Determination of genetic diversity in pepper collection by next-generation sequencing data

The pepper plant (Capsicum annuum L.) is a widely cultivated and consumed vegetable, worldwide. Therefore, pepper breeding studies aimed at improving traits such as high yield, disease resistance, and climate adaptation. Determining the genetic diversity and characterizing is crucial for more effective breeding studies in the pepper plant. In this context, the aim was to determine the genetic diversity and population structure using next-generation sequencing data in a pepper collection adapted to Mediterranean climate zone. The collection includes 99 pepper lines consisting of 21 Dolma types, 19 Charleston types, 13 Kapya types, 11 Chili types, 4 Mazamort types, 5 Chili types, 24 Sivri types, and 2 Jalapeno types. Using the ddRADSeq method, this collection characterized at the SNP level resulted in a total of 318.76 million reads and an average of %37.66 GC content. After bioinformatics analyses, 8475 SNPs were used to determine the population structure. A phylogenetic tree was created to determine genetic diversity among the lines, and it was observed that the lines clustered according to their commercial types. The STRUCTURE analysis identified two (K=2) distinct subgroups within the collection, while the PCoA analysis divided the pepper lines into five groups. The observed homozygosity (Ho) and expected heterozygosity (He) values in the population were recorded as 0.493 and 0.313, respectively. Potential parent lines were identified considering the potential heterosis effect after hybridization of genetically distant lines. The findings are expected to shed light on the development of new breeding strategies aimed at developing pepper varieties suitable for the Mediterranean climate.