Limits...
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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Related in: MedlinePlus

Map of sample locations in the present study. Our samples were collected from 5 Tibetan pig geographic populations and 25 Chinese lowland breeds. Populations tested in this study are highlighted in pink. Our previously reported and online available breeds are indicated in blue and green, respectively. Phenotypes of the 5 Tibetan pig geographic populations are shown in the left panel. BAM, Bamei; BMX, Bama Xiang; CJX, Congjiang Xiang; DHB, Dahuabai; DN, Diannanxiaoer; DS, Dongshan; EHL, Erhualian; GST, Tibetan (Gansu); GX, Ganxi; HT, Hetaodaer; JH, Jinhua; JQH, Jiangquhai; KL, Kele; LIC, Lichahei; LWU, Laiwu; LUC, Luchuan; MG, Mingguangxiaoer; MIN, Min; MS, Meishan; NJ, Neijiang; RC, Rongchang; SCT, Tibetan (Sichuan); SUT, Sutai; SZL, Shaziling; TC, Tongcheng; TT1, Tibetan (Gongbujiangda); TT2, Tibetan (Milin); WB, Chinese wild boars; WZS, Wuzhishan; YNT, Tibetan (Yunnan).
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Fig1: Map of sample locations in the present study. Our samples were collected from 5 Tibetan pig geographic populations and 25 Chinese lowland breeds. Populations tested in this study are highlighted in pink. Our previously reported and online available breeds are indicated in blue and green, respectively. Phenotypes of the 5 Tibetan pig geographic populations are shown in the left panel. BAM, Bamei; BMX, Bama Xiang; CJX, Congjiang Xiang; DHB, Dahuabai; DN, Diannanxiaoer; DS, Dongshan; EHL, Erhualian; GST, Tibetan (Gansu); GX, Ganxi; HT, Hetaodaer; JH, Jinhua; JQH, Jiangquhai; KL, Kele; LIC, Lichahei; LWU, Laiwu; LUC, Luchuan; MG, Mingguangxiaoer; MIN, Min; MS, Meishan; NJ, Neijiang; RC, Rongchang; SCT, Tibetan (Sichuan); SUT, Sutai; SZL, Shaziling; TC, Tongcheng; TT1, Tibetan (Gongbujiangda); TT2, Tibetan (Milin); WB, Chinese wild boars; WZS, Wuzhishan; YNT, Tibetan (Yunnan).

Mentions: The Tibetan pig, one of Tibetans’ domestic animals, is originally distributed in farming and farming-pastoral regions at altitudes of 2,900 - 4,300 m in the Qinghai-Tibetan Plateau [16]. Like Tibetans and other colonists in the Plateau, Tibetan pigs have several key adaptive features for coping with the harsh environment at high altitude [16]. First, they have black skin and hair with long and dense bristle that protect them from high solar radiation and cold ambient temperature in winter (Figure 1). Second, their well-developed heart and lung may be required for the increased rate of blood flow and oxygen transportation to tissues in response to hypoxia. Third, they have developed a blunted erythropoietic response to high-altitude hypoxia by exhibiting lower than expected hemoglobin concentrations relative to their lowland counterparts and acclimatized lowland pigs [17]. This feature, in contrast to Tibetan yak, goat and sheep that show elevated hemoglobin levels at high altitude, is a crucial protection mechanism for excessive erythrocytosis (a classic feature of chronic mountain sickness [18]) in Tibetans [1–3]. Forth, their alertness and agility enable them to survive in the grazing condition.Figure 1


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)

Map of sample locations in the present study. Our samples were collected from 5 Tibetan pig geographic populations and 25 Chinese lowland breeds. Populations tested in this study are highlighted in pink. Our previously reported and online available breeds are indicated in blue and green, respectively. Phenotypes of the 5 Tibetan pig geographic populations are shown in the left panel. BAM, Bamei; BMX, Bama Xiang; CJX, Congjiang Xiang; DHB, Dahuabai; DN, Diannanxiaoer; DS, Dongshan; EHL, Erhualian; GST, Tibetan (Gansu); GX, Ganxi; HT, Hetaodaer; JH, Jinhua; JQH, Jiangquhai; KL, Kele; LIC, Lichahei; LWU, Laiwu; LUC, Luchuan; MG, Mingguangxiaoer; MIN, Min; MS, Meishan; NJ, Neijiang; RC, Rongchang; SCT, Tibetan (Sichuan); SUT, Sutai; SZL, Shaziling; TC, Tongcheng; TT1, Tibetan (Gongbujiangda); TT2, Tibetan (Milin); WB, Chinese wild boars; WZS, Wuzhishan; YNT, Tibetan (Yunnan).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Map of sample locations in the present study. Our samples were collected from 5 Tibetan pig geographic populations and 25 Chinese lowland breeds. Populations tested in this study are highlighted in pink. Our previously reported and online available breeds are indicated in blue and green, respectively. Phenotypes of the 5 Tibetan pig geographic populations are shown in the left panel. BAM, Bamei; BMX, Bama Xiang; CJX, Congjiang Xiang; DHB, Dahuabai; DN, Diannanxiaoer; DS, Dongshan; EHL, Erhualian; GST, Tibetan (Gansu); GX, Ganxi; HT, Hetaodaer; JH, Jinhua; JQH, Jiangquhai; KL, Kele; LIC, Lichahei; LWU, Laiwu; LUC, Luchuan; MG, Mingguangxiaoer; MIN, Min; MS, Meishan; NJ, Neijiang; RC, Rongchang; SCT, Tibetan (Sichuan); SUT, Sutai; SZL, Shaziling; TC, Tongcheng; TT1, Tibetan (Gongbujiangda); TT2, Tibetan (Milin); WB, Chinese wild boars; WZS, Wuzhishan; YNT, Tibetan (Yunnan).
Mentions: The Tibetan pig, one of Tibetans’ domestic animals, is originally distributed in farming and farming-pastoral regions at altitudes of 2,900 - 4,300 m in the Qinghai-Tibetan Plateau [16]. Like Tibetans and other colonists in the Plateau, Tibetan pigs have several key adaptive features for coping with the harsh environment at high altitude [16]. First, they have black skin and hair with long and dense bristle that protect them from high solar radiation and cold ambient temperature in winter (Figure 1). Second, their well-developed heart and lung may be required for the increased rate of blood flow and oxygen transportation to tissues in response to hypoxia. Third, they have developed a blunted erythropoietic response to high-altitude hypoxia by exhibiting lower than expected hemoglobin concentrations relative to their lowland counterparts and acclimatized lowland pigs [17]. This feature, in contrast to Tibetan yak, goat and sheep that show elevated hemoglobin levels at high altitude, is a crucial protection mechanism for excessive erythrocytosis (a classic feature of chronic mountain sickness [18]) in Tibetans [1–3]. Forth, their alertness and agility enable them to survive in the grazing condition.Figure 1

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