Identification of SNPs in barley (Hordeum vulgare L.) by deep sequencing of six reduced representation libraries

High-density genetic markers are required for genotyping and linkage mapping in identifying genes from crops with complex genomes, such as barley. As the most common variation, single nucleotide polymorphisms (SNPs) are suitable for accurate genotyping by using the next-generation sequencing (NGS) technology. Reduced representation libraries (RRLs) of five barley accessions and one mutant were sequenced using NGS technology for SNP discovery. Twenty million short reads were generated and the proportion of repetitive sequences was reduced by more than 56%. A total of 6061 SNPs were identified, and 451 were mapped to the draft sequence of the barley genome with pairing reads. Eleven SNPs were validated using length polymorphic allele-specific PCR markers.