Han Koeun, Lee Hea-Young, Ro Na-Young, Hur On-Sook, Lee Joung-Ho, Kwon Jin-Kyung, Kang Byoung-Cheorl
Department of Plant Science, Plant Genomics and Breeding Institute, Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
National Academy of Agricultural Science, Rural Development Administration, Jeonju, Korea.
Plant Biotechnol J. 2018 Feb 6;16(9):1546-58. doi: 10.1111/pbi.12894.
Capsaicinoids are unique compounds produced only in peppers (Capsicum spp.). Several studies using classical quantitative trait loci (QTLs) mapping and genomewide association studies (GWAS) have identified QTLs controlling capsaicinoid content in peppers; however, neither the QTLs common to each population nor the candidate genes underlying them have been identified due to the limitations of each approach used. Here, we performed QTL mapping and GWAS for capsaicinoid content in peppers using two recombinant inbred line (RIL) populations and one GWAS population. Whole-genome resequencing and genotyping by sequencing (GBS) were used to construct high-density single nucleotide polymorphism (SNP) maps. Five QTL regions on chromosomes 1, 2, 3, 4 and 10 were commonly identified in both RIL populations over multiple locations and years. Furthermore, a total of 109 610 SNPs derived from two GBS libraries were used to analyse the GWAS population consisting of 208 C. annuum-clade accessions. A total of 69 QTL regions were identified from the GWAS, 10 of which were co-located with the QTLs identified from the two biparental populations. Within these regions, we were able to identify five candidate genes known to be involved in capsaicinoid biosynthesis. Our results demonstrate that QTL mapping and GBS-GWAS represent a powerful combined approach for the identification of loci controlling complex traits.
辣椒素类物质是仅在辣椒（辣椒属物种）中产生的独特化合物。几项使用经典数量性状基因座（QTL）定位和全基因组关联研究（GWAS）的研究已经鉴定出控制辣椒中辣椒素类物质含量的QTL；然而，由于所使用的每种方法的局限性，尚未鉴定出每个群体共有的QTL及其潜在的候选基因。在这里，我们使用两个重组自交系（RIL）群体和一个GWAS群体对辣椒中的辣椒素类物质含量进行了QTL定位和GWAS分析。利用全基因组重测序和测序基因分型（GBS）构建了高密度单核苷酸多态性（SNP）图谱。在多个地点和年份的两个RIL群体中共同鉴定出了位于第1、2、3、4和10号染色体上的5个QTL区域。此外，来自两个GBS文库的总共109610个SNP用于分析由208个辣椒进化枝种质组成的GWAS群体。从GWAS中总共鉴定出69个QTL区域，其中10个与从两个双亲群体中鉴定出的QTL共定位。在这些区域内，我们能够鉴定出5个已知参与辣椒素类物质生物合成的候选基因。我们的结果表明，QTL定位和GBS-GWAS是鉴定控制复杂性状基因座的一种强大的联合方法。
