Dataset Information

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment.

ABSTRACT: Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

SUBMITTER: Kim ES

PROVIDER: S-EPMC4806575 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment.

Kim E-S ES Elbeltagy A R AR Aboul-Naga A M AM Rischkowsky B B Sayre B B Mwacharo J M JM Rothschild M F MF

Heredity 20151111 3

Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of th ...[more]

PMID: 26555032

Similar Datasets

Project description:Indigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adaptive characteristics play an important role as genetic materials for improving commercial breeds. As a step toward this goal, we analyzed the genome of Korean indigenous goats within 10 goat breeds. We collected 136 goat individuals by sequencing 46 new goats and employing 90 publicly available goats. Our whole-genome data was comprised of three indigenous breeds (Korean indigenous goat, Iranian indigenous goat, and Moroccan indigenous goat; n = 29, 18, 20), six commercial breeds (Saanen, Boer, Anglo-Nubian, British Alpine, Alpine, and Korean crossbred; n = 16, 11, 5, 5, 2, 13), and their ancestral species (Capra aegagrus; n = 17). We identified that the Iranian indigenous goat and the Moroccan indigenous goat have relatively similar genomic characteristics within a large category of genomic diversity but found that the Korean indigenous goat has unique genomic characteristics distinguished from the other nine breeds. Through population analysis, we confirmed that these characteristics have resulted from a near-isolated environment with strong genetic drift. The Korean indigenous goat experienced a severe genetic bottleneck upon entering the Korean Peninsula about 2,000 years ago, and has subsequently rarely experienced genetic interactions with other goat breeds. From selection analysis and gene-set enrichment analysis, we revealed selection signals for Salmonella infection and cardiomyopathy in the genome of the Korean indigenous goat. These adaptive characteristics were further identified with genomic-based evidence. We uncovered genomic regions of selective sweeps in the LBP and BPI genes (Salmonella infection) and the TTN and ITGB6 genes (cardiomyopathy), among several candidate genes. Our research presents unique genomic characteristics and distinctive selection signals of the Korean indigenous goat based on the extensive comparison. Although the adaptive traits require further validation through biological experiments, our findings are expected to provide a direction for future biodiversity conservation strategies and to contribute another option to genomic-based breeding programmes for improving the viability of Capra hircus.

Project description:BACKGROUND:The current large spectrum of sheep phenotypic diversity results from the combined product of sheep selection for different production traits such as wool, milk and meat, and its natural adaptation to new environments. In this study, we scanned the genome of 25 Sasi Ardi and 75 Latxa sheep from the Western Pyrenees for three types of regions under selection: (1) regions underlying local adaptation of Sasi Ardi semi-feral sheep, (2) regions related to a long traditional dairy selection pressure in Latxa sheep, and (3) regions experiencing the specific effect of the modern genetic improvement program established for the Latxa breed during the last three decades. RESULTS:Thirty-two selected candidate regions including 147 annotated genes were detected by using three statistical parameters: pooled heterozygosity H, Tajima's D, and Wright's fixation index Fst. For Sasi Ardi sheep, chromosomes Ovis aries (OAR)4, 6, and 22 showed the strongest signals and harbored several candidate genes related to energy metabolism and morphology (BBS9, ELOVL3 and LDB1), immunity (NFKB2), and reproduction (H2AFZ). The major genomic difference between Sasi Ardi and Latxa sheep was on OAR6, which is known to affect milk production, with highly selected regions around the ABCG2, SPP1, LAP3, NCAPG, LCORL, and MEPE genes in Latxa sheep. The effect of the modern genetic improvement program on Latxa sheep was also evident on OAR15, on which several olfactory genes are located. We also detected several genes involved in reproduction such as ESR1 and ZNF366 that were affected by this selection program. CONCLUSIONS:Natural and artificial selection have shaped the genome of both Sasi Ardi and Latxa sheep. Our results suggest that Sasi Ardi traits related to energy metabolism, morphological, reproductive, and immunological features have been under positive selection to adapt this semi-feral sheep to its particular environment. The highly selected Latxa sheep for dairy production showed clear signatures of selection in genomic regions related to milk production. Furthermore, our data indicate that the selection criteria applied in the modern genetic improvement program affect immunity and reproduction traits.

Dataset Information

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment.

Publications

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets