reduction at temperatures of 174 - 206 oC. Natural abiogenic production of hydrocarbons, therefore, can be more ubiquitous than previously thought. The hypothesis regarding the origin of methane in Earth’s early atmosphere and its implication to the origin of life may require reconsideration.
REVIEW | doi:10.20944/preprints202012.0304.v1
Subject: Biology, Anatomy & Morphology Keywords: Vitrification; cooling; abiotic; biotic; stress; browning
Online: 14 December 2020 (08:17:26 CET)
Recent developments in the cryopreservation space has increased the trend in germplasm collections established through cryopreserved in vitro material. Cryopreservation of recalcitrant seeds through embryos and embryonic axes, is not uncommon. Tropical and sub-tropical plants are not acclimated to the cold season, therefore have no in-built natural resilience to the cold. Also, larger seeds from trees, such as avocado (Persea americana Mill.), mango (Mangifera indica) and durian (Durio zibethinus L.) are sensitive to desiccation, chilling and freezing stress, making them unsuitable for seed banking or cryopreservation. Alternatively, as seeds do not carry the same genetic make-up as the mother plant, especially in the context of woody rainforest species of which the cross-pollination is dominant; seed conservation does not serve the purpose of germplasm preservation. Other plant material and methods are needed for these plants to be successfully stored in liquid nitrogen (LN). One such method commonly used is shoot-tip cryopreservation which ensures the clonal fidelity of germplasm. There are many problems when using shoot tips of tropical recalcitrant-seeded species. These include: 1) the toxic effects of cryoprotective agents towards structural integrity; 2) optimum developmental stage for success and 3) oxidative stress associated with excision injury leading to necrosis triggering cell death and hindering regeneration for the shoot tips in culture. A pre-requisite for any cryopreservation system is the availability of an established tissue culture regeneration platform. This review will outline conservation strategies for avocado with special emphasis on attempts and improvements made in the cryopreservation space for storing this horticulturally important crop ‘avocado’ at ultra-low temperatures.
ARTICLE | doi:10.20944/preprints202201.0339.v1
Subject: Biology, Ecology Keywords: abiotic stress; proteomic; rehabilitating minelands; rhizosphere; symbiosis
Online: 24 January 2022 (10:07:29 CET)
Dioclea apurensis Kunth is native to ferruginous rocky outcrops (known as canga) in the eastern Amazon. Native cangas are considered hotspots of biological diversity and have one of the largest iron ore deposits in the world. There, D. apurensis can grow in post-mining areas where molecular mechanisms and rhizospheric interactions with soil microorganisms are expected to contribute to their establishment in rehabilitating minelands. In this study, we compare the root proteomic profile and rhizosphere-associated bacterial and fungal communities of D. apurensis growing in canga and a rehabilitating mineland to characterize the main mechanisms that allow the growth and establishment in post-mining areas. The results showed that proteins involved in response to oxidative stress, drought, excess of iron, and phosphorus deficiency were more accumulated in canga and, therefore, helped explain its high establishment rates in rehabilitating minelands. Rhizospheric selectivity of microorganisms was more evident in canga. The microbial community structure was mostly different between the two habitats, denoting that despite having its preferences, D. apurensis can associate with beneficial soil microorganisms without specificity. Therefore, its good performance in rehabilitating minelands can also be improved or attributed to its ability to cope with beneficial soil-borne microorganisms. Native plants with such adaptations must be used to enhance the rehabilitation process.
REVIEW | doi:10.20944/preprints201806.0455.v1
Online: 28 June 2018 (04:41:19 CEST)
Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence, and heavy metals. The effective management at molecular level is mandatory for thorough understanding of plant response to abiotic stress. The molecular mechanism of stress tolerance is complex and requires information at the omic level to understand it effectively. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. The emerging field of ionomics is also being employed for investigating abiotic stress tolerance in wheat. Omic approaches generate a huge amount of data, and adequate advancements in computational tools have been achieved for effective analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. In this review, we have described advances in omic tools in the view of conventional and modern approaches being used to dissect abiotic stress tolerance in wheat. Emphasis was given to approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). Comparative genomics and candidate gene approaches are also discussed considering identification of potential genomic loci, genes, and biochemical pathways involved in stress tolerance mechanism in wheat. This review also provides a comprehensive catalog of available online omic resources for wheat and its effective utilization. We have also addressed the significance of phenomics in the integrated approaches and recognized high-throughput multi-dimensional phenotyping as a major limiting factor for the improvement of abiotic stress tolerance in wheat.
