Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya

• DOI: 10.3389/fgene.2022.858923
• Publication Date: 2022-04-21T05:19:46Z
• Authors: Ruth W. Waineina; Tobias O. Okeno; Evans D. Ilatsia; Kiplangat Ngeno
• Keywords: 2. Zero hunger; signature of selection; 0303 health sciences; 03 medical and health sciences; putative regions; Genetics; Molecular Medicine; adaptation; footprints; QH426-470; candidate genes; Genetics (clinical)

Artificial and natural selection in livestock is expected to leave unique footprints on their genomes. Goat breeds Kenya have evolved for survival, breeding, production various harsh ecological areas, genomes are likely acquired alleles adaptation such diverse environments other traits of economic importance. To investigate signals some selected goat Kenya, Alpine (n = 29), Galla 12), Saanen 24), Toggenburg 31) were considered. A total 53,347 single-nucleotide polymorphisms (SNPs) generated using the Illumina GoatSNP50 BeadChip analyzed. After quality control, 47,663 autosomal remained downstream analyses. Several complementary approaches applied following analyses: integrated Haplotype Score (iHS), cross-population-extended haplotype homozygosity (XP-EHH), hapFLK, FLK. 404 top genomic regions identified across all four breeds, based Out 16 putative signature by intersection multiple-selective signal analyses, most found overlap significantly with iHS XP-EHH analyses chromosomes 3, 4, 10, 15, 22, 26. These enriched genes involved pathways associated directly or indirectly environmental regulating immune responses (e.g., HYAL1 HYAL3), milk LEPR PDE4B), adaptability MST1 PCK). The results revealed few intersect between regions. In general, this did not present typical classic signatures as predicted due complex nature traits. support that pressures challenges, artificial selection, genome admixture challenges) molded Kenya. Therefore, research provides new knowledge conservation utilization these genetic resources In-depth needed detect precise connected