Dissecting the genetic architecture of Aphanomyces root rot resistance in lentil by QTL mapping and genome-wide association study

Primary author: Yu Ma
Co-author(s): Afef Marzougui; Clarice Coyne; Sindhuja Sankaran; Dorrie Main; Lyndon Porter; Deus Mugabe; Jamin Smitchger
Faculty sponsor: Dorrie Main

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman


Lentil (Lens culinaris Medikus) is an important source of protein for people in developing countries. Aphanomyces root rot (ARR) has emerged as one of most devastating diseases affecting lentil production. In this study, we applied two complementary QTL analysis approaches to unravel the genetic architecture underlying this complex trait. A recombinant inbred line (RIL) population and an association mapping population were genotyped using genotyping by sequencing (GBS) to discover novel SNPs. QTL mapping identified 19 QTL associated with ARR resistance, while association mapping detected 38 QTL and highlighted accumulation of favorable haplotypes in most of the resistant accessions. Seven QTL clusters were discovered on six chromosomes and five putative genes involved in plant disease response were detected. Expression analysis revealed four of them, encoding an ABC transporter A family protein, a cytochrome P450 family 71 protein, a chalcone-flavanone isomerase family protein, and pectin esterase, were differentially expressed between resistant and susceptible accessions. This indicates genes involved in secondary metabolism and cell wall modification are potentially associated with ARR. Our findings provide valuable insight into the genetic control of ARR and genetic and genomic resources developed here can be used to accelerate development of lentil cultivars with high levels of partial resistance to ARR.