Desgroux Aurore, L'Anthoëne Virginie, Roux-Duparque Martine, Rivière Jean-Philippe, Aubert Grégoire, Tayeh Nadim, Moussart Anne, Mangin Pierre, Vetel Pierrick, Piriou Christophe, McGee Rebecca J, Coyne Clarice J, Burstin Judith, Baranger Alain, Manzanares-Dauleux Maria, Bourion Virginie, Pilet-Nayel Marie-Laure
INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
BMC Genomics. 2016 Feb 20;17:124. doi: 10.1186/s12864-016-2429-4.
Genome-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.
A 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.
GWA 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.
This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding.
全基因组关联（GWA）图谱绘制最近已成为一种有价值的方法，用于完善对植物病害多基因抗性的遗传基础，该方法越来越多地应用于持久作物保护的综合策略中。腐皮镰孢菌是一种世界性的豌豆和其他豆类的土传病原体，可导致造成产量损失的根腐病。连锁图谱研究报道了控制豌豆对腐皮镰孢菌抗性的数量性状位点（QTL）。然而，这些QTL的置信区间（CI）仍然很大，并且常常与不良等位基因连锁，这限制了它们在育种中的应用。本研究的目的是使用GWA方法来验证和细化先前报道的腐皮镰孢菌抗性QTL的CI，并鉴定新的抗性位点。
在九个环境中的田间感染苗圃以及在气候箱中用两种菌株对一个包含175个豌豆品系的豌豆 - 腐皮镰孢菌群体进行了评估，该群体富含源自先前研究的抗性来源的种质。使用最近开发的GenoPea Infinium® BeadChip中的13204个单核苷酸多态性（SNP）对该群体进行基因分型。
使用最近开发的多位点混合模型，GWA分析共检测到52个与对腐皮镰孢菌抗性相关的小间隔QTL。该分析验证了先前报道的七个主要腐皮镰孢菌抗性QTL中的六个，并检测到新的抗性位点。它还提供了与抗性增加相关的14个一致QTL区域的标记单倍型，并突出了最抗性品系中有利单倍型的积累。对于干豌豆育种，抗性等位基因与不期望的晚花等位基因之间的先前连锁大多得到证实，但由于分析的高分辨率，控制抗性的位点与有色花之间的连锁被打破。抗性位点潜在的推定候选基因中有很大一部分编码与胁迫相关的蛋白质，其他结果表明这些QTL参与了多种功能。
本研究提供了有价值的标记、标记单倍型和种质系，以提高豌豆育种中对腐皮镰孢菌的部分抗性水平。
