QTL mapping and identification of linked markers for anthracnose fruit rot resistance in Capsicum baccatum L

Anthracnose fruit rot caused by Colletotrichum truncatum is a major constraint in Chilli production, leading to heavy pre- and post-harvest losses. Developing resistant cultivars through marker-assisted breeding is the most sustainable management strategy. Identification of molecular markers tightly linked to anthracnose fruit rot resistance loci in Capsicum baccatum accessions will be of great use in chili crop improvement programs to introgress resistance loci into elite backgrounds. Inheritance studies in an F₂ population (IIHR 4491 × PBC81) indicated inhibitory gene action (13S:3R) governing resistance against C. truncatum isolate IIHR Ct-1. Genotyping-by-sequencing identified 8,644 high-quality single nucleotide polymorphism (SNP) markers distributed across all chromosomes, ranging from 533 on chromosome 5 to 1,130 on chromosome 3. A genome-wide association study identified 19 SNPs significantly associated with resistance mainly on chromosomes 2 and 6. The two quantitative trait locus (QTL) regions were further refined to 836.18 kb on chromosome 2 (AnR-PBC81-C2) and 135.15 kb on chromosome 6 (AnR-PBC81-C6) through target loci-based QTL mapping. Epistasis analyses indicated significant epistatic interactions between these two QTL hotspots. Seventeen candidate genes involved in plant defense mechanisms were predicted within these regions. The identified markers were also validated in another F₂ population (IHR4491 × PBC80). Meta-QTL analysis identified 36 MQTLs, with AnR-PBC81-C2 assigned to MQTL2.2. The QTL on chromosome 6 (AnR-PBC81-C6) did not colocalize with any previously reported QTLs, indicating that it represents a novel resistance locus. The refined QTLs and associated developed SSR markers can be utilized to accelerate marker-assisted introgression breeding for anthracnose fruit rot disease resistance.