ARTICLE | doi:10.20944/preprints202105.0593.v1
Online: 25 May 2021 (08:56:26 CEST)
Cacao is an understory plant cultivated under full-sun monocultures to multi-strata agroforestry systems, where cocoa trees are planted together with fruit, timber, firewood, and leguminous trees, or grown within thinned native forests. Under agroforestry systems of cultivation, cacao is subjected to excess shade due to high density of shade trees, and overgrown or unmanaged pruning of shade trees. Cacao is tolerant to shade, and the maximum photosynthetic rate occurs around irradiance of 400 μmol m−2 s−1 but excess shade reduces the irradiance further which is detrimental to photosynthesis and growth functions. Intra-specific variation is known to exist in cacao for the required saturation irradiance. A greenhouse study was implemented with 58 cacao genotypes selected from four geographically diverse groups: (i) wild cacao from river basins of the Peruvian Amazon, (PWC), (ii) Peruvian farmers’ collection (PFC), (iii) Brazilian cacao collection (BCC) and (iv) national and international cacao collections (NIC). All the cacao genotypes were subjected to 50% and 80% shade where photosynthetic photon flux density (PPFD) was 1000 and 400 μmol m-2 ּs-1 respectively. Intra-specific variations were observed for growth, physiological and nutritional traits, and tolerance to shade. Cacao genotypes tolerant to shade were: UNG-77 and UGU-130 from PWC; ICT-2173, ICT-2142, ICT-2172, ICT-1506, ICT-1087, and ICT-2171 from the PFC; PH-21, CA-14, PH-990 and PH-144 from BCC; and ICS-1, ICS-39, UF-613 and POUND-12 from NIC. Genotypes that tolerate excess shade might be useful plant types to maintain productivity and sustainability in agroforestry systems of cacao management.
REVIEW | doi:10.20944/preprints202105.0232.v1
Subject: Biology, Ecology Keywords: cyanobacteria, toxic, biotic factors, abiotic factors, interactions, allelopathy
Online: 11 May 2021 (10:36:33 CEST)
Environmental genetics-related modern methods are shown as important indicators of various cyanotoxins syntheses, and their knowledge and use are critically analyzed. Microcystins and other cyanotoxins loads and syntheses are related to different drivers, like various chemical elements and compounds (especially nutrients, such as nitrogen and phosphorus, and their ratio), then to the light, conductivity, temperature, and other climatical and hydrological factors, to which spatial and geographical features (such as the surface of the water bodies) have to be added. The biotic relationships include different specific and supraspecific, uni- and bilateral links between the cyanobacteria, and subsequently their synthesized toxins, and protozoans (or protoctists), chromists, macrophytes, different systematical and ecological groups of zooplankton, and others. The importance of, but also the gaps in, the knowledge and the scarcity of studies involving ectocrines mediated interactions between different groups of algae and plants are highlighted. The paper ends with an interesting classification of lakes' trophicity, illustrated with conceptual diagrams, based on possible scenarios of cyanobacteria behavior.
REVIEW | doi:10.20944/preprints202103.0085.v1
Subject: Biology, Anatomy & Morphology Keywords: Abiotic Stress; Ethylene; Jasomic acid; Mineral solubilization; Phytostimulants
Online: 2 March 2021 (12:17:01 CET)
This review presents a comprehensive and systematic study of the field of bacterial plant biostimulants and considers the fundamental and innovative principles underlying this technology. Plant biostimulants are an important tool for modern agriculture as part of an integrated crop management (ICM) system; helping make agriculture more sustainable and resilient. Plant biostimulants contain substance(s) and/or microorganisms whose function when applied to plants or the rhizosphere, is to stimulate natural processes to enhance plant nutrient uptake, nutrient use efficiency, tolerance to abiotic stress, biocontrol, and crop quality. The use of plant biostimulants has gained substantial and significant heed worldwide as an environment-friendly alternative for sustainable agricultural production. Presently, there is an increasing curiosity of industry and researchers in microbial biostimulants especially, bacterial plant biostimulants (BPBs) to improve crop growth and productivity. The BPBs that are based on PGPR (plant growth-promoting rhizobacteria) play plausible roles to promote/stimulate the crop plant growth through several mechanisms that include, i) nutrient acquisition by nitrogen (N2) fixation and solubilization of insoluble minerals (P, K, Zn), organic acids and siderophores, ii) antimicrobial metabolites and various lytic enzymes, iii) action of growth regulators and stress-responsive/induced phytohormones, iv) ameliorating abiotic stress like drought, high soil salinity, extreme temperatures, oxidative stress, and heavy metals by using different modes of action, and v) plant defense induction modes. Presenting here is a brief review emphasizing the applicability of BPBs as an innovative exertion to fulfill the current food crisis.
