Pakistani historical wheat panel 37K SNP data
Data files
Oct 03, 2023 version files 28.75 MB
Abstract
A collection of 196 historical wheat cultivars of Pakistan released between 1911 to 2022 were subjected to DNA fingerprinting using 16K genotyping-by-targeted sequencing (GBTS) platform. This platform is based on NGS and the 16K probes were resequenced. The resequencing data was aligned to Chinese Spring RefSeq version 1.1 and SNPcalling was performed. This resulted in 37K mSNP (multiple SNPs) DNA fingerprinting data. This is thus far the most comprehensive DNA fingerprinting data of all released cultivars of wheat so far. This data is publically available and can be used in research and publications subject to the acknowledgement.
README: Pakistani historical wheat panel 16K SNP data
https://doi.org/10.5061/dryad.xwdbrv1kb
This dataset comprised of a metadata file, a pedigree file containing all the information of cultivars, a SNP data file in vcf format and annotation file containing snp_effect information.
Sharing/Access information
In case of publication, the link will be provided here.
Code/Software
This dataset in vcf format can be directly used by any genetic analysis software like TASSEL, vcftools etc.
Methods
All the wheat cultivars seeds were provided by Dr. Muhammad Fayyz (CDRI, NARC). DNA was extracted from each cultivar following standard CTAB protocol. The DNA was sent to MolBreeding (TM), Shijiazhuang, China for 16K GBTS (liquid chip) analysis. The sequencing data was aligned to Wheat Ref Seq version 1.1, and the SNP calling was performed. The raw SNP data is provided as vcf format.