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Ag Data Commons Maintenance - Friday 03/31/23

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Data from: Genome wide association study of thyroid hormone levels following challenge with porcine reproductive and respiratory syndrome virus

    Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to PRRSV infection. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with PRRSV.

    Data from: Mapping the Quantitative Field Resistance to Stripe Rust in a Hard Winter Wheat Population ‘Overley’ × ‘Overland’

      This study was conducted to identify quantitative trait loci (QTL) associated with field resistance to stripe rust, also known as yellow rust (YR), in hard winter wheat. Stripe rust infection type and severity were rated in recombinant inbred lines (RILs, n=204) derived from a cross between hard red winter wheat cultivars ‘Overley’ and ‘Overland’ in replicated field trials in the Great Plains and Pacific Northwest.

      Data from: Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

        The following is taken directly from the introduction of the paper. In this study, we used a pure drift FST model [11] which assumes all animals originated from the same ancestral population. This model was applied to taurine and zebu animals to identify loci under selection. These two groups correspond to the main (and most ancestral) separation of domestic cattle, which in most but not all cases corresponds to animals adapted to tropical and temperate environments. The identification of such loci can aid in the identification of genes and genomic variants that are related to environmental adaptation and/or selection derived from human agro-pastoral activities.

        Data from: Estimation of pool construction and technical error

          Animals were incorporated into pools in different proportions to estimate error and evaluate factors influencing error. Animals were incorporated into 2 types of pools, sub-pools and super pools. Within phenotype, liver abscess or normal, 16 animals were combined into 4 sub-pools, 4 animals per sub-pool in parts of 1:2:3:4. Sub-pools were constructed based on crushed frozen liver tissue mass. Within phenotype, 4 sub-pools were incorporated into 2 super pools in parts of 1:2:3:4 for super pool 1 and 3:4:1:2 for super pool 2. Super pools were made based on DNA quantity. Errors in DNA quantification would create error in forming super pools from sub-pools and variation in cell content or DNA content of liver tissue would result in error in combining sub-pools from animals.

          Data from: Genetic mapping and QTL analysis for peanut smut resistance

            This collection contains supplementary information for the manuscript “Genetic mapping and QTL analysis for peanut smut resistance”, which reports the genetic map and quantitative trait loci associated with resistance to peanut smut, a disease caused by the fungus *Thecaphora frezii*. The information includes genotyping data of a 103 recombinant inbred line (RIL) population {susceptible *Arachis hypogaea* subsp. *hypogaea* × resistant synthetic amphidiploid [(*A. correntina* × *A. cardenasii*) × *A. batizocoi*]4×} and parental lines, generated with the Axiom_Arachis2 SNP array.

            Data from: Genomic regions associated with Mycoplasma ovipneumoniae presence in nasal secretions of domestic sheep

              Genotypes of significant SNPs in all breed and individual breed analysis with detected *Mycoplasma ovipneumoniae* DNA copy number and log10 *M. ovipneumoniae* DNA copy number. SNP is denoted in the column headers with its rs number and the first 7 SNP are from the all breed analysis, the following 9 SNP from the Rambouillet analysis, the following 3 from the Polypay analysis, and the final 9 from the Suffolk analysis.

              Data from: Genotypic characterization of the U.S. peanut core collection

                This collection contains supplementary data for the manuscript "Genotypic characterization of the U.S. Peanut Core Collection", which describes genotyping results for the USDA peanut core collection. Supplementary files include: descriptive information about the genotyped accessions, SNP genotype calls in several formats, a phylogenetic tree calculated from the genotype data, Structure analysis, PCA analysis, and comparisons with the diploid progenitors.