panzea

Genotypes

Download the latest public “flat file” versions of prepackaged genotypic data sets. All of them open in TASSEL 5 (GUI or command line). The genotypes come from whole genome sequencing (“HapMap”), GBS, or the MaizeSNP50 chip and traditional SNP assays.

Maize HapMap genotypes

Plot of HapMap V2 polymorphisms along maize chromosome 10

In collaboration with several projects, we have performed whole-genome Illumina sequencing on hundreds of maize lines, uncovering millions of polymorphisms. These high density genotypes have enabled GWAS in maize. Several maize HapMap versions are available, the most recent of which is HapMap V3. The BAM files used to build HapMap V3 are available through the CyVerse Data Store: instructions for accessing the BAM files.

Citation: Construction of the third generation Zea mays haplotype map. GigaScience, 2017. doi:10.1093/gigascience/gix134

  • Maize 282 association panel genotypes

    • 7x coverage
    • AGPv4
    • VCF

    Genotypes of the 282 association panel based on whole genome sequencing data. This data set includes the same markers as HapMap V3.2.1, but called from higher coverage sequencing data than the HapMap V3.2.1 release. Coordinates are uplifted to AGPv4.

    Files: hmp321_agpv4_chr*.vcf.gz

    Download VCF files File details

  • Maize HapMap V3.2.1 genotypes, imputed

    • LinkImpute
    • AGPv4
    • VCF

    Uplifted from imputed HapMap 3.2.1 AGPv3.

    Read depths added to the imputed VCF files, with minor format changes for VCF 4.1 compliance and corrected VCF tags.

    Files: hmp321_agpv4_chr*.vcf.gz

    Download VCF files File details

  • Maize HapMap V3.2.1 genotypes, not imputed

    • AGPv4
    • VCF

    Uplifted from AGPv3 genotypes.

    Minor file format changes for VCF 4.1 compliance.

    Files: hmp321_agpv4_chr*.vcf.gz

    Download VCF files File details

Maize GBS genotypes

Workflow diagram of the genotyping-by-sequencing assay

We have performed Genotyping By Sequencing (GBS) with the enzyme ApeKI and the Elshire et al. 2011 protocol on more than 60K maize samples to date. Many of these genotypes are publicly available.

  • ZeaGBS v2.7

    • 955,690 SNPs
    • 17,280 public samples
    • HDF5
    • HapMap

    The current ZeaGBS build, containing genotypes for 955,690 SNPs at more than 60K taxa (samples), 17,280 of which are public. For the public samples, both raw and partially imputed genotypes are available as HDF5 files with AGPv2 coordinates, which open in TASSEL 5. Variants and genotypes are also uplifted to AGPv3 and AGPv4 coordinates in HapMap and TASSEL HDF5 formats.

    File details

Legacy SNPs

SNP genotype cluster plot

We also have SNP genotypic data from more traditional SNP assays, including the Illumina MaizeSNP50 BeadChip, the Illumina GoldenGate SNP assay, and the Sequenom single-base extension assay.

If a download link doesn't open, try right-clicking it and opening it in a new tab. Looking for other data? See Phenotypes and GWAS results.