Table_3_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.

所有现代辣椒种质材料均源自野生辣椒属（Capsicum）物种的驯化过程。然而，由于全基因组关联分析（genome-wide association study, GWAS）数据以及各类性状选择信号的可获得性有限，目前尚未在辣椒中鉴定出与驯化相关的基因。为解决这一研究难题，本研究利用覆盖全球辣椒属种质资源的351份高度多样化辣椒种质材料，采集了与果实相关的主要驯化性状数据：包括果实长度、果实宽度、单果质量、果皮厚度及果实着生位置。采用基因型分型测序（genotype-by-sequencing, GBS）技术，本研究在230份一年生辣椒（C. annuum）种质材料中开发了187,966个全基因组范围内的高质量单核苷酸多态性（single nucleotide polymorphism, SNP）标记。连锁不平衡（linkage disequilibrium, LD）分析结果显示，连锁不平衡块的平均长度为149 kb。通过全基因组关联分析（GWAS），本研究鉴定出与64个显著连锁不平衡块相关的111个基因。本研究利用17个果实相关数量性状位点（quantitative trait locus, QTL）对全基因组关联分析结果进行了交叉验证，并鉴定出16个与果实形态相关驯化性状相关的候选因果基因，其分子功能涵盖细胞分裂与细胞扩张过程。本研究鉴定出的显著连锁不平衡块与候选基因，为解析辣椒属的驯化历史提供了独特的分子线索。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调控基因的克隆工作。