Lens orientalis contributes quantitative trait loci and candidate genes associated with Ascochyta blight resistance in lentil

Purpose: The goal of this study is to construct an interspecific genetic linkage map using SNP markers generated using a genotyping by sequencing transcript approach. Methods: mRNA profiles of 14-day-old parents and 140 recombinant inbred lines were generated by high-throughput sequencing using Illumina HiSeq 3000 system. The sequence reads that passed filtering were mapped to lentil cultivar Cassab reference transcriptome using Burrows Wheeler Aligner and the SNPs generated were then clustered to linkage groups (LG) to construct a high-density linkage map using the 'mstmap' function from within the ASMap R package (v1.0-4) (Taylor and Butler, 2017). Results: A total of 694,694,624 paired end reads (150-bp) were generated by sequencing multiplexed cDNA libraries on the Illumina HiSeq 3000 platform with an average of 4,997,803 reads per RIL progeny. Variant calling and sequential filtering led to identification of 2,363 SNP markers which were used to construct a genetic linkage map spanning 545.5 cM with 8 linkage groups. Conclusions: The study has utilized a novel interspecific-derived RIL population to add an array of SNPs to the existing marker data for lentil, which will be of use in future genetic and genomic analyses. Overall design: mRNA profiles of 14-day-old Lens orientalis (ILWL 180) and Lens culinaris (ILL 6002) accessions and 140 recombinant inbred lines.