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.

Show MeSH

Related in: MedlinePlus

Genomic signatures of selection in each and all Tibetan pig populations. (A) Genome-wide distribution of LSBL values. From top to bottom panels, LSBL outliers are shown for each Tibetan pig population from Gansu, Tibet and Sichuan & Yunnan (SCYN) provinces as well as all Tibetan pigs. The chromosomes are plotted along the x-axis, and LSBL values are plotted along the y-axis. Chromosomes are indicated by different colors, and the threshold indicating signature of selection is denoted with a dashed grey line. The strongest candidate genes corresponding to the top SNP outliers are indicated by red arrows in each panel, and the gene names are labeled above the arrows. Two flanking genes (HFM1 and ZNF644) are shown for one intergenic SNP. (B) A heat map of allele frequencies at the top SNP loci for each and overall of the tested populations. A spectrum of heat map colors indicates different allele frequencies at these loci.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Genomic signatures of selection in each and all Tibetan pig populations. (A) Genome-wide distribution of LSBL values. From top to bottom panels, LSBL outliers are shown for each Tibetan pig population from Gansu, Tibet and Sichuan & Yunnan (SCYN) provinces as well as all Tibetan pigs. The chromosomes are plotted along the x-axis, and LSBL values are plotted along the y-axis. Chromosomes are indicated by different colors, and the threshold indicating signature of selection is denoted with a dashed grey line. The strongest candidate genes corresponding to the top SNP outliers are indicated by red arrows in each panel, and the gene names are labeled above the arrows. Two flanking genes (HFM1 and ZNF644) are shown for one intergenic SNP. (B) A heat map of allele frequencies at the top SNP loci for each and overall of the tested populations. A spectrum of heat map colors indicates different allele frequencies at these loci.

Mentions: We identified a total of 207 SNP outliers (0.5% of empirical LSBL distribution), corresponding to 140, 129 and 124 candidate genes (50 kb up- and downstream of each SNP outliers) in Gansu, Tibet and SCYN populations, respectively (Additional file 6: Table S2). Few common signals were found between the three Tibetan populations (Figure 3, Additional file 7: Figure S5). C9ORF3, GRIN2B and GRID1, three functionally plausible genes (See Discussion), exhibited the most significant signals of selection in Gansu, Tibet and SCYN populations, respectively (Figure 4A). These SNPs showed a marked allele frequency difference between one Tibetan population and the other Tibetan and lowland populations (Figure 4B).Figure 3


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)

Genomic signatures of selection in each and all Tibetan pig populations. (A) Genome-wide distribution of LSBL values. From top to bottom panels, LSBL outliers are shown for each Tibetan pig population from Gansu, Tibet and Sichuan & Yunnan (SCYN) provinces as well as all Tibetan pigs. The chromosomes are plotted along the x-axis, and LSBL values are plotted along the y-axis. Chromosomes are indicated by different colors, and the threshold indicating signature of selection is denoted with a dashed grey line. The strongest candidate genes corresponding to the top SNP outliers are indicated by red arrows in each panel, and the gene names are labeled above the arrows. Two flanking genes (HFM1 and ZNF644) are shown for one intergenic SNP. (B) A heat map of allele frequencies at the top SNP loci for each and overall of the tested populations. A spectrum of heat map colors indicates different allele frequencies at these loci.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Genomic signatures of selection in each and all Tibetan pig populations. (A) Genome-wide distribution of LSBL values. From top to bottom panels, LSBL outliers are shown for each Tibetan pig population from Gansu, Tibet and Sichuan & Yunnan (SCYN) provinces as well as all Tibetan pigs. The chromosomes are plotted along the x-axis, and LSBL values are plotted along the y-axis. Chromosomes are indicated by different colors, and the threshold indicating signature of selection is denoted with a dashed grey line. The strongest candidate genes corresponding to the top SNP outliers are indicated by red arrows in each panel, and the gene names are labeled above the arrows. Two flanking genes (HFM1 and ZNF644) are shown for one intergenic SNP. (B) A heat map of allele frequencies at the top SNP loci for each and overall of the tested populations. A spectrum of heat map colors indicates different allele frequencies at these loci.
Mentions: We identified a total of 207 SNP outliers (0.5% of empirical LSBL distribution), corresponding to 140, 129 and 124 candidate genes (50 kb up- and downstream of each SNP outliers) in Gansu, Tibet and SCYN populations, respectively (Additional file 6: Table S2). Few common signals were found between the three Tibetan populations (Figure 3, Additional file 7: Figure S5). C9ORF3, GRIN2B and GRID1, three functionally plausible genes (See Discussion), exhibited the most significant signals of selection in Gansu, Tibet and SCYN populations, respectively (Figure 4A). These SNPs showed a marked allele frequency difference between one Tibetan population and the other Tibetan and lowland populations (Figure 4B).Figure 3

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