Genome-wide association study and candidate gene identification for yield components, quality, and disease resistance traits in Capsicum species

Capsicum is an important crop for both fresh consumption and industrial use. This study investigated the genetic loci associated with 11 agronomic traits in Capsicum species using genome-wide association studies (GWAS) and genotyping-by-sequencing (GBS). A collection of 100 diverse Capsicum genotypes was evaluated under field conditions over 2 years. Genotyping was conducted using the Illumina platform. For most traits, the phenotypic coefficient of variance (21.22–56.40) exceeded the genotypic coefficient of variance (18.75–54.75). Hierarchical clustering grouped the genotypes into three clusters. Analysis of GBS data identified 16,745 high-quality SNPs, with the highest number (3202) located on chromosome 3. Linkage disequilibrium (LD) analysis across the 12 chromosomes identified 835 LD blocks. STRUCTURE software predicted three distinct sub-populations (K = 3). GWAS identified 34 SNPs significantly associated with 28 QTL regions. The study identified candidate genes putatively associated with traits such as plant height (Transcription factor MYB4), fruit length (Putative glycine-rich cell wall structural protein 1), fruit width (Pentatricopeptide repeat-containing protein At2g20540), fruit orientation (Bidirectional sugar transporter N3-like), fruit colour (Metallocarboxypeptidase inhibitor), pungency (Probable LRR receptor-like serine/threonine-protein kinase At1g53420), number of fruits per plant (Ankyrin repeat domain-containing protein 13B), fruit weight (Putative F-box protein At5g50220), yield per plant (Photosynthetic NDH subunit of lumenal location 1, chloroplastic), chilli leaf curl virus resistance (Formin-like protein 3), and anthracnose resistance (Acyl-CoA-binding protein). A few candidate genes were validated by qRT-PCR. These findings provide valuable genomic resources and identify candidate genes for key traits relevant to Capsicum breeding.