QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum 

First author: Koeun Han; Affiliations: Seoul National University (首尔国立大学): Seoul, Korea

Corresponding author: Byoung-Cheorl Kang

Capsaicinoids (辣椒素) 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; 测序基因分型) 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 (双亲群体). 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.

辣椒素是只在辣椒中特异存在的一种化合物。已经又一些研究通过数量性状位点（QTL）图谱和全基因组关联分析（GWAS）鉴定了一些控制辣椒中辣椒素含量的相关基因，然而由于每个方法每次都是单独使用，存在不可弥补的缺陷，导致并未有共同的QTL位点或是潜在的候选基因被鉴定出来。本文综合利用了QTL图谱和GWAS两种方法对两个重组自交系群体（RIL）和一个GWAS群体进行了分析。基因组重测序分析和测序基因分型被用来构建高密度的单核苷酸变异图谱。在两个RIL群体多地点和多年生的数据中鉴定到了来自1、2、3、4和10号染色体上共同的5个QTL区域。此外，总共109610个来源于GBS库的SNPs被用于对包含208个辣椒个体的GWAS群体进行分析。总共鉴定出69个QTL区域，其中10个与双亲群体中鉴定到的QTL共定位。在这些鉴定到的区域中，作者进一步获取了5个已知参与辣椒素生物合成的候选基因。本文的工作显示了QTL图谱和GBS-GWAS的组合使用可以有效定位控制复杂性状的遗传位点。

doi: 10.1111/pbi.12894

Journal: Plant Biotechnology Journal

First Published date: 02 March, 2018

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