We collected 155 barley materials, including wild barley, landrace, cultivated barley and Tibetan hul-less barley accessions representative of different ecological regions around the world, and conducted whole genome resequencing to compose the chip background dataset. After a selection pipeline and genotyping quality evaluation, 40,529 SNP loci were successfully obtained for chip development.
In the barley 40K SNP liquid array, more variation occurred on chromosome arms than within centromeres. The average interval length between adjacent SNPs was 113.1 kb, with 67.5% primarily distributed from 0 to 100 kb, and 0.9% had an interval larger than 1 Mb. According to the annotation of the barley reference genome, most of probes located in intergenic region (66.1%). Of the polymorphisms located in gene regions, 42.9% were exonic variations, and 57.1% were intronic variations.