Genomic signatures of high-altitude adaptation in Ethiopian sheep populations

Edea, Zewdu; Dadi, Hailu; Dessie, Tadelle; Kim, Kwan‐Suk

doi:10.1007/s13258-019-00820-y

Cited by 54 publications

(36 citation statements)

References 72 publications

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“…Second was the MITF gene (melanocyte inducing transcription factor) ( di value = 8.36), which was selected for adaptation to high levels of ultraviolet radiation in Tibetan goats. Similar results have been found for Tibetan sheep [ 23 ] and Ethiopian sheep [ 24 ]. Another, RGCC (regulator of cell cycle) ( di value = 9.21) had a physical interaction with HIF1α and VEGF , which are key mediators in the cellular response to hypoxia [ 31 ] and also identify in Tibetan pigs [ 25 ].…”

Section: Resultssupporting

confidence: 89%

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Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet

Jin

Lü

Fei

et al. 2020

Animals

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Tibetan goat is an ancient breed, which inhabits the adverse conditions of the plateaus in China. To investigate the role of selection in shaping its genomes, we genotyped Tibetan goats (Nagqu Prefecture, above 4500 m) and three lowland populations (Xinjiang goats, Taihang goats and Huanghuai goats). The result of PCA, neighbor-joining (N-J) tree and model-based clustering showed that the genetic structure between the Tibetan goat and the three lowland populations has significant difference. As demonstrated by the di statistic, we found that some genes were related to the high-altitude adaptation of Tibetan goats. Functional analysis revealed that these genes were enriched in the VEGF (vascular endothelial growth factor) signaling pathway and melanoma, suggesting that nine genes (FGF2, EGFR, AKT1, PTEN, MITF, ENPEP, SIRT6, KDR, and CDC42) might have important roles in the high-altitude adaptation of Nagqu Tibetan goats. We also found that the LEPR gene was under the strongest selection (di value = 16.70), and it could induce upregulation of the hypoxic ventilatory response. In addition, five genes (LEPR, LDB1, EGFR, NOX4 and FGF2) with high di values were analyzed using q-PCR. Among them, we found that LEPR, LDB1 and FGF2 exhibited higher expression in the lungs of the Tibetan goats; LEPR, EGFR and LDB1 exhibited higher expression in the hearts of the Huanghuai goat. Our results suggest that LEPR, LDB1, EGFR and FGF2 genes may be related to the high-altitude adaptation of the goats. These findings improve our understanding of the selection of the high-altitude adaptability of the Nagqu Tibetan goats and provide new theoretical knowledge for the conservation and utilization of germplasm resources.

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Section: Resultssupporting

confidence: 89%

“…Thirdly, we obtained 261 specific selected SNPs that contained 459 genes without the LOC symbols and Gene IDs ( Table S2 ). In accordance with gene function and previous study, finally, we found 16 potential genes associated with hypoxia and angiogenesis, energy metabolism, or melanogenesis [ 23 , 24 , 25 ].…”

Section: Resultssupporting

confidence: 89%

Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet

Jin

Lü

Fei

et al. 2020

Animals

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“…Phosphorylation of the PPP1R12A (also called MYPTI) gene is known to increase as the level of oxygen decreases [85,86]. In a study comparing Ethiopian sheep breeds that are adapted to different ecological regions, Edea et al [87] identified four genes including PPP1R12A that showed signatures of selection likely related to high altitude adaptation. Gene expression analyses revealed SLC16A3 as one of the significant up-regulated genes (p-value = 1.77E − 02) in response to high altitude adaptation of sheep fetal carotid arteries [88].…”

Section: Body Size and Cold Acclimationmentioning

confidence: 99%

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

et al. 2020

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Background: Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results: Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8,

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“…Another adaptive mechanism to decrease energy demands is the modification of morphological traits, e.g. Tibetan sheep have smaller body sizes (Yang et al ) and high‐altitude Ethiopian sheep breeds have distinctive coat features, such as colour, texture and length (Edea et al ), compared with lowland breeds.…”

Section: Effects Of High Altitude On the Mammalian Body And Physiologmentioning

confidence: 99%

Selection signatures for high‐altitude adaptation in ruminants

Friedrich

Wiener

2020

Animal Genetics

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Summary High‐altitude areas are important socio‐economical habitats with ruminants serving as a major source of food and commodities for humans. Living at high altitude, however, is extremely challenging, predominantly due to the exposure to hypoxic conditions, but also because of cold temperatures and limited feed for livestock. To survive in high‐altitude environments over the long term, ruminants have evolved adaptation strategies, e.g. physiological and morphological modifications, which allow them to cope with these harsh conditions. Identification of such selection signatures in ruminants may contribute to more informed breeding decisions, and thus improved productivity. Moreover, studying the genetic background of altitude adaptation in ruminants provides insights into a common molecular basis across species and thus a better understanding of the physiological basis of this adaptation. In this paper, we review the major effects of high altitude on the mammalian body and highlight some of the most important short‐term (coping) and genetically evolved (adaptation) physiological modifications. We then discuss the genetic architecture of altitude adaptation and target genes that show evidence of being under selection based on recent studies in various species, with a focus on ruminants. The yak is presented as an interesting native species that has adapted to the high‐altitude regions of Tibet. Finally, we conclude with implications and challenges of selection signature studies on altitude adaptation in general. We found that the number of studies on genetic mechanisms that enable altitude adaptation in ruminants is growing, with a strong focus on identifying selection signatures, and hypothesise that the investigation of genetic data from multiple species and regions will contribute greatly to the understanding of the genetic basis of altitude adaptation.

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Genomic signatures of high-altitude adaptation in Ethiopian sheep populations

Cited by 54 publications

References 72 publications

Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet

Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

Selection signatures for high‐altitude adaptation in ruminants

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