Epistatic Interactions Governing Fruit Quality Trait Architecture in Tomato (Solanum lycopersicum) Breeding Lines Developed for Nigerian Production Environments

Tomato fruit quality in Nigerian markets is defined by a complex multi-trait phenotype encompassing firmness, shelf life, total soluble solids content, lycopene concentration, and color uniformity. While individual quantitative trait loci for these traits have been reported in international literature, the epistatic interactions governing fruit quality trait architecture in tomato breeding lines specifically adapted to Nigerian production environments have not been investigated. This dissertation characterizes epistatic interaction networks for fruit quality traits in a recombinant inbred line population derived from crosses between locally adapted Nigerian tomato accessions and AVRDC-released tropical-adapted parents. A total of 280 RILs were genotyped using a 6,000 SNP tomato array and phenotyped across three environments in Kano, Ibadan, and Benue states. Composite interval mapping and epistasis-enriched QTL analysis were performed using R/qtl2. Significant epistatic interactions were detected for lycopene content and fruit firmness involving loci on chromosomes 2, 9, and 11, with a novel cis-acting QTL identified for shelf life colocalizing with a candidate ethylene receptor gene. The results provide actionable knowledge for genomics-assisted breeding of fruit quality-improved tomato for the Nigerian market. Keywords: epistasis, tomato, fruit quality, QTL mapping, Nigerian breeding environments