Table_1_Uncovering Candidate Genes Controlling Major Fruit-Related Traits in Pepper via Genotype-by-Sequencing Based QTL Mapping and Genome-Wide Association Study.xlsx

All modern pepper accessions are products of the domestication of wild Capsicum species. However, due to the limited availability of genome-wide association study (GWAS) data and selection signatures for various traits, domestication-related genes have not been identified in pepper. Here, to address this problem, we obtained data for major fruit-related domestication traits (fruit length, width, weight, pericarp thickness, and fruit position) using a highly diverse panel of 351 pepper accessions representing the worldwide Capsicum germplasm. Using a genotype-by-sequencing (GBS) method, we developed 187,966 genome-wide high-quality SNP markers across 230 C. annuum accessions. Linkage disequilibrium (LD) analysis revealed that the average length of the LD blocks was 149 kb. Using GWAS, we identified 111 genes that were linked to 64 significant LD blocks. We cross-validated the GWAS results using 17 fruit-related QTLs and identified 16 causal genes thought to be associated with fruit morphology-related domestication traits, with molecular functions such as cell division and expansion. The significant LD blocks and candidate genes identified in this study provide unique molecular footprints for deciphering the domestication history of Capsicum. Further functional validation of these candidate genes should accelerate the cloning of genes for major fruit-related traits in pepper.

所有现代辣椒种质资源均源自野生辣椒属物种的驯化过程。然而，由于目前全基因组关联分析（GWAS）数据以及多种性状选择信号的可用资源有限，辣椒中尚未发现与驯化相关的功能基因。为解决这一问题，本研究利用涵盖全球辣椒属种质资源的351份高度多样化辣椒种质资源群体，获取了主要果实相关驯化性状的表型数据，包括果实长度、宽度、单果重、果皮厚度及果实着生位置。本研究采用基因型测序分型（GBS）技术，在230份一年生辣椒（C. annuum）种质资源中开发出187966个覆盖全基因组的高质量单核苷酸多态性（SNP）标记。连锁不平衡（LD）分析结果显示，连锁不平衡区块的平均长度为149 kb。通过全基因组关联分析（GWAS），本研究共鉴定出与64个显著连锁不平衡区块相关的111个基因。本研究利用17个果实相关数量性状基因座（QTL）对全基因组关联分析结果进行了交叉验证，最终鉴定出16个被认为与果实形态相关驯化性状有关的因果基因，其分子功能涵盖细胞分裂与细胞扩张过程。本研究鉴定得到的显著连锁不平衡区块与候选基因，为解析辣椒属植物的驯化历史提供了独特的分子足迹。对这些候选基因开展进一步的功能验证，将有助于加速辣椒主要果实相关性状功能基因的克隆工作。