In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping‐by‐sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome‐wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.

中文翻译：

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辣椒中马铃薯病毒Y种群大小暗示的QTL的全基因组关联映射：广泛的QTL金字塔抗性证据。

在这项研究中，我们寻找了辣椒（Capsicum annuum）种质中的遗传因素，这些遗传因素控制进入植物的马铃薯病毒Y（PVY）颗粒的数量（即接种时的有效种群大小）和系统水平的PVY积累（即人口普查）。在256个辣椒种质的核心集合中，通过序列基因分型（GBS），我们获得了覆盖整个基因组的10 307个单核苷酸多态性（SNP）。全基因组关联研究（GWAS）在7、4、6、9和12号染色体上检测到了7个与病毒种群大小在接种和/或系统水平上显着相关的SNP。主要抗性基因pvr2编码真核起始因子4E。在其他染色体的置信区间中没有发现明显的抗性候选物。在6号和12号染色体上检测到的SNP与先前鉴定为双亲种群的抗性定量性状基因座（QTL）共定位。这些结果表明GBS和GWAS在金黄色葡萄球菌中的效率，表明GWAS和经典QTL作图之间的结果高度一致，并表明以双亲种群鉴定的抗性QTL代表了辣椒品种的大量收集。此外，在核心集合中，这些不同基因座的抗性等位基因的合并频率比偶然预期的要高，这表明抗性QTL的广泛金字塔化以及抗性QTL和主要效应基因的广泛组合。这样的金字塔可以增加电阻效率和/或耐久性。