Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea

Abstract

BackgroundGenome-wide association (GWA) mapping has recently emerged as a valuable approach for refining the genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil-borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. Linkage mapping studies reported quantitative trait loci (QTL) controlling resistance to A. euteiches in pea. However the confidence intervals (CIs) of these QTL remained large and were often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to use a GWA approach to validate and refine CIs of the previously reported Aphanomyces resistance QTL, as well as identify new resistance loci.MethodsA pea-Aphanomyces collection of 175 pea lines, enriched in germplasm derived from previously studied resistant sources, was evaluated for resistance to A. euteiches in field infested nurseries in nine environments and with two strains in climatic chambers. The collection was genotyped using 13,204 SNPs from the recently developed GenoPea Infinium® BeadChip.ResultsGWA analysis detected a total of 52 QTL of small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven previously reported main Aphanomyces resistance QTL and detected novel resistance loci. It also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of favourable haplotypes in the most resistant lines. Previous linkages between resistance alleles and undesired late-flowering alleles for dry pea breeding were mostly confirmed, but the linkage between loci controlling resistance and coloured flowers was broken due to the high resolution of the analysis. A high proportion of the putative candidate genes underlying resistance loci encoded stress-related proteins and others suggested that the QTL are involved in diverse functions.ConclusionThis study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2429-4) contains supplementary material, which is available to authorized users.

Insights to plant–microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

“…Improved phenotypic scoring of resistance among assessed accessions (e.g., digital image analysis; Desgroux et al, 2018) will further contribute to improving QTL analysis and it seems likely that in the near future, mapping studies will identify more genomic regions, candidate genes, and markers for potential MAS. Hamon et al (2013) Most importantly, the study by Desgroux et al (2016) included various field conditions and controlled condition assays with two distinct pathogen strains, making the identified genomic regions a valuable resource for future breeding efforts in pea. Although they detected QTL consistent over the different environments, significant plant genotype × environment (G × E) and plant genotype × pathogen strain interactions were observed.…”

“…Resistance to Fusarium and Aphanomyces root rot has been mapped in common bean, with a colocalization of resistance and root morphology‐related QTL, indicating that a combination of physiological mechanisms and root architecture traits is responsible for disease resistance (Hagerty et al, ; Nakedde et al, ; Navarro, Sass, & Nienhuis, ; Schneider et al, ). In pea, extensive mapping studies have been conducted for Fusarium and Aphanomyces root rots, and colocalization of root‐architecture and resistance QTL have been evidenced, too (Coyne et al, ; Desgroux et al, ; Desgroux et al, , ; Feng et al, ; Hamon et al, ; Li et al, ; Pilet‐Nayel et al, , ). Regarding D. pinodes , the most virulent pathogen of the Ascochyta complex, several QTL studies identified and reconfirmed genomic regions controlling resistance in pea (Carrillo et al, ; Fondevilla et al, , ).…”

“…This analysis integrated data of 29 field environments on 2 continents and 12 controlled condition‐assays over several years. Similarly, Desgroux et al () used 13,204 SNP to genotype 175 pea accessions and performed resistance screenings in field and controlled conditions for resistance to A. euteiches . Using GWAS, they found 52 QTL of small‐size intervals and validated most previously defined resistance QTL.…”

“…Most importantly, the study by Desgroux et al () included various field conditions and controlled condition assays with two distinct pathogen strains, making the identified genomic regions a valuable resource for future breeding efforts in pea. Although they detected QTL consistent over the different environments, significant plant genotype × environment (G × E) and plant genotype × pathogen strain interactions were observed.…”

Genome-Wide Association Mapping for Heat Stress Responsive Traits in Field Pea

“…In pea, association and linkage mapping has been employed to uncover the genetic bases of several traits including agronomic and seed quality traits [30,35], disease resistance [32,36], seed mineral concentrations [37], seed lipid content [38], salinity tolerance [31], and frost tolerance [33]. Despite its importance, only limited studies have been carried out to identify genomic regions associated with pea stress tolerance [28].…”