ARTICLE | doi:10.20944/preprints202205.0231.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: vegetation indices; precision farming; hybrid; phenotyping; remote sensing
Online: 17 May 2022 (12:47:44 CEST)
Abstract: Early assessment of crop development is a key aspect of precision agriculture. Shortening the time of response before a deficit of irrigation, nutrients and damage by diseases is one of the usual concerns in agriculture. Early prediction of crop yields can increase profitability in the farmer's economy. In this study we aimed to predict the yield of four maize commercial hybrids (Dekalb7508, Advanta9313, MH_INIA619 and Exp_05PMLM) using remotely sensed spectral vegetation indices (VI). A total of 10 VI (NDVI, GNDVI, GCI, RVI, NDRE, CIRE, CVI, MCARI, SAVI, and CCCI) were considered for evaluating crop yield and plant cover at 31, 39, 42, 46 and 51 days after sowing (DAS). A multivariate analysis was applied using principal component analysis (PCA), linear regression, and r-Pearson correlation. In the present study, highly significant correlations were found between plant cover with VIs at 46 (GNDVI, GCI, RVI, NDRE, CIRE and CCCI) and 51 DAS (GNDVI, GCI, NDRE, CIRE, CVI, MCARI and CCCI). The PCA indicated a clear discrimination of the dates evaluated with VIs at 31, 39 and 51 DAS. The inclusion of the CIRE and NDRE in the prediction model contributed to estimate the performance, showing greater precision at 51 DAS. The use of RPAS to monitor crops allows optimizing resources and helps in making timely decisions in agriculture in Peru.
ARTICLE | doi:10.20944/preprints202301.0345.v1
Subject: Life Sciences, Genetics Keywords: Fabaceae; bioinformatics; molecular markers; neglected crop; genomics
Online: 19 January 2023 (03:57:25 CET)
Lupinus mutabilis Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have been mainly focused on morphological features, however, the have not been molecularly characterized. Currently, it is possible to explore genetic parameters of plants with reliable and modern methods like genotyping-by-sequencing (GBS). We here for the first time used single nucleotide polymorphisms (SNPs) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, similar to the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59 %) and indicated that variability within populations is 92.41 %. Population divergence (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, similar to other Lupinus species, tarwi also depends on cross-pollination. SNPs markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.
DATA DESCRIPTOR | doi:10.20944/preprints202208.0349.v1
Subject: Life Sciences, Genetics Keywords: NGS; Andean; neglected breed; genome
Online: 18 August 2022 (11:12:25 CEST)
The Peruvian creole cattle (PCC) is a neglected breed, and is an essential livestock resource in the Andean region of Peru. To develop a modern breeding program and conservation strategies for the PCC, a better understanding of the genetics of this breed is needed. We sequenced the whole genome of the PCC using a paired-end 150 strategy on the Illumina HiSeq 2500 platform, obtaining 320 GB of sequencing data. The obtained genome size of the PCC was 2.77 Gb with a contig N50 of 108Mb and 92.59% complete BUSCOs. Also, we identified 40.22% of repetitive DNA of the genome assembly, of which retroelements occupy 32.39% of the total genome. A total of 19,803 protein-coding genes were annotated in the PCC genome. We downloaded proteomes and genomes of the Bovinae subfamily, and conducted a comparative analysis with our draft genome. Phylogenomic analysis showed that PCC is related to Bos indicus. Also, we identified 7,746 family genes shared among the Bovinae subfamily. This first PCC genome is expected to contribute to a better understanding of its genetics to adapt to the tough conditions of the Andean ecosystem, and evolution.