Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study.

Yu Ma,Deus Mugabe,Lyndon D Porter,Chongyuan Zhang,Stephen P Ficklin,Clarice J Coyne,Sindhuja Sankaran,Md Nurul Amin,Jamin A Smitchger,Rebecca J Mcgee,Naser Rasheed,Afef Marzougui,Dorrie Main

doi:10.3390/ijms21062129

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 the most devastating diseases affecting lentil production. In this study, we applied two complementary quantitative trait loci (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 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 15 putative genes were identified within the QTL clusters. To validate QTL mapping and genome-wide association study (GWAS) results, expression analysis of five selected genes was conducted on partially resistant and susceptible accessions. Three of the genes were differentially expressed at early stages of infection, two of which may be associated with ARR resistance. 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.

Highlights

Lentil (Lens culinaris Medikus), an important grain legume, is widely grown throughout the world with an annual production of 7.8 million tons [1]
In terms of the environmental effects, there were no significant differences for most of the traits; shoot dry weight loss per plant (SDL), root dry weight loss per plant (RDL), average intensity of blue channel acquired from an Red-Green-Blue (RGB) camera (RGB.blue), above ground index (AGI), and canopy area acquired from a multispectral camera (Multispectral.canopy) showed significant environmental effects
Frequency distributions of most traits fit normal curves, whereas SDL, RDL, number of pixels loss per plant in shoot acquired from an RGB camera (RGB.SPL), and number of pixels loss per plant in root acquired from an RGB camera (RGB.RPL) had moderately skewed distributions toward high scores

Summary

Introduction

Lentil (Lens culinaris Medikus), an important grain legume, is widely grown throughout the world with an annual production of 7.8 million tons [1]. Root rot disease caused by Aphanomyces euteiches Drechs. Is one of most devastating diseases in lentil production and can cause yield losses up to 80% [3]. Aphanomyces root rot (ARR) was first described by Jones and Drechsler in 1927 and was reported as a prevalent pathogen in pea fields worldwide. Further testing of lentil cultivars with a French isolate confirmed the lack of resistance in lentil lines [7]. While it was known previously, lentil root rot caused by A. euteiches was first identified in the US in 2008 [11] and in Canada in 2012 [12]. The most effective, economical, and sustainable management of ARR is utilizing genetic resistance in the development of cultivars with high levels of partial resistance

Methods

Results

Conclusion