Complete genome sequencing and analysis of <Emphasis Type="Italic">Capsicum annuum</Emphasis> varieties

Peppers (Capsicum spp.), economically important crops of the nightshade family, are used as vegetables, spices, and medicines. Bacterial wilt (BW), one of the most devastating bacterial plant diseases, causes heavy losses in many crops, including peppers. The aim of this study was to develop DNA-based molecular markers that could be used in future marker-assisted breeding for BW resistance. Genome-wide discovery of single-nucleotide polymorphisms (SNPs was achieved by comparing whole-genome resequencing data from two pepper varieties, Saengryeg 211 (susceptible to BW) and 82PR66 (resistant to BW) with the reference genome of Capsicum annuum cv. CM334. A total of 118,588,231 and 148,774,861 paired raw reads with an average length of 151 bp were recorded for Saengryeg 211 and 82PR66, respectively. Data mining revealed 6,804,889 and 4,293,534 SNPs for Saengryeg 211 and 82PR66, respectively. The SNPs, were assorted into 12 chromosomes. A total of 5,514,563 polymorphic SNPs were discovered between the two varieties, and 42,236 high-resolution melting marker primer sets were selected for use in future experiments. Our results reveal numerous DNA-based molecular markers that might be useful in molecular breeding and QTL mapping in pepper.