Genomic Selection and Its Application to Accelerating Genetic Gain in Clarias gariepinus Breeding Programmes in Nigeria

This research investigated the application of genomic selection as a strategy for accelerating genetic gain in Clarias gariepinus breeding programmes in Nigeria, addressing the absence of modern molecular breeding tools in the country's catfish aquaculture sector. Genomic selection uses dense genome-wide marker information to predict breeding values with greater accuracy than phenotypic selection alone, offering the potential to shorten generation intervals and increase selection intensity. A reference population of 600 catfish from five diverse hatchery and wild-source populations spanning the Niger, Cross, and Benue river basins was genotyped using genotyping-by-sequencing, generating over 12,000 SNP markers. Phenotypic records for growth traits, disease resistance indicators, and feed conversion efficiency were collected over two generations. Genomic estimated breeding values were predicted using genomic best linear unbiased prediction models, and prediction accuracies were compared against pedigree-based BLUP models. Results demonstrated that genomic selection increased prediction accuracy for body weight at harvest by 0.31 units over pedigree-based models, with accuracy gains largest for disease resistance traits of low heritability. Simulation of a two-year selection cycle indicated a projected 28 percent increase in annual genetic gain under genomic selection compared to conventional mass selection. Genomic inbreeding coefficients revealed elevated relatedness in hatchery populations compared to wild counterparts, highlighting the need for managed diversity maintenance within breeding programmes. The study provides the first genomic selection analysis for catfish in Nigeria and recommends the establishment of a national catfish genomic reference population database and genotyping infrastructure as a platform for sustainable genetic improvement. Keywords: genomic selection, Clarias gariepinus, breeding programme, genetic gain, SNP markers