Genotypes
From this page you can obtain the latest public "flat file" versions of prepackaged, genotypic data sets. All of these can be opened with the TASSEL 5 (GUI or command line). The genotypes were obtained by whole genome sequencing ("HapMap"), GBS, or with MaizeSNP50 chip or traditional SNP assays.

We are working on restoring the download links for Hapmap genotypes. Please email qisun(at)cornell.edu if you need the file now. . 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 maize HapMapV3. The bam files used for construction of HapMapV3 are available though CyVerse Data Store. Click here for instruction to access the bam files. Citation: Construction of the third generation Zea mays haplotype map. Gigascience. 2017 Dec 30. doi: 10.1093/gigascience/gix134. [Epub ahead of print]

Maize 282 association panel genotypes (7x, AGPv4 coordinates) [more] Genotypes of 282 association panel based on the whole genome sequencing data. This data set include the same markers as in HapMap V3.2.1, but called from higher coverage sequencing data than the HapMapV3.2.1 release. These files have their coordinates uplifted to agpv4 The VCF files can be downloaded from CyVerse in the directory: /iplant/home/shared/panzea/hapmap3/hmp321/unimputed/282_libs_2015/uplifted_APGv4. The file names are hmp321_agpv4_chr*.vcf.gz. You can use this icommand to download all files: iget -K -r /iplant/home/shared/panzea/hapmap3/hmp321/unimputed/282_libs_2015/uplifted_APGv4 Maize HapMapV3.2.1 genotypes (with imputation by LinkImpute, AGPv4) [more] Uplifted from imputed HapMap3.2.1 agpv3. 2016.10.5 Read depths are added to the imputed VCF files. There are minor changes in the file format to be compliant with VCF 4.1 specification. The new files with read depth and correct vcf tags are located in /iplant/home/shared/panzea/hapmap3/hmp321/imputed/uplifted_APGv4. The files are named hmp321_agpv4_chr*.vcf.gz Maize HapMapV3.2.1 genotypes (without imputation, AGPv4) [more] Uplifted from agpv3 genotypes. 2016.10.5 There are minor changes in the file format to be compliant with VCF 4.1 specification. The files are located in /iplant/home/shared/panzea/hapmap3/hmp321/unimputed/uplifted_APGv4, and named hmp321_agpv4_chr*.vcf.gz.

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 publically available.

ZeaGBSv2.7 [more] This is the current ZeaGBS build, containing genotypes for 955,690 SNPs at more than 60K taxa (samples), 17,280 of which are public. For these public samples, both raw and partially imputed genotypes are available as HDF5 files with AGPv2 coordinates which can be opened with TASSEL 5. In addition, the variants and genotypes were uplifted to AGPv3 and AGPv4 coordinates in hapmap and Tassel HDF5 formats.

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