Subject: Biology, Plant Sciences Keywords: sunflower; growth-regulating factor; expression pattern; abiotic stress
Online: 11 December 2019 (04:58:22 CET)
Growth-regulating factor (GRF) is a plant-specific transcription factor family, which is involved in nearly all of the central developmental processes in plants. However, little is known about GRF family genes in cultivated sunflower. In this study, 17 GRF genes were identified and characterized from sunflower genome. Their gene structures, conserved motifs, chromosomal distributions and phylogenetic relationships were analyzed. The expression patterns of these genes were detected in various tissues of sunflower inbred line SK02R, which revealed that the 10 seed-specific GRF genes may play important roles during seed development in sunflower. Additionally, transcripts changes of the GRFs under two major abiotic stresses and phytohormones showed that most of the detected GRFs were reduced significantly by GA3 treatment, and other treatments(ABA, NaCl and PEG6000) differently regulated various sunflower growth-regulating factors at different time points. MiR396 target analysis indicated that there may exist a complicated homeostasis between miR396 and its targets GRF and WRKY transcription factor genes in cultivated sunflower. The phylogenetic and expression analyses of the GRF gene family in sunflower would be useful for further cloning and function exploration of the HaGRF genes.
REVIEW | doi:10.20944/preprints202205.0279.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Melatonin; NO; ROS; abiotic stress; NOmela; H2S; NRS; PTMs
Online: 20 May 2022 (13:35:00 CEST)
Melatonin (MEL), a ubiquitous indolamine, is a molecule whose regulatory role in plan metabolism has gained interest in the last decades. Likewise, nitric oxide (NO), a gasotransmitter, can also affect plant molecular pathways due to its function as a signalling molecule. Both MEL and NO can interact at multiple levels under abiotic stress, starting by their own biosynthetic pathways and inducing a particular signalling response in plants. This review summarizes the role of these molecules during plant development and fruit ripening, as well as their interactions. Due to the impact of climate change‐related abiotic stresses on agriculture, this review has also focused on their role in mediating abiotic stress tolerance and the mechanisms by which they operate, from upregulation of the whole antioxidant defence system to posttranductional modifications of important molecules. Their interactions and crosstalk with phytohormones and H2S is also discussed. Finally, we introduce NOmela, an emerging and very unknown molecule which seems to have a stronger potential than MEL and NO separately in mediating plant stress response.
REVIEW | doi:10.20944/preprints202006.0016.v1
Subject: Life Sciences, Genetics 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.
REVIEW | doi:10.20944/preprints201812.0028.v1
Subject: Biology, Plant Sciences Keywords: stomatal movement; calcium sensing receptor; phosphorylation; abiotic stress; calcium signaling
Online: 3 December 2018 (14:02:28 CET)
The calcium-sensing receptor (CAS), as a chloroplast thylakoid membrane protein, involved in the process of [Ca2+] ext-induced [Ca2+]cyt increase (CICI) in the plant. However, the underlying mechanism regulating this process is lacking. Furthermore, recent evidence suggests that CAS may perform additional roles in the plant. Here, we provide an update covering the multiple roles of CAS in stomatal movement regulation and calcium signaling in the plant. We also analysis the possible phosphorylation mechanism of CAS by light and discuss the role of CAS in abiotic stress (drought, salt stress) and biotic stresses (plant immune signaling). Finally, we provide a perspective for future experiments which are required to fill gaps in our understanding of the biological function of CAS in the plant.
