Hot pepper and sweet pepper, Agronomic traits, Genome-wide association study (GWAS), Specific-locus amplified fragment sequencing (SLAF-seq), Biotechnology, TP248.13-248.65, Genetics, QH426-470

Abstract Background Utilizing Single Nucleotide Polymorphism (SNP) marker technology, a phylogenetic and agronomic trait network analysis was conducted on the collected hot pepper and sweet pepper germplasm resources, providing a theoretical basis for parental selection and new varieties. Results Specific-locus amplified fragment sequencing (SLAF-seq) technology was employed for a genome-wide association study (GWAS) on 197 hot pepper and sweet pepper germplasm resources, generating 1404.88 Mb clean reads data with an average Q30 of 91.5% and mean GC content of 37.96%. Through sequencing data analysis, a total of 639,815 SLAF tags were obtained with an average sequencing depth of 12.16x, among which 86,381 were polymorphic SLAF tags, leading to the development of 18,145,155 SNP markers. The identified SNP markers were used for cluster analysis of the genetic structure and phylogenetic relationships of hot pepper and sweet pepper germplasm resources, dividing the 197 hot pepper and sweet pepper germplasm resources into 9 clusters. Additionally, a genome-wide association analysis was conducted on 25 agronomic traits of the 197 hot pepper and sweet pepper materials, yielding a substantial number of significantly associated SNP loci with agronomic traits. A correlation network analysis diagram was drawn among the various agronomic traits, preliminarily determining the relationships between the 25 agronomic characteristics of hot pepper and sweet pepper and the positions of 15 agronomic traits (p