Partial resistances, often controlled by quantitative trait loci (QTL), are considered to be more durable than monogenic resistances. Therefore, a precursor to developing efficient breeding programs for polygenic resistance to pathogens should be a greater understanding of genetic diversity and stability of resistance QTL in plants. In this study, we deciphered the diversity and stability of resistance QTL to Aphanomyces euteiches in pea towards pathogen variability, environments and scoring criteria, from two new sources of partial resistance (PI 180693 and 552), effective in French and USA infested fields. Two mapping populations of 178 recombinant inbred lines each, derived from crosses between 552 or PI 180693 (partially resistant) and Baccara (susceptible), were used to identify QTL for Aphanomyces root rot resistance in controlled and in multiple French and USA field conditions using several resistance criteria. We identified a total of 135 additive-effect QTL corresponding to 23 genomic regions and 13 significant epistatic interactions associated with partial resistance to A. euteiches in pea. Among the 23 additive-effect genomic regions identified, five were consistently detected, and showed highly stable effects towards A. euteiches strains, environments, resistance criteria, condition tests and RIL populations studied. These results confirm the complexity of inheritance of partial resistance to A. euteiches in pea and provide good bases for the choice of consistent QTL to use in marker-assisted selection schemes to increase current levels of resistance to A. euteiches in pea breeding programs.

BackgroundDevelopment of durable plant genetic resistance to pathogens through strategies of QTL pyramiding and diversification requires in depth knowledge of polygenic resistance within the available germplasm. Polygenic partial resistance to Aphanomyces root rot, caused by Aphanomyces euteiches, one of the most damaging pathogens of pea worldwide, was previously dissected in individual mapping populations. However, there are no data available regarding the diversity of the resistance QTL across a broader collection of pea germplasm. In this study, we performed a meta-analysis of Aphanomyces root rot resistance QTL in the four main sources of resistance in pea and compared their genomic localization with genes/QTL controlling morphological or phenological traits and with putative candidate genes.ResultsMeta-analysis, conducted using 244 individual QTL reported previously in three mapping populations (Puget x 90–2079, Baccara x PI180693 and Baccara x 552) and in a fourth mapping population in this study (DSP x 90–2131), resulted in the identification of 27 meta-QTL for resistance to A. euteiches. Confidence intervals of meta-QTL were, on average, reduced four-fold compared to mean confidence intervals of individual QTL. Eleven consistent meta-QTL, which highlight seven highly consistent genomic regions, were identified. Few meta-QTL specificities were observed among mapping populations, suggesting that sources of resistance are not independent. Seven resistance meta-QTL, including six of the highly consistent genomic regions, co-localized with six of the meta-QTL identified in this study for earliness and plant height and with three morphological genes (Af, A, R). Alleles contributing to the resistance were often associated with undesirable alleles for dry pea breeding. Candidate genes underlying six main meta-QTL regions were identified using colinearity between the pea and Medicago truncatula genomes.ConclusionsQTL meta-analysis provided an overview of the moderately low diversity of loci controlling partial resistance to A. euteiches in four main sources of resistance in pea. Seven highly consistent genomic regions with potential use in marker-assisted-selection were identified. Confidence intervals at several main QTL regions were reduced and co-segregation among resistance and morphological/phenological alleles was identified. Further work will be required to identify the best combinations of QTL for durably increasing partial resistance to A. euteiches.

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.

La production de lin ol eagineux en France peine a se stabiliser et a satisfaire la demande d'op erateurs d'aval qui valorisent la graine riche en om ega 3 (acide alphalinol enique) dans des fili eres animales en vue de fournir des aliments (produits laitiers, oeufs, jambon) enrichis naturellement en om ega 3. Et pourtant, les el ements de contexte sont favorables a un regain de cette culture : que ce soit un march e europ een largement d eficitaire en graines de lin ol eagineux ou les evolutions environnementales demand ees a l'agriculture. C'est pourquoi l'Organisation nationale interprofessionnelle des ol eagineux (Onidol) et le Centre technique interprofessionnel des ol eagineux m etropolitains et du chanvre industriel (Cetiom) ont lanc e en 2008 un diagnostic de la fili ere du lin français. Cette etude avait pour objectifs de conduire un etat des lieux depuis la production jusqu' a l'utilisation du lin français et d'en d eduire quelques perspectives pour le futur. Pour b en eficier d'un panorama actualis e de l'ensemble des maillons de la fili ere lin, des enquêtes ont et e men ees aupr es de l'ensemble des op erateurs selon des techniques adapt ees a chaque secteur. Une attention particuli ere a et e port ee sur la progression de l'offre vari etale dans la mesure o u le diff erentiel de rendement du lin ol eagineux par rapport a d'autres cultures de l'assolement en France est probablement une des causes majeures de la stagnation de la culture. La synth ese des r esultats de cette etude permet de tracer quelques perspectives encourageantes pour l'avenir de la production française de lin.Une source v eg etale in egal ee en om ega 3Le lin ol eagineux (Linum usitatissimum) est cultiv e d'abord pour sa graine a la diff erence de son parent, le lin textile, s electionn e, lui, en priorit e pour sa paille riche en fibres. Sa graine de petite taille (5 a 10 g pour 1 000 grains) est riche en huile (38 a 40 % pour une graine brute a 9 % d'humidit e) et moyennent dot ee en prot eines (22 %). Son originalit e provient de son profil en acides gras domin e par la pr esence de l'acide alphalinol enique (C18:3 appartenant a la famille des om ega 3), a plus de 54 % en moyenne du total (figure 1). L'usage de son huile a connu un fort d eveloppement en Europe au cours du XX e si ecle dans les secteurs non alimentaires. Ainsi, grâce a la forte siccativit e et r eactivit e de son huile, le lin s'est av er e une mati ere premi ere de choix pour la fabrication du linol eum (revêtement de sol), de peintures et d'encres mais aussi de savons. En parall ele les tourteaux, co-produits de l'huile lors de la trituration de la graine, ont connu un vif succ es en alimentation animale et notamment aupr es des eleveurs de bovins, probablement en raison de la teneur encore elev ee en Abstract: Linseed oil crop production does not succeed in reaching stable acreage in France and does not meet the demand coming from users which incorporate linseeds, which display high content in omega 3 (alpha-linolenic acid), in animal feeding in order to de...