Genomic Selection and Breeding Programme Optimisation for Productivity and Trypanotolerance in Nigerian Cattle Populations

This study develops a genomic selection framework and optimises breeding programme parameters for simultaneously improving productivity traits and maintaining trypanotolerance in Nigerian cattle populations, contributing an original contribution to tropical livestock genomics and breeding system design. Trypanotolerance, the ability to survive and produce under trypanosome challenge without treatment, is a critical adaptive trait of N'Dama and Muturu cattle breeds in Nigeria's tsetse-endemic zones. Designing improvement programmes that enhance milk and beef production while preserving this essential adaptive characteristic requires advanced genomic selection tools that have not been applied to Nigerian cattle. This study generates genomic data from 1,500 cattle of N'Dama, Muturu, and Bunaji breeds using 50K SNP arrays across experimental herds at NAPRI Shika, Nigerian Stored Products Research Institute, and Ibadan. Reference population construction and GBLUP and ssGBLUP methods are applied to estimate genomic breeding values for growth rate, milk production, heat tolerance, and trypanotolerance indices derived from experimental trypanosome challenge data. Breeding programme simulation uses ADAM software to optimise selection intensity, generation interval, and constraint parameters for maintaining allelic diversity at trypanotolerance-associated loci. Findings reveal that genomic selection increases expected annual genetic gain for yearling weight by 34 percent above conventional pedigree selection while constraining inbreeding rate within acceptable limits. Genomic regions on chromosomes 2, 7, and 22 show consistent significant associations with trypanotolerance across breeds. The study contributes an original Nigerian cattle genomic selection methodology and recommends establishment of a national cattle genotyping and evaluation infrastructure.

Keywords: genomic selection, trypanotolerance, Nigerian cattle, breeding programme, SNP markers.