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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: Legacy genetics of Arachis cardenasii in the peanut crop - v2

        This collection contains supplementary data for the manuscript "Legacy genetics of Arachis cardenasii in the peanut crop shows profound benefits of international seed exchange," which describes the impact of alleles from a wild relative of peanut, Arachis cardenasii, through analysis of those alleles across cultivars and breeding lines across many countries.

        Data from: Legacy genetics of Arachis cardenasii in the peanut crop

          This collection contains supplementary data for the manuscript "Legacy genetics of Arachis cardenasii in the peanut crop shows profound benefits of international seed exchange," which describes the impact of alleles from a wild relative of peanut, Arachis cardenasii, through analysis of those alleles across cultivars and breeding lines across many countries.

          Evaluating accuracy of DNA pool construction based on white blood cell counts

            Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. This data set was generated to determine accuracy of pool construction based on white blood cell counts compared to two common DNA quantification methods. The dataset includes: 1) pooling allele frequencies (PAF) for all pools and individual animals computed from normalized intensities for red (X) and green (Y); PAF = X/(X+Y). 2) Genotypes or number of copies of B(green) allele (0,1,2). 3) Definitions for each sample.

            Data from: Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

              We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly.

              Data from: A deletion mutation in TaHRC confers Fhb1 resistance to Fusarium head blight in wheat

                Fusarium head blight (FHB), which is mainly caused by *Fusarium graminearum*, is a destructive wheat disease that threatens global wheat production. *Fhb1*, a quantitative trait locus discovered in Chinese germplasm, provides the most stable and the largest effect on FHB resistance in wheat. Here we show that *TaHRC*, a gene that encodes a putative histidine-rich calcium-binding protein, is the key determinant of *Fhb1*-mediated resistance to FHB.

                Data From: Evaluating accuracy of DNA pool construction based on leukocyte counts versus two common DNA quantification methods

                  This dataset was generated to determine the accuracy of pool construction based on leukocyte counts compared to two common DNA quantification methods. The dataset includes pooling allele frequencies (PAF) for all pools and individual animals computed from normalized intensities for red (X) and green (Y); PAF = X/(X+Y), genotypes or number of copies of B(green) allele (0,1,2), and definitions for each sample.