Identification of QTLs associated with resistance to bacterial wilt in pepper (Capsicum annuum L.) through bi-parental QTL mapping and genome-wide association analysis

Ralstonia solanacearum is responsible for causing bacterial wilt (BW) disease in solanaceous crops, leading to significant crop losses. The challenge in controlling this disease lies in its soil-borne nature and the complex genetic architecture of R. solanacearum. Moreover, the complex oligogenic nature of resistance genes makes breeding resistant cultivars in peppers difficult. In this study, we combined bi-parental quantitative trait loci (QTL) mapping and a genome-wide association study (GWAS) to map loci associated with BW resistance. An F5:7 recombinant inbred lines were subjected to genotyping by sequencing (GBS) and the GWAS panel was genotyped using an Illumina PepperSNP 16 K array genotyping platform. A significant QTL (QTL.Bw5) was identified on the telomeric region of chromosome 5. GWAS analysis also identified four loci associated with BW resistance (GWAS.Bw.4, GWAS.Bw.5, GWAS.Bw.8.1, and GWAS.Bw.8.2) on chromosomes 4, 5, and 8. Our study revealed 13 candidate genes within QTL regions and in the vicinity of GWAS single-nucleotide polymorphisms (SNPs) based on their biological gene functions. A majority of these candidate genes were associated with plant stress, defense, or hormone signaling pathways. The QTLs and GWAS-SNPs related to BW resistance will provide valuable information for further characterizing resistance genes and developing markers to facilitate the breeding of resistant pepper cultivars.