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

Abstract

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

Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds

“…Results of GO and KEGG for the list of candidate genes identified in the current study support the assumption that pathways associated with adaptation mechanisms to harsh environmental conditions, such as regulation of immune response may be under positive selection in Egyptian goat breeds. These findings agree with previous reports in Egyptian [ 5 ] and Ugandan [ 8 ] goat breeds and indicates that adaptation to local environmental conditions requires a complex network of multiple genes [ 93 ], which is an important feature of indigenous breeds to increase their adaptation capacity.…”

A Review on Indigenous Goats of East Africa: A Case for Conservation and Management

“…The lack of defined genotypes leaves local goat populations in East Africa identified through a confusing array of regional and tribe names as well as the colors and patterns of their coats. For instance, the Sukuma goat, which is named after the Sukuma tribe in Tanzania, and the Galla goat, which is named after the Galla tribe in Kenya [ 31 , 32 , 35 ]. In Tanzania, the common indigenous goat breeds include Ujiji, mostly found around Lake Tanganyika; Sukuma, found in the south of Lake Victoria; Maasai, Pare, and Sonjo in the northern region; while Gogo and Newala goats are found in the central and southern part of the country [ 32 ].…”

“…Therefore, it is hypothesized that the indigenous goat population may have distinct genes responsible for this adaptation. For instance, the HSPA2 gene variations in indigenous goats have been linked to improved heat tolerance, allowing these breeds to support homeostasis and productivity in high-temperature situations [ 35 ]. In addition, studies on the genome-wide characterization of selection signatures and runs of homozygosity in Ugandan goat breeds have also reported the presence of IL10RB and IL23A genes responsible for the immune system [ 31 ].…”

Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

“…Compared to microarray methods, the whole-genome resequencing method offers a more comprehensive detection of genetic variations, providing deeper insight into the genetic landscape [ 26 , 27 , 28 ]. Furthermore, the iHS analysis applied to whole-genome resequencing and SNP microarray data have proven effective in identifying genomic regions under positive selection in goats; this approach facilitated the identification of genes associated with key traits such as productivity, disease resistance, and climate adaptability [ 4 , 29 , 30 ].…”