Genome-wide association study and candidate gene identification for agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum

Abstract Pepper agronomic traits serve as pivotal indicators for characterizing germplasm attributes and correlations. Investigating genotypic disparities through phenotypic variations holds significant scientific merit Whole genome resequencing facilitates comprehensive examination of diverse individuals with known references, enabling subsequent differential analyses to pinpoint single nucleotide polymorphisms(SNPs) linked to pepper agrnomic. This study ,conducted a genome-wide association study(GWAS) encompassing 26 agronomic traits in 182 pepper specimens. Rigorous measures, including phylogenetic analysis, population structure analysis, population principal component analysis, kinship analysis, and linkage disequilibrium analysis, were employed to ensure the precision and reliability of GWAS results. The optimal statistical model. Was determined through these analyses. A total of 929 SNPs significantly associated with 26 agronomic traits, were identified, alongside the detection of 519 candidate genes within 100kb region adjacent to these SNPs. Additionally, through gene annotation and expression pattern scrutiny, genes such as SCPL13, extensin-1-like, and DDB1 correlated with fruit traits in Capsicum frutescens and Capsicum annuum were validated via qRT-PCR. 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.