Genomic dissection of Botrytis grey mould resistance in chickpea (Cicer arietinum L.) using QTL-seq approach

Eight QTLs linked to Botrytis grey mould resistance in chickpea were identified, enabling marker-assisted selection and candidate gene discovery for the development of resistant cultivars. Botrytis grey mould (BGM), caused by Botrytis cinerea Pers. ex. Fr., is a destructive disease limiting chickpea production globally. To control this disease, breeding for the development of resistant chickpea cultivars is one of the most economic and effective method. Hence, identification and mapping of resistance genes/quantitative trait loci (QTL(s)) are critical. However, there are limited reports on QTL mapping and the identification of candidate genes for BGM resistance in chickpea. The present study employed bulked segregant analysis and whole-genome sequencing (BSA-seq) approach for the detection of candidate genomic regions controlling BGM resistance. A total of eight QTLs were mapped with three on chromosome 1 (BGM1.1, qBGM1.2, qBGM1.3), one on chromosome 3 (qBGM3.1), two each on chromosome 4 (qBGM4.1, qBGM4.2) and chromosome 7 (qBGM7.1, and qBGM7.2). Based on high ΔSNP-index and G' values, qtlBGM4.2 (2.36 Mb region) was selected for subsequent validation by KASP primers. Linkage mapping with KASP primers derived from six polymorphic SNPs with high read depth identified a 506.16 kb genomic region equaling 0.84 cM on the genetic map linked with BGM resistance. The results presented herein provide insights for further cloning and functional analysis of candidate genes (Leucine-rich repeat extension-like kinases, rust resistance kinase Lr10, and F-box proteins) related to BGM resistance. Additionally, BGM-specific KASP markers developed in this study will be highly useful for marker-assisted selection (MAS) to accelerate chickpea breeding programmes for BGM resistance.