REVIEW | doi:10.20944/preprints202103.0066.v1
Subject: Biology, Anatomy & Morphology Keywords: GRAS protein, DELLA, Intrinsically Disordered Proteins, Arbuscular Mycorrhizal association, abiotic stress
Online: 2 March 2021 (10:01:42 CET)
The GAI‐RGA ‐ and ‐SCR (GRAS) proteins belong to the plant-specific transcription factor gene family and involved in several developmental processes, phytohormone and phytochrome signaling, symbiosis, stress responses etc. GRAS proteins have a conserved GRAS domain at C-terminal and hypervariable N-terminal. The C-terminal conserved domain directly affects the function of the GRAS proteins. For instance, in Arabidopsis, mutations in this domain in Slender rice 1 (SLR1) and Repressor of GA (RGA) proteins cause significant phenotypic changes. GRAS proteins have been reported in more than 30 plant species and till now it has been divided into 17 subfamilies. This review highlighted GRAS protein's importance during several biological processes in plants, structural features of GRAS proteins, their expansion and diversification in the plants, GRAS-interacting proteins complexes and their role in biological processes. We also summarized available recent research that utilized CRISPR-Cas9 technology to manipulate GRAS genes in a plant for different traits. Further, the exploitation of GRAS genes in crop improvement programs has also been discussed
Subject: Chemistry, Analytical Chemistry Keywords: untargeted metabolomics; internal standard; deoxynivalenol; abiotic stress of wheat; matrix effects
Online: 6 October 2020 (13:37:38 CEST)
Stable isotope-assisted approaches can improve untargeted LC-HRMS metabolomics studies. Here, we demonstrate at the example of chemically stressed wheat that metabolome-wide internal standardization by globally 13C-labeled metabolite extract (GLMe-IS) of experimental-condition-matched biological samples can help to improve coverage of treatment-relevant metabolites and aid in the post-acquisition assessment of putative matrix effects in samples obtained upon different treatments. For this, native extracts of toxin- and mock-treated (control) wheat ears were standardized by the addition of uniformly-13C-labeled wheat ear extracts that were cultivated under similar experimental conditions (toxin-treatment and control) and measured with LC-HRMS. The results show that 996 wheat-derived metabolites were detected with the non-condition-matched 13C-labeled metabolite extract, while another 68 were only covered by the experimental-condition-matched GLMe-IS. Additional testing is performed with the assumption that GLMe-IS enables compensation for matrix effects. Although on average no severe matrix differences between both experimental conditions were found, individual metabolites may be affected as is demonstrated by wrong decisions with respect to the classification of significantly altered metabolites. When GLMe-IS was applied to compensate for matrix effects, 272 metabolites showed significantly altered levels between treated and control samples, 42 of which would not have been classified as such without GLMe-IS.
REVIEW | doi:10.20944/preprints202207.0404.v1
Subject: Biology, Plant Sciences Keywords: Abiotic stress; biotic stress; biotechnology; climate change; CRISPR; crop improvement; genome editing
Online: 26 July 2022 (10:44:22 CEST)
Climate change poses a serious threat to global agricultural activity and food production. To address this issue, plant genome editing technologies have been developed to provide an alternative solution for crop improvement. Unlike conventional breeding techniques (e.g., selective breeding and mutation breeding), modern genome editing tools offer more targeted and specific alterations of the plant genome to produce crops with desired traits, such as higher yield and/or stronger resilience to the changing environment. In this review, we discuss the current development and future applications of genome editing technologies in mitigating the impacts of biotic and abiotic stresses on agriculture. We focus specifically on the CRISPR/Cas system, which has been the center of attention in the last few years as a revolutionary genome-editing tool in various species. We also conducted a bibliographic analysis on CRISPR-related papers published from 2012 to 2021 (10 years) to identify trends and possible gaps in the CRISPR/Cas-related plant research. In addition, this review article outlines the current shortcomings and challenges of employing genome editing technologies in agriculture with notes on future prospective. We believe combining conventional and more innovative technologies in agriculture would be the key to optimizing crop improvement beyond the limitations of traditional agricultural practices.
REVIEW | doi:10.20944/preprints202109.0364.v1
Subject: Biology, Horticulture Keywords: stress tolerance; biological mechanisms; biotic/Abiotic stress; hybrid priming; high-quality seeds
Online: 21 September 2021 (14:02:07 CEST)
Farmers and seed companies constantly require high-quality seeds with excellent agronomic performance. However, faced with environmental adversity, limited natural resources and increasing food demand around the globe, more attention has turned to improving crop plant production by implementing efficient strategies. Seed priming technology has shown promising biological improvements leading to suitable agronomic performance in crop plants under adverse environmental conditions. Seeds are subjected to controlled conditions that are conducive to complex physiological, biochemical, and molecular changes, conferring specific stress tolerance to subsequent germination and growth conditions. In this review paper, we aimed to study the recent approaches in the efficiency of hydropriming, osmopriming, chemopriming, hormopriming, nanopriming, matrix priming, biopriming, physical priming and hybrid priming procedures in the production of crop plants under environmental adversity, as well as their biological mechanism changes. All priming methods demonstrated relevant changes in the biological mechanism related to crop plant production by mitigating salinity effects, heavy metals, and flooding stress and enhancing chilling, heat, drought and phytopathogen tolerance. We strongly recommend that researchers combine multiple priming methods, known as hybrid priming, in their investigations to provide novel technologies and additional biological approaches to enhance the knowledge of crop plant science. Thus, the findings shed light on the use of seed priming technology as a key strategy to increase crop plant production under environmental adversity by acquiring stress tolerance and enhancing agronomic traits to meet the global food demand.
REVIEW | doi:10.20944/preprints202012.0274.v1
Subject: Biology, Anatomy & Morphology Keywords: seed dormancy; germination; light-mediated process; abiotic stress; epigenetic control; translational control
Online: 11 December 2020 (10:30:09 CET)
The transition from a dormant to a germinating seed represents a crucial developmental switch in the life cycle of a plant. Subsequent transition from a germinating seed to an autotrophic organism also requires a robust and multi-layered control. Seed germination and seedling growth are multistep processes, involving both internal and external signals, which lead to a fine-tuning control network.
