Single-nucleotide polymorphism matrices for a large diversity panel of wheat (Triticum aestivum L.)

A total of 8,070 wheat samples were characterized using genotyping-by-sequencing (GBS) while whole genome shotgun sequencing (WGS) was carried out on 768 samples. For all characterizations, DNA was extracted from 10-cm-long leaves of 10-days-old seedlings. Among GBS samples, 7,745 trace back to accessions of the German federal ex situ genebank bank hosted at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben. The 325 remaining GBS samples correspond to European elite cultivars. Regarding WGS, 446 samples trace back to the IPK genebank while 191 are European elite cultivars and 131 correspond to modern German breeding lines. High-quality sequence reads were aligned against the hexaploid wheat reference genome assembly cv. Chinese Spring (IWGSC RefSeq v1.0). Bi-allelic SNPs with minimum QUAL ? 40, minimum read depth for homozygous call ? 1, and minimum read depth for heterozygous calls ? 2 were retained and VCF files generated.