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34 results for “Diversity Panel”
DATASET: characterization of the seed coat extractable phenolic profile and color in 308 common bean lines of the Spanish Diversity Panel
<p>Characterizarion of the seed coat extractable phenolic profile and color in 308 common bean lines of the Spanish Diversity Panel</p>
WEST Diversity Panel GBS information (Ferguson et al., 2020)
<p>Genotyping by sequencing information (5,512,653 SNPs on 850 individuals [842 unique]) used in the manuscript "Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions" (Ferguson et al., 2020) DOI:10.1101/2020.11.02.365213</p> <p>The information, data, or work presented herein was funded in part by the Advanced Research Projects Agency-Energy (ARPA-E), U.S. Department of Energy, under Award Number DE-DE-AR0000661. The views and opinions of the authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.</p>
DATASET: Genotyping by sequencing of the common bean Spanish Diversity Panel
<p>Genotyping by sequencing of 308 common bean lines included in the Spanish Diversity Panel. The ApeKI restriction enzyme was used. The sequencing reads were aligned using the reference genome V2.1 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris). A total of 11,763 SNP markers are included in this dataset after filtering for missing values (< 10%) and minor allele frequency (MAF> 0.05). </p>
Natural variation across Arabidopsis diversity panel in early responses to salt stress
<p>The data of Arabidopsis thaliana accessions which were grown according to the established protocol for studying salt stress in soil experiment (described in detail here dx.doi.org/10.17504/protocols.io.4xzgxp6), in the PSI facility, Czech Republic. </p>
Spatially corrected dataset for natural variation across Arabidopsis diversity panel in early responses to salt stress
<p>The spatially corrected data of Arabidopsis thaliana accessions, which were grown according to the established protocol for studying salt stress in soil experiment (described in detail here dx.doi.org/10.17504/protocols.io.4xzgxp6), in the PSI facility, Czech Republic.</p> <p>The spatial correction was done using the asreml package. The data was subsequently used for the Genome-Wide Association Study. </p>
F I G U R E 3 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 3 A priori discriminant analysis of principal components (DAPC) plot of Camel trout. Each point represents the genotype of an individual fish, with centroids for each site labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis
F I G U R E 1 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 1 Map showing the location of rivers sampled for brown trout within the UK, France and Ireland. The left panel shows the rivers used to assess the performance of the single nucleotide polymorphisms (SNP) panel at characterising genetic parameters within and outside the target region. The top right (blue) panel shows the locations of the four sampled rivers in Mount's Bay, Cornwall (Case Study 1). The bottom right (red) panel shows the location of the sample locations in the Camel catchment (Case Study 2). The red box within the bottom right panel gives the position of the impassable De Lank quarry site
F I G U R E 2 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 2 A priori discriminant analysis of principal components (DAPC) of trout genotypes from rivers flowing into Mount's Bay, Cornwall. Individuals are represented by individual points, with centroids for each river labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis
F I G U R E 4 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 4 Correlation between geographic distance (km) against genetic distance (linear FST) for the trout samples from the River Camel. The red points represent those between the De Lank and all other sites, the black points for all pair-wise comparisons excluding the De Lank. Linear regression for all sites including the De Lank is given by the red line (r2 = 0.321, P = 0.231), and linear regression for all pair-wise sites excluding the De Lank is given by the black line (r2 = 0.658, P = 0.0671)
Performance of a durum wheat diversity panel under different management systems
<p>Raw data of a 3-year durum wheat trial carried out at Martonvásár, Hungary, from 2020 to 2022 under three different management systems, i.e. conventional high-input, conventional low-input and certified organic.</p>
Description of the HealthyMinorCereals oat (Avena sativa L.) diversity panel and best linear unbiased estimators (BLUEs) of agro-morphological traits
<p>Best linear unbiased estimators (BLUEs) of various agro-morphological traits of oat (Avena sativa) germplasm evaluated in Estonia and the Czech Republic between 2014 and 2019 (9 environments in total) within the FP7 HealthyMinorCereals project.</p>
k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase II) Part 1/3
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k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase) Part 3/3
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k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase II) Part 2/3
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Characterization data for the EtNAM population and Ethiopian durum wheat landraces diversity panel
<p>In smallholder, low-input farming systems diffused in the Global South, farmers select and propagate crop varieties based on their traditional knowledge and experience. A quantitative integration of their knowledge into breeding pipelines may support the sustainable intensification of local farming. This data entry combines genomics with socioeconomics to tap into traditional knowledge in smallholder farming systems, focusing on durum wheat (<em>Triticum durum </em>Desf.). Data refer to a large nested association mapping (EtNAM) population that we developed by recombining elite international breeding line with Ethiopian traditional varieties maintained by local farmers. This entry carries also molecular and phenotypic data produced on a diversity panel (DP) of Ethiopian landraces previously characterized in four year-location combinations and published in Mengistu et al 2016 (<a href="https://doi.org/10.1111/pbi.12538">https://doi.org/10.1111/pbi.12538</a>). </p> <p>EtNAM lines and DP genotypes were evaluated for agronomic performances and farmers' appreciation in multiple locations, reveailing that gender and location can influence farmers' preference and that women and men farmers can consistently identify the best durum wheat genotypes. We used this data to train a genomic selection (GS) model with farmer scores to show that their prediction accuracy over grain yield was higher than that of the benchmark GS model trained on grain yield. The data was also used in a genome wide association mapping (GWAS) and quantitative trait locus (QTL) mapping to identify genetic determinants of agronomic traits and farmer scores. Our data shows that farmers' traditional knowledge can be integrated in a quantitative framework to increase genetic gain in pre-breeding programs, supporting genomics-driven breeding for local adaptation.</p> <p>The Rdata files contain phenotypic and molecular characterization data for 1,200 recombinant inbred lines (RILs) deriving from the EtNAM and phenotypic and molecular characterization data for 400 durum wheat genotypes in the Ethiopian DP.</p>
Vegetative biomass production under different inorganic nitrogen forms of the USDA rice (Oryza sativa L.) diversity panel 1
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Characterization data for the EtNAM population and Ethiopian durum wheat landraces diversity panel
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Data from: Genome assembly of a diversity panel of Chenopodium quinoa
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NBS-LRR PacBio sequencing from a Glycine max diversity panel
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Data from: Genetic analysis of sugarcane mosaic virus resistance in the Wisconsin Diversity Panel of maize
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