Abstract
Population structure and relationship information among goats is critical for genetic improvement, utilization, and conservation. This study explored population structure and level of introgression among four goat breeds in Kenya: the indigenous Galla (n = 12) and three imported breeds, the Alpine (n = 29), Toggenburg (n = 31), and Saanen (n = 24). Genetic diversity was analyzed using four indices (polymorphic SNPs, mean allele frequency, observed and expected heterozygosity and inbreeding coefficient) within each breed. Population structure assessed using model-based clustering (ADMIXTURE) revealed four breeds according to their geographic regions in Kenya. Kenyan Alpine goats were the most admixed breed with about 10 % of its genome derived from Galla, 10 % and 6 % from Saanen and Toggenburg respectively. The association of Galla with other breeds was anticipated since the Galla breed was used as the founder population for crossbreeding with Saanen, Alpine and Toggenburg breeds. The relationship information evaluated by computing Reynolds genetic distance revealed five distinctive clusters: Alpine, Galla, Saanen, Toggenburg and some mixture of Alpine and Toggenburg. Saanen and Galla breeds seem to be the most genetically distinct among the sampled populations. The genetic variation among the goat populations observed will provide a good opportunity for sustainable utilization, conservation, and future genetic resource improvement programmes in goat breeds in Kenya.
Highlights
Goats are known to be the most adaptable and widespread species of domestic animals, thriving across various geographical conditions, ranging from mountains to deserts and the tropics, Africa included
Of the excluded single-nucleotide polymorphisms (SNP), 2,235 had less than 0.1 missing per SNP, 663 SNPs significantly deviated from Hardy Weinberg Equilibrium (HWE) (P < 0.001) and 644 SNPs had Minor Allele Frequency (MAF) lower than 0.05
The Galla breed had the highest number of SNPs excluded in total (10,688), whereas Alpine revealed the lowest number of SNPs excluded (5,129)
Summary
Goats are known to be the most adaptable and widespread species of domestic animals, thriving across various geographical conditions, ranging from mountains to deserts and the tropics, Africa included. The importance of goats in supporting rural household economies in developing countries is well documented (Deshingkar et al, 2008; Herrero et al, 2013). The diminishing land sizes in the medium to high potential areas for agriculture due to human population pressure, expansion of urban areas and climate change-related challenges, call for alternative farming practices such as intensive dairy goat production, which offers more multi-functionality, flexibility, and adaptability to varied production conditions (Scarpa et al, 2003).
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