Genetic Diversity and Population Structure of Dairy Goat Populations in Kenya

Abstract

This study aimed to decipher the genetic diversity and structure of different dairy goat populations kept at KALRO-research station Naivasha to facilitate national genetic improvement program. We used 49,773 genome-wide SNP data to quantify levels of and patterns of genetic diversity among 243 individuals from five goat populations: Toggenburg (n=69), Alpine (n=54), Saneen (n=24), Toggenburg Kenya Dual Purpose goat (TKDPG) (n=4), Kenya Dual Purpose Goat (KDPG)(n=11) and crosses (n=81). Inbreeding coefficient, observed and expected heterozygosity ranged from-0.01-0.07, 0.56- 0.60 and 0.57 respectively. Principal component analysis clustered the populations into three distinct clusters namely; cluster one-Saanen, Alpine and their crosses, cluster two-Toggenburg, Alpine, TKDPG and their crosses, and cluster three-KDPG, Toggenburg, TKDPG, Alpine and their crosses. Genetically admixed genotypes were identified in each cluster, indicating intermixing within the populations. High number of ROH proofed there is some level of homozygosity in the goat genotypes in Kenya. Results provided understandings into genomic variations and relationships which is vital in furthering genetic improvement and conservation of goat kept at Kenya Agricultural and Livestock Research Organization (KALRO) research station and Kenya as a whole.