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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.

        Data from: Genetic variation among 481 diverse soybean accessions

          This data is from the manuscript titled: "Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing". SNP calls were obtained from resequencing 481 diverse soybean lines comprising 52 wild (*Glycine soja*) and 429 cultivated (*Glycine max*). A total of 7.8 million SNPs were identified between the 481 re-sequenced accessions.


            The genosim package simulates genotypes, breeding values, and phenotypes; simulates DNA sequence read depth (numbers of A and B alleles); and resolves SNP conflicts between parent and offspring genotypes.


              The findmap.f90 program aligns sequence reads to reference map, calls previous variants, and identifies new variants.


                The findhap.f90 program finds haplotypes and imputes genotypes using multiple chip sets and sequence data.