High-altitude adaptation: Role of genetic and epigenetic factors

2021 ◽  
Vol 46 (4) ◽  
Author(s):  
Nipa Basak ◽  
Kumarasamy Thangaraj
Keyword(s):  
High Altitude ◽  
Epigenetic Factors ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

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

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1599
Author(s):  
Meilin Jin ◽  
Jian Lu ◽  
Xiaojuan Fei ◽  
Zengkui Lu ◽  
Kai Quan ◽  
...  
Keyword(s):  
High Altitude ◽  
Growth Factor Signaling ◽  
Vascular Endothelial ◽  
Model Based Clustering ◽  
Adverse Conditions ◽  
High Altitude Adaptation ◽  
Significant Difference ◽  
Altitude Adaptation ◽  
Endothelial Growth Factor

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.

scholarly journals Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rahul K. Verma ◽  
Alena Kalyakulina ◽  
Cristina Giuliani ◽  
Pramod Shinde ◽  
Ajay Deep Kachhvah ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
High Altitude ◽  
Dna Sequences ◽  
Large Scale ◽  
Framework Analysis ◽  
Mt Dna ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
The Impact

AbstractNetworks have been established as an extremely powerful framework to understand and predict the behavior of many large-scale complex systems. We studied network motifs, the basic structural elements of networks, to describe the possible role of co-occurrence of genomic variations behind high altitude adaptation in the Asian human population. Mitochondrial DNA (mtDNA) variations have been acclaimed as one of the key players in understanding the biological mechanisms behind adaptation to extreme conditions. To explore the cumulative effects of variations in the mitochondrial genome with the variation in the altitude, we investigated human mt-DNA sequences from the NCBI database at different altitudes under the co-occurrence motifs framework. Analysis of the co-occurrence motifs using similarity clustering revealed a clear distinction between lower and higher altitude regions. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral ‘RSRS50’ variant 10,398 was found to co-occur only at higher altitudes supporting the fact that a separate route of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence interactions specific to high altitude at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding the role of co-occurrence of mitochondrial variations in high altitude adaptation.

scholarly journals Role of mitochondrial genetic interactions in determining adaptation to high altitude in human population around the globe

2021 ◽  
Author(s):  
Rahul K Verma ◽  
Alena Kalyakulina ◽  
Ankit Mishra ◽  
Mikhail Ivanchenko ◽  
Sarika Jalan
Keyword(s):  
High Altitude ◽  
Human Population ◽  
Nadh Dehydrogenase ◽  
Gene Interaction ◽  
Genetic Networks ◽  
Genetic Interactions ◽  
High Altitude Adaptation ◽  
Evolutionary Forces ◽  
Altitude Adaptation

Physiological and haplogroup studies performed to understand high-altitude adaptation in humans are limited to individual genes and polymorphic sites. Due to stochastic evolutionary forces, the frequency of a polymorphism is affected by changes in the frequency of a nearby polymorphism on the same DNA sample making them connected in terms of evolution. Here, first, we provide a method to model these mitochondrial polymorphisms as 'co-mutation networks' for three high-altitude populations, Tibetan, Ethiopian and Andean. Then, by transforming these co-mutation networks into weighted and undirected gene-gene interaction (GGI) networks, we were able to identify functionally enriched genetic interactions ofCYBandCO3genes in Tibetan and Andean populations, while NADH dehydrogenase genes in the Ethiopian population playing a significant role in high altitude adaptation. These co-mutation-based genetic networks provide insights into the role of different sets of genes in high-altitude adaptation human sub-populations.

scholarly journals Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cheng Quan ◽  
Yuanfeng Li ◽  
Xinyi Liu ◽  
Yahui Wang ◽  
Jie Ping ◽  
...  
Keyword(s):  
High Altitude ◽  
Structural Variation ◽  
Tibet Plateau ◽  
Base Pairs ◽  
Adaptation Studies ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
And Function ◽  
Genomic Regions

Abstract Background Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little is known of adaptive introgressed SVs in Tibetans so far. Results Here, we generate a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% are sequence-resolved for the first time. We systematically assess the distribution of these SVs across repeat sequences and functional genomic regions. Through genotyping in additional 276 genomes, we identify 69 Tibetan-Han stratified SVs and 80 candidate adaptive genes. We also discover a few adaptive introgressed SV candidates and provide evidence for a deletion of 335 base pairs at 1p36.32. Conclusions Overall, our results highlight the important role of SVs in the evolutionary processes of Tibetans’ adaptation to the Qinghai-Tibet Plateau and provide a valuable resource for future high-altitude adaptation studies.

scholarly journals Characterization of Structural Variation in Tibetans Reveals New Evidence of High-altitude Adaptation and Introgression

2020 ◽  
Author(s):  
Cheng Quan ◽  
Yuanfeng Li ◽  
Yahui Wang ◽  
Jie Ping ◽  
Yiming Lu ◽  
...  
Keyword(s):  
High Altitude ◽  
Structural Variation ◽  
Tibet Plateau ◽  
Base Pairs ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
And Function ◽  
Genomic Regions ◽  
Qinghai Tibet Plateau

AbstractStructural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. To investigate the role of SVs in high-altitude adaptation (HAA), we here generated a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using the nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% were sequence-resolved for the first time. We systemically assessed the distribution of these SVs across repeat sequences and functional genomic regions. Through genotyping in additional 189 genomes, we identified 90 Tibetan-Han stratified SVs and 124 candidate adaptive genes. Besides, we discovered 15 adaptive introgressed SV candidates and provided evidence for a deletion of 335 base pairs at 1p36.32. Overall, our results highlight the important role of SVs in the evolutionary processes of Tibetans’ adaptation to the Qinghai-Tibet Plateau and provide a valuable resource for future HAA studies.

scholarly journals Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

2021 ◽  
Author(s):  
Pamela Wiener ◽  
Christelle Robert ◽  
Abulgasim Ahbara ◽  
Mazdak Salavati ◽  
Ayele Abebe ◽  
...  
Keyword(s):  
High Altitude ◽  
Environmental Variables ◽  
Large Scale ◽  
Sequence Data ◽  
Strong Association ◽  
Environmental Adaptation ◽  
Whole Genome Sequence ◽  
Single Nucleotide Variants ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

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