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Kumar C, Song S, Jiang L, He X, Zhao Q, Pu Y, Malhi KK, Kamboh AA, Ma Y. Sequence Characterization of DSG3 Gene to Know Its Role in High-Altitude Hypoxia Adaptation in the Chinese Cashmere Goat. Front Genet 2018; 9:553. [PMID: 30510564 PMCID: PMC6254015 DOI: 10.3389/fgene.2018.00553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/29/2018] [Indexed: 12/29/2022] Open
Abstract
The Tibetan cashmere goat is one of the main goat breeds used by people living in the plateau. It exhibits the distinct phenotypic characteristics observed in lowland goats, allowing them to adapt to the challenging conditions at high altitudes. It provides an ideal model for understanding the genetic mechanisms underlying high-altitude adaptation and hypoxia-related diseases. Our previous exome sequencing of five Chinese cashmere breeds revealed a candidate gene, DSG3 (Desmoglein 3), responsible for the high-altitude adaptation of the Tibetan goat. However, the whole DSG3 gene (44 kbp) consisting of 16 exons in the goat genome was not entirely covered by the exome sequencing. In this study, we resequenced all the 16 exons of the DSG3 gene in ten Chinese native goat populations. Twenty-seven SNP variants were found between the lowland and highland goat populations. The genetic distance (FST) of significant SNPs between the lowland and highland populations ranged from 0.42 to 0.58. By using correlation coefficient analysis, linkage disequilibrium, and haplotype network construction, we found three non-synonymous SNPs (R597E, T595I, and G572S) in exon 5 and two synonymous SNPs in exons 8 and 16 in DSG3. These mutations significantly segregated high- and low-altitude goats in two clusters, indicating the contribution of DSG3 to the high-altitude hypoxia adaptation in the Tibetan goat.
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Affiliation(s)
- Chandar Kumar
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tando Jam, Pakistan
| | - Shen Song
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Jiang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohong He
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qianjun Zhao
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yabin Pu
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kanwar Kumar Malhi
- Department of Veterinary Microbiology, Faculty of Animal Husbandry and Veterinary Science, Sindh Agriculture University, Tando Jam, Pakistan
| | - Asghar Ali Kamboh
- Department of Veterinary Microbiology, Faculty of Animal Husbandry and Veterinary Science, Sindh Agriculture University, Tando Jam, Pakistan
| | - Yuehui Ma
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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E G, Zhao Y, Chen L, Ma Y, Chu M, Li X, Hong Q, Li L, Guo J, Zhu L, Han Y, Gao H, Zhang J, Jiang H, Jiang C, Wang G, Ren H, Jin M, Sun Y, Zhou P, Huang Y. Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA. Ecol Evol 2018; 8:5111-5123. [PMID: 29876086 PMCID: PMC5980450 DOI: 10.1002/ece3.4100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/21/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D-loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high-frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low-frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.
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Affiliation(s)
- Guang‐Xin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Yong‐Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Li‐Peng Chen
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Yue‐Hui Ma
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Ming‐Xing Chu
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiang‐Long Li
- College of Animal Science and TechnologyHebei Normal University of Science & TechnologyQinghuangdaoChina
| | - Qiong‐Hua Hong
- Yunnan Animal Scinence and Veterinary InstituteKunmingChina
| | - Lan‐Hui Li
- College of Animal Science and TechnologyAgricultural University of HebeiBaoding, HebeiChina
| | - Ji‐Jun Guo
- Animal Husbandry Station of Qinghai ProvinceXining, QinghaiChina
| | - Lan Zhu
- Yunnan Animal Scinence and Veterinary InstituteKunmingChina
| | - Yan‐Guo Han
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Hui‐Jiang Gao
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Jia‐Hua Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Huai‐Zhi Jiang
- Animal Science and Technology CollegeJilin Agriculture UniversityChangchun, JilinChina
| | - Cao‐De Jiang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Gao‐Fu Wang
- Chongqing Academy of Animal SciencesChongqingChina
| | | | - Mei‐Lan Jin
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Yuan‐Zhi Sun
- Wuhan Tianyi Huiyuan Bioscience & Technology IncWuhanChina
| | - Peng Zhou
- Chongqing Academy of Animal SciencesChongqingChina
| | - Yong‐Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
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Du X, Cao J, Han X, Hao H, Yu M, Zhang G, Zhao S. Genetic diversity and population structure among eight Chinese indigenous goat breeds in the Yellow River valley. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.12.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Song S, Yao N, Yang M, Liu X, Dong K, Zhao Q, Pu Y, He X, Guan W, Yang N, Ma Y, Jiang L. Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). BMC Genomics 2016; 17:122. [PMID: 26892324 PMCID: PMC4758086 DOI: 10.1186/s12864-016-2449-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/09/2016] [Indexed: 12/27/2022] Open
Abstract
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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Affiliation(s)
- Shen Song
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China.
| | - Na Yao
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Min Yang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Xuexue Liu
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Kunzhe Dong
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Qianjun Zhao
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Yabin Pu
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Xiaohong He
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Weijun Guan
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Ning Yang
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China.
| | - Yuehui Ma
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Lin Jiang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
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