ARTICLE | doi:10.20944/preprints202008.0684.v1
Subject: Biology, Ecology Keywords: Chlorophyll Fluorescence; SIF; Drought; Spectral Vegetation Indices; GOME-2; Abiotic Stress; Caatinga
Online: 30 August 2020 (18:24:28 CEST)
Sun-Induced chlorophyll Fluorescence (SIF) relates directly to photosynthesis yield and stress but there are still uncertainties in its interpretation. Most of these uncertainties concern the influences of the emitting vegetation’s structure (e.g., leaf angles, leaf clumping) and biochemistry (e.g., chlorophyll content, other pigments) on the radiative transfer of fluorescent photons. The Caatinga is a large region at northeast Brazil of semiarid climate and heterogeneous vegetation, where such biochemical and structural characteristics can vary greatly even within a single hectare. With this study we aimed to characterize eleven years of SIF seasonal variation from Caatinga vegetation (2007 to 2017) and to study its responses to a major drought in 2012. Orbital SIF data from the instrument GOME-2 was used along with MODIS MAIAC EVI and NDVI. Environmental data included precipitation rate (TRMM), surface temperature (MODIS) and soil moisture (ESA CCI). To support the interpretation of SIF responses we have used red and far-red SIF adjusted by the Sun’s zenith angle (SIF-SZA) and by daily Photosynthetically Active Radiation (dSIF). Furthermore, we have also adjusted SIF through two contrasting formulations using NDVI data as proxy for structure and biochemistry, based on previous leaf-level and landscape level studies: SIF-Yield and SIF-Prod. Data was tested with time-series decomposition, rank correlation, spatial correlation and Linear Mixed Models (LMM). Results show that GOME-2 SIF and adjusted SIF formulations responded consistently to the observed environmental variation and showed a marked decrease in SIF emissions in response to a 2012 drought, that was generally larger than the corresponding NDVI and EVI decreases. Drought sensitivity of SIF, as inferred from LMM slopes, was correlated to land cover at different regions of the Caatinga. This is the first study to show correlation between landscape-level SIF and an emergent property of ecosystems (i.e., resilience), showcasing the value of remotely sensed fluorescence for ecological studies.
REVIEW | doi:10.20944/preprints202010.0532.v1
Subject: Biology, Anatomy & Morphology Keywords: Biotic stress; Abiotic stress; climate change; Plant Transcription Factors; Food Security; Crop Improvement
Online: 26 October 2020 (14:26:31 CET)
Crop plants should be resilient to climatic factors in order to feed ever-increasing populations. Plants have developed stress-responsive mechanisms by changing their metabolic pathways and switching the stress-responsive genes. The discovery of plant transcriptional factors (TFs) as key regulators of different biotic and abiotic stresses have opened up new horizons for plant scientists. TFs perceive the signal and switch certain stress-responsive genes on and off by binding to different cis-regulatory elements. The above 50 species of plant TFs have been reported in nature. DREB, bZIP, MYB, NAC, Zinc-finger, HSF, Dof, WRKY, and NF-Y are important with respect to biotic and abiotic stresses whereas the role of many TFs is yet to explore. In this review, we summarize the role of different stress-responsive TFs with respect to biotic and abiotic stresses. Further, challenges and future opportunities linked with TFs for developing climate-resilient crops are also elaborated.
REVIEW | doi:10.20944/preprints202010.0639.v1
Subject: Life Sciences, Biochemistry Keywords: Plants; polyamines; abiotic stresses; biotic stresses; transgenic plants; Plant-pathogen interaction; Plants-fungal interaction
Online: 30 October 2020 (13:10:51 CET)
The biotic and abiotic stresses are the main causes of the loss of agricultural crops productivity, their normal growth and development in the environment. It has been calculated that two-thirds of the major crops are frequently lost due to adverse environmental conditions. The productivity of crops under unfavorable environmental stresses is apparently the main challenge to the breeders and farmers where polyamines (PAs) play diverse roles in environmental stimuli. PAs (putrescine, spermidine, and spermine) are low molecular weight positively charge compounds have the active potential power to negative charge molecules (DNA, RNA, and proteins) is widely distributed in all living organisms. Evidence showed that PAs contribute a lot of different physiological and biological functions, such as cell growth and development, controlling the cell cycle, involve in gene expression, cell signaling, replication, transcription, translation, and membrane stabilization. Naturally occurring polyamines activity acuminated to their involvement with different biotic and abiotic stresses and contribute to the survival of the plant in the environment. Here, we have described the potential mechanisms, synthesis, and various roles of PAs during stresses tolerant and disease resistance.
