Signatures analysis of divergent selection revealed genes associated with different biological aspects of goats in Kenya

Abstract

The identification of genes and mutations linked to phenotypic features significant for livestock species may be revealed through the detection of selection signatures. This study aimed to decipher the selection signatures and mutational load of different dairy goat populations kept at KALRO-research station Naivasha. Analysis was done on the following breeds; Galla (n=12), and exotic dairy goats imported from South Africa (n=16). DNA was extracted from whole blood and genotyped using the Illumina GoatSNP50 BeadChip where 49773 single-nucleotide polymorphisms (SNPs) were generated. Analysis of selection signatures was carried out using fixation index (Fst) and nucleotide diversity (Pi). Two breeds, the Galla and imported dairy goats from South Africa were assessed based on the 0.05% top and lowest Fst and Pi respectively. The genes linked to pathways that are either directly or indirectly related to environmental adaptability were found to be more abundant in certain locations. These was revealed by genes associated with the immune response, organ development (TBC1D32, ADAMTS18), memory (SORCS3), sensory receptors and signaling (CDH23, CEP350, KCND2). We found genomic regions that could offer background information to comprehend the mechanisms influencing economic traits in the different goat breeds. Furthermore, the findings of this study are useful in furthering the genetic improvement of goat breeds kept at the KALRO research station and Kenya as a whole.