Genome-Wide Association Study of Resistance Genes Against Anthracnose (Colletotrichum gloeosporioides) in Nigerian Pepper (Capsicum annuum) Germplasm

Anthracnose, caused by Colletotrichum gloeosporioides and related species, is the most economically destructive post-harvest disease of pepper (Capsicum annuum) in Nigeria, causing losses of 40 to 60 percent in storage and transit. Breeding for durable resistance is the most cost-effective long-term management strategy, yet the genetic architecture of anthracnose resistance in Nigerian pepper germplasm remains uncharacterized. This dissertation conducts the first genome-wide association study (GWAS) of anthracnose resistance in a diverse panel of 200 Nigerian Capsicum annuum accessions assembled from six geopolitical zones. A high-density genotyping-by-sequencing approach generating over 50,000 SNPs was combined with phenotypic screening for anthracnose lesion area, disease severity index, and resistance category under both controlled inoculation and field conditions across two seasons. Population structure analysis, linkage disequilibrium mapping, and mixed linear model GWAS were applied. Twelve significant marker-trait associations were identified on chromosomes 1, 6, and 10, with two loci explaining over 30 percent of phenotypic variance for disease severity. Candidate gene annotation reveals probable roles for nucleotide-binding leucine-rich repeat genes and reactive oxygen species pathway genes in resistance. The study establishes a foundational genetic resource for marker-assisted selection for anthracnose resistance in Nigerian pepper breeding programs. Keywords: GWAS, anthracnose, Capsicum annuum, resistance genes, marker-assisted selection