ARTICLE | doi:10.20944/preprints202104.0018.v1
Subject: Biology, Anatomy & Morphology Keywords: abiotic stress; acetaldehyde; hexenal; LOX products; mass spectrometry; methanol; proton-transfer reaction; tropical crop species
Online: 1 April 2021 (12:50:17 CEST)
Leaf mechanical wounding triggers a rapid, within minutes, release of a blend of volatile organic compounds (VOCs). Wounding-induced VOC blend is mainly composed of oxygenated ubiquitous stress volatiles such as methanol and volatile products of lipoxygenase (LOX) pathway (mainly C5 and C6 alcohols and aldehydes and their derivatives), but also includes multiple minor VOCs that collectively act as infochemicals inducing defences in non-damaged plant leaves, neighbouring plants and attracting herbivore enemies. Till present, interspecific variability of the rate of induction and magnitude of wounding-induced emissions, and the extent to which plant structural traits and physiological activity alter these emissions are poorly known. Particularly scarce is the information of the induced emissions in tropical agricultural plant species despite their economic importance and large area of cultivation at regional to global scales. We chose five tropical crops with varying photosynthetic activity and leaf structural characteristics: Abelmoschus esculentus, Amaranthus cruentus, Amaranthus hybridus, Solanum aethiopicum and Telfairia occidentalis to characterize the kinetics and magnitude of wounding-induced emissions, hypothesizing that the induced emission response is greater and faster in physiologically more active species with greater photosynthetic activity than in less active species. Rapid highly repeatable leaf wounds (12-mm cuts) were generated by a within-leaf-chamber cutting knife. Wounding-induced VOC emissions were measured continuously with a proton-transfer reaction time-of-flight mass spectrometer and gas-chromatography mass spectrometry was used to separate isomers. Twenty-three ion VOCs and twelve terpenoid molecule structures were identified, whereas ubiquitous stress volatiles methanol (on average 40% of total emissions), hexenal (24%), and acetaldehyde (11%) were the main compounds across the species. Emissions of low-weight oxygenated compounds (LOC, 70% of total), and LOX products (29%) were positively correlated across species, but minor VOC components, monoterpenoids and benzenoids were negatively correlated with LOC and LOX, indicating a reverse relationship between signal specificity and strength. There was a large interspecific variability in the rate of induction and emission magnitude, but the hypothesis of a stronger emission response in physiologically more active species was only partly supported. In addition, the overall emission levels were somewhat lower with different emission blend compared to the data reported for wild species, as well as different shares for the VOCs in the blend. The study demonstrates that wounding-dependent emissions from tropical agricultural crops can significantly contribute to atmospheric volatiles, and these emissions cannot be predicted based on current evidence of wild plant model systems.
REVIEW | doi:10.20944/preprints202007.0333.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Abiotic stress; Biotic stress; Adaptation; Climate change; Diaseases; Diversity; Genetic Resources; Gene bank; Wild relatives
Online: 15 July 2020 (11:21:07 CEST)
Abstract: A large number of collecting expeditions were launched in regions of ‘centers of diversity’ and hundreds of thousands of sample have been collected and stored in gene banks as ‘genetic resources’. So far, only a small number of the samples have been evaluated for their biotic and abiotic stress tolerance. Now, their time to become useful has come. A new global phenomenon has arisen – climate change. The crop genetic resources and their wild progenitors that have survived countless years of changing environment during the last 11,000 years could harbor genes that may be useful under the new growing conditions and environmental factors thrown up by climate change and global warming. With the deployment of modern bio-engineering techniques selected genes or gene fragments can be transferred from genetic resources to modern varieties of crop plants to make them well-prepared to mitigate the effects of global warming and climate change. The latter is the most serious issue facing plant breeders today. New pests and diseases could affect crop production. These review paper discusses various impacts and issues as a result of this phenomenon and suggest ways to safeguard our most important crops through better management of crop plant genetic resources in the near future.
