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

A total of 588 wheat (Triticum aestivum L.) samples were characterized using whole genome resequencing. DNA was extracted from 10-cm-long leaves of 10-day-old seedlings. The raw sequenced data of 131 parental lines and 5 checks was released at the European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena/) under Project IDs PRJEB48738. The newly 452 wheat samples' raw sequenced data have been deposited at ENA under the project IDs PRJEB82869. High-quality sequence reads were aligned against the hexaploid wheat reference genome assembly cv. Chinese Spring (IWGSC RefSeq v2.1). 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. The SNPs with missing rate less than 30%, homozygous genotypes for each allele more than 10 and heterozygosity less than 1% were kept in this dataset.