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

Authors: MA, YU - Washington State University; Coyne, Clarice - Clare; SANKARAN, SINDHUJA - Washington State University; MAIN, DORRIE - Washington State University; Porter, Lyndon; MUGABE, DEUS - Washington State University; SMITCHGER, JAMIN - Washington State University; ZHANG, CHONGYUAN - Washington State University; AMIN, MD NURUL - Washington State University; FASHEED, NASER - University Of Faisalabad; FICKLIN, STEPHEN - Washington State University; McGee, Rebecca

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2020
Publication Date: 3/20/2020
Citation: Ma, Y., Coyne, C.J., Sankaran, S., Main, D., Porter, L.D., Mugabe, D., Smitchger, J., Zhang, C., Amin, M., Fasheed, N., Ficklin, S., McGee, R.J. 2020. Dissecting genetic architecture of Aphanomyces root rot resistance in lentil by QTL mapping and genome-wide association. International Journal of Molecular Sciences. 21(6):2129. https://doi.org/10.3390/ijms21062129.
DOI: https://doi.org/10.3390/ijms21062129

Interpretive Summary: Lentil (Lens culinaris Medikus), an important grain legume, is widely grown throughout the world with annual production of 6.3 million tons (FAOSTAT, 2018). In 2016, the major producers of lentils were Canada (50.1%), India (16.3%), Turkey (5.7%), United States (3.9%), and Nepal (3.9%). With high protein, minerals, carbohydrates and fiber, it is an inexpensive food source and can alleviate malnutrition in developing countries. Associated with nitrogen fixation, it significantly benefits cereal-based cropping system. Aphanomyces root rot (ARR) disease, which is caused by the soilborne pathogen Aphanomyces euteiches, is one of most devastating diseases in lentil production and can cause yield loss up to 80%. There are currently no lentil cultivars that are resistant to Aphanomyces Root Rot (ARR) and no practical means to control the disease once it is established in a field. In this study, we used two complementary approaches and modern molecular methods to identify genes associated with resistance to ARR. We found seven clusters of genes associated with ARR resistance. When we investigated the function of the genes, we found that they are associated with cell wall modification and secondary metabolism. This is consistent with gene function of other plants in response to diseases. This study provides valuable genetic resources to aid in the development of lentil varieties resistant to ARR. Future analysis of the genes we discovered will enable us to better understand the molecular basis of resistance in lentil to ARR.

Technical Abstract: 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 effecting lentil production. In this study we applied two complementary methods of quantitative trait loci (QTL) analysis to unravel the genetic architecture underling this complex trait. A RIL population and an association mapping population were genotyped to discover novel single nucleotide polymorphisms (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 genes encoding ABC transporter A family protein, cytochrome P450 family 71 protein, chalcone-flavanone isomerase family protein, and pectin esterase that were differentially expressed between resistant and susceptible accessions. This indicates that 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 improved resistance to ARR.