U.S. flag

An official website of the United States government

UPIC

    Unique Pattern Informative Combinations (UPIC), a decision tool for the cost-effective design of DNA fingerprinting/genotyping experiments using simple-sequence/tandem repeat (SSR/STR) markers.

    Data from: Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection

      Virulence shifts in populations of *Puccinia striiformis* f. sp. *tritici* (*Pst*), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of *Pst*, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments.

      Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans

        The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs, to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses.

        SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley"

          The 318 sampled wild barley accensions, known as the Wild Barley Diversity Collection (WBDC), were genotyped using the Illumina Golden Gate Genotyping Assay with two Barley Oligo Pool assay chips (BOPA1 and BOPA2). The genotype calls were based on machine-scored data using the program ALCHEMY and the SNPs were annotated using the program SNPMeta. The BOPA1 & 2 files contains the output of the ALCHEMY program.

          Musa Germplasm Information System

            The Musa Germplasm Information System (MGIS) contains key information on Musa germplasm diversity, including passport data, botanical classification, morpho-taxonomic descriptors, molecular studies, plant photographs and GIS information on 4616 accessions managed in 21 collections around the world, making it the most extensive source of information on banana genetic resources.

            Switchgrass ESTs and SNPs

              As part of our project, “Developing Association Mapping in Polyploid Perennial Biofuel Grasses” (DOE-USDA Plant Feedstock Genomics for Bioenergy Program grant DE-A102-07ER64454)*, two SNP discovery initiatives were carried out. The earlier one (2009) was an approach based on EST sequences. The latest initiative (2011-12) adopted a more powerful approach, based on GBS (Genotyping by Sequencing). We believe that the SNP markers identified in these studies will greatly enhance breeding efforts that target the improvement of key biofuel traits and the development of new switchgrass cultivars.