Genomics & Genetics | Ag Data Commons

Genomes To Fields 2014

Phenotypic, genotypic, and environment data for the 2014 field season: The data is stored in [CyVerse](http://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/Carolyn_Lawrence_Dill_G2F_Nov_2016_V.3).

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The effects of different feed additives on bird performance and the gastrointestinal microbiome of Salmonella-challenged broilers

This dataset contain raw sequence data for 16S amplicon microbiome profiling of broilers challenged with Salmonella and fed several different intervention strategies. Files are tar archives containing zipped fastq raw data files for each sample.

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A consistent and predictable commercial broiler chicken bacterial microbiome in antibiotic-free production displays strong correlations with performance

This dataset includes forward and reverse raw sequencing reads for 2,309 broiler chicken gut, respiratory, and litter samples surveyed using 16S amplicon profiling.

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Genomes To Fields (G2F) Inbred Ear Imaging Data 2017

A subset of ~30 inbreds were evaluated in 2014 and 2015 to develop an image based ear phenotyping tool. The data is stored in [CyVerse](http://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/Edgar_Spalding_G2F_Inbred_Ear_Imaging_June_2017).

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maize-GAMER Annotations for maize B73 RefGen_V4 Zm00001d.2

This dataset from maize-GAMER is a new high-coverage and reproducible functional annotation of maize protein coding genes based on Gene Ontology (GO) term assignments that covers all genes in the B73 RefGen_V4 Zm00001d.2.

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Maize-GAMER: Maize B73 RefGen_v3 5b+

This dataset from maize-GAMER is a new high-coverage and reproducible functional annotation of maize (*Zea mays*) protein coding genes based on Gene Ontology (GO) term assignments that covers all genes in the B73 RefGen_v3 5b+ set. Data are compressed gzip (.gz) files.

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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.

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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.

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Barley Genotyping SNPs Annotated using SNPMeta

These are SNPs on two Illumina GoldenGate genotyping arrays and one 9k iSelect genotyping array.

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Variants from "The role of deleterious substitutions in crop genomes"

SNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.

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