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Population history and genomic signatures for high-altitude adaptation in Tibetan pigs.

Ai H, Yang B, Li J, Xie X, Chen H, Ren J - BMC Genomics (2014)

Bottom Line: Several geographically isolated pig populations are distributed throughout the Plateau.Tibetan pig populations have experienced substantial genetic differentiation.Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, P, R China. renjunjxau@hotmail.com.

ABSTRACT

Background: The Tibetan pig is one of domestic animals indigenous to the Qinghai-Tibet Plateau. Several geographically isolated pig populations are distributed throughout the Plateau. It remained an open question if these populations have experienced different demographic histories and have evolved independent adaptive loci for the harsh environment of the Plateau. To address these questions, we herein investigated ~ 40,000 genetic variants across the pig genome in a broad panel of 678 individuals from 5 Tibetan geographic populations and 34 lowland breeds.

Results: Using a series of population genetic analyses, we show that Tibetan pig populations have marked genetic differentiations. Tibetan pigs appear to be 3 independent populations corresponding to the Tibetan, Gansu and Sichuan & Yunnan locations. Each population is more genetically similar to its geographic neighbors than to any of the other Tibetan populations. By applying a locus-specific branch length test, we identified both population-specific and -shared candidate genes under selection in Tibetan pigs. These genes, such as PLA2G12A, RGCC, C9ORF3, GRIN2B, GRID1 and EPAS1, are involved in high-altitude physiology including angiogenesis, pulmonary hypertension, oxygen intake, defense response and erythropoiesis. A majority of these genes have not been implicated in previous studies of highlanders and high-altitude animals.

Conclusion: Tibetan pig populations have experienced substantial genetic differentiation. Historically, Tibetan pigs likely had admixture with neighboring lowland breeds. During the long history of colonization in the Plateau, Tibetan pigs have developed a complex biological adaptation mechanism that could be different from that of Tibetans and other animals. Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau.

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Comparison of our highlighted candidate genes with previous reports. A venn diagram showing shared and distinct candidate genes for high-altitude adaptation between our findings, the 247 previously reported hypoxia genes [14] and 215 positively selected genes (PSGs) recently identified in the Tibetan wild boars [20].
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Fig5: Comparison of our highlighted candidate genes with previous reports. A venn diagram showing shared and distinct candidate genes for high-altitude adaptation between our findings, the 247 previously reported hypoxia genes [14] and 215 positively selected genes (PSGs) recently identified in the Tibetan wild boars [20].

Mentions: As shown in Figure 5, a majority of candidate genes implicated in the current study are distinct from those hypoxia genes identified in Tibetans [4–9], other highlanders [11–13] and Tibetan antelope [14] and yak [15]. We argue that Tibetan pigs may have evolved a different biological adaptation mechanism. Even compared with the recent findings of hypoxia-related genes in Tibetan pigs based on the whole-genome sequence data [19], most of candidate genes including those ranking in the top list of the current study (such as PLA2G12A, RGCC, C9ORF3, GRIN2B and GRID1) are reported for the first time.Figure 5


Population history and genomic signatures for high-altitude adaptation in Tibetan pigs.

Ai H, Yang B, Li J, Xie X, Chen H, Ren J - BMC Genomics (2014)

Comparison of our highlighted candidate genes with previous reports. A venn diagram showing shared and distinct candidate genes for high-altitude adaptation between our findings, the 247 previously reported hypoxia genes [14] and 215 positively selected genes (PSGs) recently identified in the Tibetan wild boars [20].
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4197311&req=5

Fig5: Comparison of our highlighted candidate genes with previous reports. A venn diagram showing shared and distinct candidate genes for high-altitude adaptation between our findings, the 247 previously reported hypoxia genes [14] and 215 positively selected genes (PSGs) recently identified in the Tibetan wild boars [20].
Mentions: As shown in Figure 5, a majority of candidate genes implicated in the current study are distinct from those hypoxia genes identified in Tibetans [4–9], other highlanders [11–13] and Tibetan antelope [14] and yak [15]. We argue that Tibetan pigs may have evolved a different biological adaptation mechanism. Even compared with the recent findings of hypoxia-related genes in Tibetan pigs based on the whole-genome sequence data [19], most of candidate genes including those ranking in the top list of the current study (such as PLA2G12A, RGCC, C9ORF3, GRIN2B and GRID1) are reported for the first time.Figure 5

Bottom Line: Several geographically isolated pig populations are distributed throughout the Plateau.Tibetan pig populations have experienced substantial genetic differentiation.Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, P, R China. renjunjxau@hotmail.com.

ABSTRACT

Background: The Tibetan pig is one of domestic animals indigenous to the Qinghai-Tibet Plateau. Several geographically isolated pig populations are distributed throughout the Plateau. It remained an open question if these populations have experienced different demographic histories and have evolved independent adaptive loci for the harsh environment of the Plateau. To address these questions, we herein investigated ~ 40,000 genetic variants across the pig genome in a broad panel of 678 individuals from 5 Tibetan geographic populations and 34 lowland breeds.

Results: Using a series of population genetic analyses, we show that Tibetan pig populations have marked genetic differentiations. Tibetan pigs appear to be 3 independent populations corresponding to the Tibetan, Gansu and Sichuan & Yunnan locations. Each population is more genetically similar to its geographic neighbors than to any of the other Tibetan populations. By applying a locus-specific branch length test, we identified both population-specific and -shared candidate genes under selection in Tibetan pigs. These genes, such as PLA2G12A, RGCC, C9ORF3, GRIN2B, GRID1 and EPAS1, are involved in high-altitude physiology including angiogenesis, pulmonary hypertension, oxygen intake, defense response and erythropoiesis. A majority of these genes have not been implicated in previous studies of highlanders and high-altitude animals.

Conclusion: Tibetan pig populations have experienced substantial genetic differentiation. Historically, Tibetan pigs likely had admixture with neighboring lowland breeds. During the long history of colonization in the Plateau, Tibetan pigs have developed a complex biological adaptation mechanism that could be different from that of Tibetans and other animals. Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau.

Show MeSH
Related in: MedlinePlus