Genomic signatures of divergent selection for production and adaptation in domestic goats (Capra hircus)

Abstract

Background : Goats are distributed worldwide and include many breeds with marked phenotypic variation. Both natural and human driven processes have shaped their genomes. Here, 52K genome-wide SNP genotypes were used to investigate signatures of divergent selection between indigenous goats from an arid hot environment in Egypt and breeds developed under temperate environments in Europe. Three selection signature approaches were used, the di derivative of F ST , iHS and Rsb. Results: Out of a total of 36 candidate regions that were detected to be under selection by the three approaches, the analysis detected nine regions with the strongest selection signatures spanning 134 genes of which 68 were the most significantly functionally enriched. In addition to well-known genes affecting dairy traits ( LAP3 , ABCG2 , MEPE , IBSP , MED28 ) and body weight and stature ( LCORL , NCAPG , CCSER1 , DCAF16 ) in several mammalian species, we found evidence for selection in regions spanning genes implicated in the regulation of fatty acid synthesis and metabolic pathways ( PI4K2B and PPARGC1A ), inflammatory gene expression and autoimmune response pathways ( CXCL8 , HERC5 , RGS18 , TROVE2 ) and spermatogenesis ( SPATA18 , LAP3 ). Other genes not reported before in goats included SLIT2 , PACRGL , GRP125 , DHX15 , SOD3 and KCNIP4 which have been associated with thermal nociception in mice. We also detected a paralog of TBC1D12 , namely TBC1D14 , in one of the candidate regions. TBC1D12 has been linked to environmental adaptation in sheep. Gene ontology analysis revealed the 68 candidate genes were highly enriched in two biological processes viz regulation of G protein-coupled receptor signaling pathway (GO:0045744) and cellular response to stress (GO:0033554). Conclusions: Our results provide evidence that goat genomes have evolved, in part, via diverse positive selection directed at breed formation, at past and recent genetic improvement and adaptation to environments. Based on their uniqueness, these breed-group specific signatures of selection can be considered to be footprints of divergence which may be useful in characterizing genome architecture and diversity in domestic animals and for targeted genetic improvement.

Investigation of phenotypic, genetic and genomic background of Milk spectra in Sarda dairy sheep

“…Mwacharo et al. (2019) reported that the Phosphatidylinositol 4‐Kinase Type 2 Beta ( PI4K2B ) gene could be involved in the fatty acids synthesis (adipogenesis) and metabolic pathways in goats. The Anomalous Homeobox ( ANHX ) gene was found to be differently expressed between two groups of pigs with high and low feed efficiency (Xu et al., 2020).…”

“…The NPY gene has been also reported to be associated with feed intake in sheep (Wagner et al, 2004), whereas the Phytanoyl-CoA 2-Hydroxylase Interacting Protein Like (PHYHIPL) gene has been reported to have an additive effect on residual feed intake in beef cattle by (Abo-Ismail et al, 2018). Mwacharo et al (2019) reported that the Phosphatidylinositol 4-Kinase Type 2 Beta (PI4K2B) gene could be involved in the fatty acids synthesis (adipogenesis) and metabolic pathways in goats. The Anomalous Homeobox (ANHX) gene was found to be differently expressed between two groups of pigs with high and low feed efficiency (Xu et al, 2020).…”

The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data

“…Another signal on CHI6 shared by the two approaches identified a region from about 37.7 to 39.1 Mb, which was detected in both the PAL-MAJ and TIN-TIS window-based F ST comparisons as well as in the Majorera ROH analysis. To our knowledge, this region is of particular interest as it has also been detected as a candidate in a comparison between several other indigenous goats breeds from an arid hot environment in Egypt and European breeds that are raised under temperate environments [ 49 ]. This region encompasses five genes ( FAM184B , DCAF16 , NCAPG , LCORL and TRNAC-GCA ), that have been suggested to be involved in body weight and stature in cattle, sheep and humans [ 50 , 51 ].…”