Table_3_Advanced backcross QTL analysis and comparative mapping with RIL QTL studies and GWAS provide an overview of QTL and marker haplotype diversity for resistance to Aphanomyces root rot in pea (Pisum sativum).xlsx

Aphanomyces euteiches is the most damaging soilborne pea pathogen in France. Breeding of pea resistant varieties combining a diversity of quantitative trait loci (QTL) is a promising strategy considering previous research achievements in dissecting polygenic resistance to A. euteiches. The objective of this study was to provide an overview of the diversity of QTL and marker haplotypes for resistance to A. euteiches, by integrating a novel QTL mapping study in advanced backcross (AB) populations with previous QTL analyses and genome-wide association study (GWAS) using common markers. QTL analysis was performed in two AB populations derived from the cross between the susceptible spring pea variety “Eden” and the two new sources of partial resistance “E11” and “LISA”. The two AB populations were genotyped using 993 and 478 single nucleotide polymorphism (SNP) markers, respectively, and phenotyped for resistance to A. euteiches in controlled conditions and in infested fields at two locations. GWAS and QTL mapping previously reported in the pea-Aphanomyces collection and from four recombinant inbred line (RIL) populations, respectively, were updated using a total of 1,850 additional markers, including the markers used in the Eden x E11 and Eden x LISA populations analysis. A total of 29 resistance-associated SNPs and 171 resistance QTL were identified by GWAS and RIL or AB QTL analyses, respectively, which highlighted 10 consistent genetic regions confirming the previously reported QTL. No new consistent resistance QTL was detected from both Eden x E11 and Eden x LISA AB populations. However, a high diversity of resistance haplotypes was identified at 11 linkage disequilibrium (LD) blocks underlying consistent genetic regions, especially in 14 new sources of resistance from the pea-Aphanomyces collection. An accumulation of favorable haplotypes at these 11 blocks was confirmed in the most resistant pea lines of the collection. This study provides new SNP markers and rare haplotypes associated with the diversity of Aphanomyces root rot resistance QTL investigated, which will be useful for QTL pyramiding strategies to increase resistance levels in future pea varieties.

嗜根腐丝囊霉（Aphanomyces euteiches）是法国境内危害最为严重的豌豆土传病原菌。结合多种数量性状位点（QTL）培育豌豆抗病品种，鉴于此前在解析嗜根腐丝囊霉多基因抗性方面的研究成果，是极具前景的育种策略。本研究旨在整合一项针对高级回交（AB）群体的新型QTL定位研究、既往QTL分析以及采用共同标记开展的全基因组关联分析（GWAS），系统梳理抗嗜根腐丝囊霉相关QTL与标记单倍型的多样性。本研究构建了两个高级回交群体，均由感病春豌豆品种"Eden"分别与两份新的部分抗源"E11"和"LISA"杂交获得。两个AB群体分别采用993个和478个单核苷酸多态性（SNP）标记进行基因型鉴定，并在可控环境与两处侵染性田间环境中开展抗嗜根腐丝囊霉表型鉴定。本研究还对既往在豌豆-嗜根腐丝囊霉关联群体中开展的GWAS，以及来自4个重组自交系（RIL）群体的QTL定位结果进行了更新，共新增1850个标记，涵盖本研究中"Eden×E11"与"Eden×LISA"群体分析所用的标记。通过GWAS分析与RIL、AB群体QTL定位，分别鉴定得到29个与抗性相关的SNP位点以及171个抗性QTL，共锁定10个保守遗传区域，验证了既往报道的QTL。从"Eden×E11"与"Eden×LISA"两个AB群体中均未检测到新的保守抗性QTL。不过，在11个保守遗传区域所在的连锁不平衡（LD）区块中，鉴定到了丰富的抗性单倍型多样性，尤其是在豌豆-嗜根腐丝囊霉关联群体的14份新抗源材料中。在该群体中高抗豌豆品系内，已证实这11个区块存在优势单倍型的富集现象。本研究鉴定得到一批与嗜根腐丝囊霉根腐病抗性QTL多样性相关的新型SNP标记与稀有单倍型，可为未来通过QTL聚合策略提升豌豆品种抗性水平提供有力支撑。