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Abstract：
Pepper agronomic traits serve as pivotal indicators for characterizing germplasm attributes and correlations. It is important to study differential genotypic variation through phenotypic differences of target traits. Whole genome resequencing was used to sequence the whole genome among different individuals of species with known reference genomes and annotations, and based on this, differential analyses of individuals or populations were carried out to identify SNPs for agronomic traits related to pepper. This study conducted a genome-wide association study encompassing 26 key agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum. The population structure (phylogenetics, population structure, population principal component analysis, genetic relationship) and linkage disequilibrium analysis were realized to ensure the accuracy and reliability of GWAS results, and the optimal statistical model was determined. A total of 929 SNPs significantly associated with 26 agronomic traits, were identified, alongside the detection of 519 candidate genes within 100 kb region adjacent to these SNPs. Additionally, through gene annotation and expression pattern scrutiny, genes such as GAUT1, COP10, and DDB1 correlated with fruit traits in Capsicum frutescens and Capsicum annuum were validated via qRT-PCR. In the CH20 (Capsicum annuum) and YB-4 (Capsicum frutescens) cultivars, GAUT1 and COP10 were cloned with cDNA lengths of 1065 bp and 561 bp, respectively, exhibiting only a small number of single nucleotide variations and nucleotide deletions. This validation provides a robust reference for molecular marker-assisted breeding of pepper agronomic traits, offering both genetic resources and theoretical foundations for future endeavors in molecular marker-assisted breeding for pepper.
摘要：
辣椒农艺性状是表征种质属性和相关性的关键指标。重要的是通过目标性状的表型差异来研究差异基因型变异。全基因组重测序用于对具有已知参考基因组和注释的不同物种个体之间的全基因组进行测序。基于此,进行了个体或种群差异分析，以鉴定与辣椒相关的农艺性状的SNP。这项研究进行了一项全基因组关联研究，其中包括182个向上生长的C.frutescens和C.annuum的26个关键农艺性状。种群结构(系统发育学，人口结构,人口主成分分析，遗传关系）和连锁不平衡分析，以确保GWAS结果的准确性和可靠性，并确定了最优统计模型。共有929个SNP与26个农艺性状显著相关，被确认,同时在与这些SNP相邻的100kb区域内检测519个候选基因。此外,通过基因注释和表达模式审查，通过qRT-PCR验证了与辣椒和辣椒果实性状相关的GAUT1，COP10和DDB1基因。在CH20（辣椒）和YB-4（辣椒）品种中，克隆了GAUT1和COP10，cDNA长度分别为1065bp和561bp，分别,仅表现出少量的单核苷酸变异和核苷酸缺失。该验证为辣椒农艺性状的分子标记辅助育种提供了可靠的参考，为未来辣椒分子标记辅助育种工作提供遗传资源和理论基础。
