SNP discovery and genetic mapping using Genotyping by Sequencing of Whole Genome genomic DNA from a pea RIL population. PEAPOL

HiSeq2000 whole genome sequencing of four pea lines, followed by direct identification of SNP markers without assembly using the discoSnp tool, discovered 419,024 SNPs. Subsequent filtering led to the identification of 131,850 highly designable SNPs polymorphic between at least two of the four pea lines. Short read sequencing on a subpopulation of 48 sequenced RILs from the cross 'Baccara' x 'PI180693' allowed the construction of a WGGBS-derived pea genetic map. Sequencing of four additional pea lines showed that mapped SNPs are polymorphic and can be used in other crosses.