REVIEW | doi:10.20944/preprints201801.0223.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: abiotic stress; antioxidant defense; enzyme regulations; oxidative stress; plant nutrients; reactive oxygen species; soil fertility
Online: 24 January 2018 (07:01:05 CET)
Among the plant nutrients potassium (K) is one of the vital elements required for plant growth and physiology. Potassium is not only a constituent of plant structure but also plays regulatory function in several biochemical processes related to protein synthesis, carbohydrate metabolism, enzyme activation. There are several physiological processes like stomatal regulation and photosynthesis are dependent on K. In the recent decades K was found to provide abiotic stress tolerance. Under salt stress, K helps in maintaining ion homeostasis and regulation of osmotic balance. Under drought stress condition K regulates the stomatal opening and makes the plants adaptive to water deficit. Many reports provided the notion that K enhances the antioxidant defense in plants and therefore, protects the plants from oxidative stress under various environmental adversities. Also, it provides some cellular signaling alone or in association with other signaling molecules and phytohormones. Although a considerable progress in understanding K-induced abiotic stress tolerance in plants has been achieved the exact molecular mechanisms of such protections are still under research. In this review, we summarized the recent literature on the biological functions of K, its uptake, and translocation and its role in plant abiotic stress tolerance.
ARTICLE | doi:10.20944/preprints202006.0228.v1
Subject: Biology, Horticulture Keywords: crop genetics; Solanum tuberosum; abiotic stress; phenylpropanoids; essential amino acid; transcriptome; small RNA; comparative genomics; nutrition
Online: 18 June 2020 (09:15:21 CEST)
Potato is among one of the most important food crops, yet maintaining plant productivity in this drought-sensitive crop has become a challenge. Competition for scarce water resources and the continued effects of global warming exacerbate current constraints on crop production. While plants’ response to drought in above-ground tissues has been well documented, the regulatory cascades in developing tubers have been largely unexplored. Using the commercial Canadian cultivar ‘Vigor’, plants were subjected to a drought treatment under high-tunnels causing a 4 ℃ increase in canopy temperature when compared to the well-watered control. Tubers were sampled for RNAseq and metabolite analysis. Approximately 2600 genes and 3898 transcripts were differentially expressed by at least four-fold in drought-stressed potato tubers, with 75 % and 69 % being down-regulated respectively. A further 229 small RNAs were implicated in gene regulation during drought. The comparison of protein homologues between Solanum tuberosum L. and Arabidopsis thaliana L. indicates that downregulated genes are associated with phenylpropanoid, carotenoid, and patatin biosynthesis. This suggests that there may be nutritive implications to drought stress occurring during the potato tuber bulking phase in sensitive cultivars.
ARTICLE | doi:10.20944/preprints202004.0235.v1
Subject: Earth Sciences, Environmental Sciences Keywords: abiotic stress; metro-scale; physiological acclimation; urban leaf morphology; red maple trees; stomate size; urban forests
Online: 15 April 2020 (09:32:30 CEST)
Environmental conditions, such as temperature, carbon dioxide, and nutrient availability, are altered by urban conditions at regional scales with potential for impact on tree leaf structure. Our goal was to compare leaf morphological characteristics driven by physiological acclimation in red maple (Acer rubrum L.) trees in deciduous forests embedded in a small (Newark, DE) and a large (Philadelphia, PA) city. The study was conducted in six urban forests on eighteen mature red maple trees in a long-term urban forest network. We hypothesized that red maples in Philadelphia forests compared to Newark forests will have a thicker upper epidermal layer, spongy palisade and mesophyll layer, longer and wider stomates, and lower stomate density. Additionally, we hypothesized that red maples in Philadelphia forests compared to Newark forests will have lower leaf water content and specific leaf area, and greater leaf thickness, fresh leaf weight, dry leaf weight, and leaf dry matter content. Our results for stomate length and stomate width supported our predictions; red maple leaves had longer and wider stomates in Philadelphia forests than in Newark forests. The increased stomate size in red maple trees suggests potential altered gas exchange behavior and mutual abiotic stress mitigation responses in red maple to greater urbanization impacts in Philadelphia forests. This supports previous findings of possible physiological and biochemical acclimation of red maple trees to urban conditions. Furthermore, the findings from this study suggest red maple trees may be a good biomonitor of regional scale impacts in urban environments.
ARTICLE | doi:10.20944/preprints202204.0208.v1
Subject: Life Sciences, Molecular Biology Keywords: sulfate deficiency; Arabidopsis thaliana; Solanum lycopersicum; Triticum aestivum; LSU; response to low sulfur; abiotic stress; sulfur nutrition
Online: 22 April 2022 (03:32:19 CEST)
LSU (RESPONSE TO LOW SULFUR) proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. However, little is known about the LSU gene repertoire and evolution of this family in land plants. In this work, a total of 270 LSU family members were identified using 134 land plant species with whole genome sequence available. Phylogenetic analysis revealed that LSU genes belong to a Spermatophyta-specific gene family, and their homologs are distributed in three major groups, two for dicotyledons and one group for monocotyledons. Moreover, we analyzed the expression of LSU genes in one representative species of each phylogenetic group (wheat, tomato and Arabidopsis) and found a conserved response to S-deficiency, suggesting that these genes might play a key role in S stress responses. Accordingly, Arabidopsis lsu2 knockout mutant plants showed increased levels of internal sulfate content and lower levels of expression of different key genes involved in S deficiency and metabolism like SDI2 and APR3. In summary, our results indicate that LSU genes are evolutionarily conserved in angiosperms and that specific members of this family might play an important role regulation of S transport and assimilation.
