Development of a Genomic Selection Framework for Resistance to Columnaris Disease in African Catfish Breeding Programmes in Nigeria

Columnaris disease caused by Flavobacterium columnare represents a significant source of mortality in African catfish hatcheries and juvenile rearing operations in Nigeria, and the development of disease-resistant catfish strains through genomic selection offers a sustainable alternative to antibiotic-dependent disease management. This study develops an original genomic selection framework for resistance to Flavobacterium columnare infection in Clarias gariepinus, constituting the first genomic selection study for disease resistance in this species in Nigeria. The study was conducted at the National Institute for Freshwater Fisheries Research in Niger State and involved the construction of a reference population of 1,200 full-sibling families genotyped using a custom 65,000 single nucleotide polymorphism array developed specifically for this project. Phenotypic disease resistance was characterised through a standardised challenge protocol in which juveniles were exposed to a pathogenic Flavobacterium columnare isolate and survival was recorded over 14 days. Genomic estimated breeding values for disease resistance were computed using genomic best linear unbiased prediction implemented in the GBLUP framework. Genome-wide association analysis identified 12 significant quantitative trait loci for disease resistance on five chromosomes, explaining 38% of total genetic variance. Cross-validation of genomic prediction accuracy using a leave-one-family-out scheme yielded a mean accuracy of 0.67, superior to pedigree-based BLUP predictions (0.41). The study establishes the theoretical and empirical foundations for incorporating genomic selection for disease resistance into the national catfish selective breeding programme, providing a pathway to replacing antibiotic dependence in Nigerian hatcheries.

Keywords: genomic selection, Clarias gariepinus, Flavobacterium columnare, disease resistance, breeding programme