Single nucleotide polymorphism genotyping of 323 wheat accessions from Pakistan, Mexico and Australia

DNA was extracted from 21 day old seedlings using the Wizard Genomic DNA Purification Kit (Promega, UK). Quantity and quality was checked using an ND-1000 spectrophotometer (Thermo Fisher Scientific, USA) and a Qubit 2.0 fluorometer using a Qubit dsDNA quantification kit (Invitrogen, UK). The quality thresholds were as follows: an OD260/OD280 ratio of between 1.8 and 2.0 and a OD260/OD230 ratio greater than 1.5. High-throughput SNP genotyping of 323 genotypes was performed using the TaNG v1.1 Affymetrix Axiom genotyping array (Thermo Fisher Scientific, UK) at the University of Bristol Genomics facility, University of Bristol, UK. Genotype calling was performed using the Best Practices Workflow in the Axiom Analysis Suite (AxAS) following the default SNP quality control thresholds where DCQ (dish quality control) ≥ 0.82 and CR (call rate) cut-off ≥ 97%. Markers were then classified and filtered based on the Axiom recommended criteria. Subsequently, markers that were monomorphic, had a minor allele frequency (MAF) of <5%, a missing call rate of >20%, or a heterozygote frequency >25% were removed. After filtering, a total of 6,315 best recommended and high-quality markers were retained and were used to generate the HapMap-formatted data.

This dataset is under embargo and will be made available by 1 June 2027 at the latest   Find out more »