ARTICLE | doi:10.20944/preprints202104.0344.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Lysine; Rice; Amino Acids; Saline Stress; Abiotic Stress; Gene Regulatory Network; Bayesian Network; Parameter Estimation; Inference; RNA Seq
Online: 13 April 2021 (10:52:26 CEST)
Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the human body’s healthy functioning. Rice is a staple food for large proportion of the global population, thus increasing the lysine content in rice will improve its nutritional value. In this paper, we studied the lysine biosynthesis pathway in rice (Oryza Sativa) to identify the regulators of the lysine reporter gene LYSA (LOC_Os02g24354). Genetically intervening at the regulators has the potential to increase the overall lysine content in rice. We modeled the lysine biosynthesis pathway in rice seedlings under normal and saline (NaCl) stress conditions using Bayesian networks. We estimated the model parameters using experimental data and identified the gene DAPF(LOC_Os12g37960) as a positive regulator of the lysine reporter gene LYSA under both normal and saline stress conditions. Based on this analysis, we conclude that the gene DAPF is a potent candidate for genetic intervention. Upregulating DAPF using methods such as CRISPR-Cas9 has the potential to upregulate the lysine reporter gene LYSA and increase the overall lysine content in rice.
REVIEW | doi:10.20944/preprints202102.0136.v1
Subject: Life Sciences, Biochemistry Keywords: endophytes; resistance inducers; biological control; abiotic stress; plant-microbe interactions; sustainability; integrated pest management; microorganisms; plant disease control
Online: 4 February 2021 (12:07:42 CET)
Plant diseases cause losses of approximately 16% globally. Thus, management measures must be implemented to mitigate losses and guarantee food production. In addition to traditional management measures, resistance induction and biological control have gained ground in agriculture due to their enormous potential. Endophytic fungi colonize plant tissues internally and have the potential to act as biological control agents, as elicitors in the process of resistance induction and in attenuating abiotic stresses. In this review, we list the action of this group of microorganisms as potential agents which can act in controlling plant diseases and describe several examples in which endophytes were able to reduce the damage caused by pathogens and adverse conditions. This is due to their arsenal of molecules generated during the interaction by which they form a kind of biological shield in the plant. Studies on these microorganisms have grown due to the existing diversity and the multiple benefits they can offer. Finally, considering that endophytic fungi can be an important tool in managing diseases due to the large amount of biologically active substances produced, bioprospecting this class of microorganisms is tending to increase and generate valuable products.
REVIEW | doi:10.20944/preprints202006.0123.v1
Subject: Life Sciences, Molecular Biology Keywords: Lignocellulosic biomass crops; biofuels; plant miRNAs; miR156; miR156/SPL-system; plant biotechnology; abiotic and biotic stresses; bio-confinement
Online: 9 June 2020 (11:52:23 CEST)
Currently, energy security and environmental degradation are the two biggest challenges before humanity that can be surmounted with the use of green and sustainable biofuels produced from lignocellulosic crops. In the future, to ensure adequate and cost-effective supply of biofuels, it requires a sufficient amount of amenable and quality lignocellulosic feedstocks. Therefore, agricultural yields of lignocellulosic biomass crops should be substantially increased by intense genetic maneuvering of key gene regulatory mechanisms and signaling pathways that control plant biomass yield. Recently, numerous miRNAs families are identified, characterized, and validated across the plant kingdom. Plant microRNAs (miRNAs) are 21 to 24 nucleotides long, non-coding small RNAs, act as regulators of their target genes via inducing modifications in transcription, translation, and epigenome. MiRNAs represent many hallmark characteristics like sequence-specific regulation, tissue, and species-specific expression, evolutionary conservation, and functional diversity. They coordinate well physiological and life cycle processes in plants under adverse environmental conditions. Hence, miRNAs offer accurate, precise, and efficient regulatory switches in the miRNA-targeted genetic networks. It is evident from the study of the miR156 family and its target SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes network that controls highly significant agronomic traits in crop plants. The miR156/SPL module acts as a master circuit that synchronizes many intricate complex biological functions such as growth and development, and metabolic processes by sensing internal and external environmental signals in plants. Therefore, miR156 can prove a potential target for miRNAs based plant biotechnology to harmonize complex biofuel traits and improve biomass yield in lignocellulosic biomass crops.