数字农科院2.0

Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus)

文献类型： 外文期刊

作者： Song, Shen;Yao, Na;Yang, Min;Liu, Xuexue;Dong, Kunzhe;Zhao, Qianjun;Pu, Yabin;He, Xiaohong;Guan, Weijun;Ma, Yuehui;Jiang, Lin;Song, Shen;Yang, Ning

作者机构：

关键词： Cashmere goat;Population genetics;High altitude;Hypoxia

期刊名称： BMC GENOMICS

ISSN： 1471-2164

年卷期： 2016 年 17 卷

页码：

收录情况： SCI

摘要： Background: The Tibetan cashmere goat (Capra hircus), one of the most ancient breeds in China, has historically been a critical source of meat and cashmere production for local farmers. To adapt to the high-altitude area, extremely harsh climate, and hypoxic environment that the Tibetan cashmere goat lives in, this goat has developed distinct phenotypic traits compared to lowland breeds. However, the genetic components underlying this phenotypic adaptation remain largely unknown. Results: We obtained 118,700 autosomal SNPs through exome sequencing of 330 cashmere goats located at a wide geographic range, including the Tibetan Plateau and low-altitude regions in China. The great majority of SNPs showed low genetic differentiation among populations; however, approximately 2-3 % of the loci showed more genetic differentiation than expected under a selectively neutral model. Together with a combined analysis of high-and low-altitude breeds, we revealed 339 genes potentially under high-altitude selection. Genes associated with cardiovascular system development were significantly enriched in our study. Among these genes, the most evident one was endothelial PAS domain protein 1 (EPAS1), which has been previously reported to be involved in complex oxygen sensing and significantly associated with high-altitude adaptation of human, dog, and grey wolf. The missense mutation Q579L that we identified in EPAS1, which occurs next to the Hypoxia-Inducible Factor-1 (HIF-1) domain, was exclusively enriched in the high-altitude populations. Conclusions: Our study provides insights concerning the population variation in six different cashmere goat populations in China. The variants in cardiovascular system-related genes may explain the observed phenotypic adaptation of the Tibetan cashmere goat.

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[1]Additional file 9: Table S6. of Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Xiaohong He,Jiang, Lin,Yuehui Ma,Qianjun Zhao,Weijun Guan,Yang, Ning,Kunzhe Dong,Yao, Na,Song, Shen,Yang, Min,Yabin Pu,Xuexue Liu

[2]Additional file 2: Figure S1. of Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Yang, Ning,Yang, Min,Jiang, Lin,Xiaohong He,Weijun Guan,Yao, Na,Yuehui Ma,Song, Shen,Qianjun Zhao,Kunzhe Dong,Xuexue Liu,Yabin Pu

[3]Additional file 1: Table S1. of Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Song, Shen,Yabin Pu,Qianjun Zhao,Xuexue Liu,Kunzhe Dong,Jiang, Lin,Xiaohong He,Yuehui Ma,Weijun Guan,Yang, Ning,Yao, Na,Yang, Min

[4]Additional file 8: Figure S3. of Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Jiang, Lin,Song, Shen,Kunzhe Dong,Yabin Pu,Qianjun Zhao,Yang, Min,Xiaohong He,Yuehui Ma,Weijun Guan,Xuexue Liu,Yang, Ning,Yao, Na

[5]Additional file 7: Table S5. of Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Xiaohong He,Yabin Pu,Xuexue Liu,Jiang, Lin,Qianjun Zhao,Yang, Ning,Kunzhe Dong,Song, Shen,Weijun Guan,Yao, Na,Yuehui Ma,Yang, Min

[6]Additional file 6: Figure S2. of Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Jiang, Lin,Qianjun Zhao,Yabin Pu,Yao, Na,Yuehui Ma,Yang, Ning,Kunzhe Dong,Xuexue Liu,Song, Shen,Xiaohong He,Yang, Min,Weijun Guan

[7]Additional file 5: Table S4. of Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Xiaohong He,Yang, Min,Weijun Guan,Yuehui Ma,Xuexue Liu,Yang, Ning,Song, Shen,Jiang, Lin,Yao, Na,Yabin Pu,Kunzhe Dong,Qianjun Zhao

[8]Additional file 3: Table S2. of Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Kunzhe Dong,Xiaohong He,Yao, Na,Yuehui Ma,Weijun Guan,Song, Shen,Yabin Pu,Xuexue Liu,Yang, Min,Yang, Ning,Qianjun Zhao,Jiang, Lin

[9]Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Song, Shen,Yabin Pu,Weijun Guan,Yang, Ning,Kunzhe Dong,Qianjun Zhao,Yang, Min,Jiang, Lin,Yuehui Ma,Xuexue Liu,Yao, Na,Xiaohong He

[10]Additional file 4: Table S3. of Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). Xuexue Liu,Xiaohong He,Jiang, Lin,Song, Shen,Weijun Guan,Yabin Pu,Kunzhe Dong,Yang, Min,Yuehui Ma,Qianjun Zhao,Yao, Na,Yang, Ning

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