Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome‐wide association study

Anthracnose, caused by Colletotrichum lentis , is a devastating disease of lentil ( Lens culinaris Medik.) in western Canada. Growing resistant lentil cultivars is the most cost‐effective and environmentally friendly approach to prevent seed yield losses that can exceed 70%. To identify loci conferring resistance to anthracnose race 1 in lentil, biparental quantitative trait loci (QTL) mapping of two recombinant inbred line (RIL) populations was integrated with a genome‐wide association study (GWAS) using 200 diverse lentil accessions from a lentil diversity panel. A major‐effect QTL ( qAnt 1 .Lc‐ 3) conferring resistance to race 1 was mapped to lentil chromosome 3 and colocated on the lentil physical map for both RIL populations. Clusters of candidate nucleotide‐binding leucine‐rich repeat (NB‐LRR) and other defense‐related genes were uncovered within the QTL region. A GWAS detected 14 significant single nucleotide polymorphism (SNP) markers associated with race 1 resistance on chromosomes 3, 4, 5, and 6. The most significant GWAS SNPs on chromosome 3 supported qAnt 1 .Lc‐ 3 and delineated a region of 1.6 Mb containing candidate resistance genes. The identified SNP markers can be directly applied in marker‐assisted selection (MAS) to accelerate the introgression of race 1 resistance in lentil breeding.