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Ag Data Commons migration begins October 18, 2023

The Ag Data Commons is migrating to a new platform – an institutional portal on Figshare. Starting October 18 the current system will be available for search and download only. Submissions will resume after the launch of our portal on Figshare in November. Stay tuned for details!

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.

    Breedbase

      The Breedbase system has evolved from the Sol Genomics Network (SGN) and Cassavabase and related sites (see RTBbase.org).Breedbase is striving to be a complete breeding management system, including field management, data collection, crossing utilities, and advanced trial analysis.

      CottonGen Sequence Retrieval

        Sequence Retrieval allows users to download nucleotide and protein sequences including chromosomes, scaffolds, genes, mRNAs, transcript coding sequences, protein, reftrans contigs and unigene contigs. For the sequences aligned to larger sequences, such as genes, mRNAs and transcript coding sequences, a numeric value specifying the number of upstream bases and downstream bases can be entered.

        CottonGen Map Viewer

          MapViewer is a graphical tool for viewing and comparing *Gossypium* spp. genetic maps. It includes dynamically scrollable maps, correspondence matrices, dot plots, links to details about map features, and exporting functionality. It was developed by the MainLab at Washington State University and is available for download for use in other Tripal databases.

          CottonGen JBrowse

            CottonGen has an instance of the JBrowse genome browser for viewing genome data. A list of the Whole Genomes and Chloroplast Genomes is available together with a JBrowse tutorial for more details about how to navigate and use JBrowse.

            CottonGen BLAST

              CottonGen offers BLAST with genome, transcriptome, peptide and marker sequence databases from *Gossypium* species. This can be done using nucleotide sequences or peptide sequences. BLAST functionality is similar to that on NCBI.