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Dondup D, Yang Y, Xu D, Namgyal L, Wang Z, Shen X, Dorji T, kyi N, Drolma L, Gao L, Ga Z, Sang Z, Ga Z, Mu W, Zhuoma P, Taba X, Jiao G, Liao W, Tang Y, Zeng X, Luobu Z, Wu Y, Wang C, Zhang J, Qi Z, Guo W, Guo G. Genome diversity and highland-adaptative variation in Tibet barley landrace population of China. Front Plant Sci 2023; 14:1189642. [PMID: 37235004 PMCID: PMC10206316 DOI: 10.3389/fpls.2023.1189642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Barley landraces accumulated variation in adapting to extreme highland environments during long-term domestication in Tibet, but little is known about their population structure and genomic selection traces. In this study, tGBS (tunable genotyping by sequencing) sequencing, molecular marker and phenotypic analyses were conducted on 1,308 highland and 58 inland barley landraces in China. The accessions were divided into six sub-populations and clearly distinguished most six-rowed, naked barley accessions (Qingke in Tibet) from inland barley. Genome-wide differentiation was observed in all five sub-populations of Qingke and inland barley accessions. High genetic differentiation in the pericentric regions of chromosomes 2H and 3H contributed to formation of five types of Qingke. Ten haplotypes of the pericentric regions of 2H, 3H, 6H and 7H were further identified as associated with ecological diversification of these sub-populations. There was genetic exchange between eastern and western Qingke but they shared the same progenitor. The identification of 20 inland barley types indicated multiple origins of Qingke in Tibet. The distribution of the five types of Qingke corresponded to specific environments. Two predominant highland-adaptative variations were identified for low temperature tolerance and grain color. Our results provide new insights into the origin, genome differentiation, population structure and highland adaptation in highland barley which will benefit both germplasm enhancement and breeding of naked barley.
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Affiliation(s)
- Dawa Dondup
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
- College of Plant Science, Tibet Agricultural and Husbandry University, Linzhi, China
| | - Yang Yang
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Dongdong Xu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lhundrup Namgyal
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Xia Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tsechoe Dorji
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Tibetan Plateau Earth Science, Chinese Academy of Sciences, Beijing, China
| | - Nyima kyi
- Tibet Climate Center, Tibet Meteorological Bureau, Lhasa, China
| | - Lhakpa Drolma
- Tibet Institute of Plateau Atmospheric and Environmental Sciences, Tibet Meteorological Bureau, Lhasa, China
- Key Laboratory of Atmospheric Environment of Tibet Autonomous Region, Tibet Meteorological Bureau, Lhasa, China
| | - Liyun Gao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zhuo Ga
- College of Plant Science, Tibet Agricultural and Husbandry University, Linzhi, China
| | - Zha Sang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zhuo Ga
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Wang Mu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Pubu Zhuoma
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Xiongnu Taba
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Guocheng Jiao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Wenhua Liao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Yawei Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zhaxi Luobu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chunchao Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Jing Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Ganggang Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
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Wu D, Liu Y, Chen W, Shao J, Zhuoma P, Zhao D, Yu Y, Liu T, Yu R, Gan Y, Yuzheng B, Huang Y, Zhang H, Bi X, Tao C, Lai S, Luo Q, Zhang D, Wang H, Zhaxi P, Zhang J, Qiao J, Zeng C. How placenta promotes the successful reproduction in high-altitude populations: a transcriptome comparison between adaptation and acclimatization. Mol Biol Evol 2022; 39:6596365. [PMID: 35642306 PMCID: PMC9206416 DOI: 10.1093/molbev/msac120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
As the best adapted high altitude population, Tibetans feature a relatively high offspring survival rate. Genome-wide studies have identified hundreds of candidate SNPs related to high altitude adaptation of Tibetans, although most of them have unknown functional relevance. To explore the mechanisms behind successful reproduction at high altitudes, we compared the placental transcriptomes of Tibetans, sea level Hans (SLHan), and Han immigrants (ImHan). Among the three populations, placentas from ImHan showed a hyperactive gene expression pattern. Their increased activation demonstrates a hypoxic stress response similar to sea level individuals experiencing hypoxic conditions. Unlike ImHan, Tibetan placentas were characterized by the significant up-regulation of placenta-specific genes, and the activation of autophagy and the tricarboxylic acid (TCA) cycle. Certain conserved hypoxia response functions, including the antioxidant system and angiogenesis, were activated in both ImHan and Tibetans, but mediated by different genes. The coherence of specific transcriptome features linked to possible genetic contribution was observed in Tibetans. Furthermore, we identified a novel Tibetan-specific EPAS1 isoform with a partial deletion at exon six, which may be involved in the adaption to hypoxia through the EPAS1-centred gene network in the placenta. Overall, our results show that the placenta grants successful pregnancies in Tibetans by strengthening the natural functions of the placenta itself. On the other hand, the placenta of ImHan was in an inhabiting time-dependent acclimatization process representing a common hypoxic stress response pattern.
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Affiliation(s)
- Deng Wu
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Yunao Liu
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Wei Chen
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China.,Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, China
| | - Jianming Shao
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Pubu Zhuoma
- Department of Obstetrics and Gynecology, The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Dexiong Zhao
- Department of Obstetrics and Gynecology, Qinghai Red Cross Hospital, Xining, Qinghai China
| | - Yang Yu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Tianzi Liu
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Ruoxuan Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yongna Gan
- Department of Obstetrics and Gynecology, Qinghai Red Cross Hospital, Xining, Qinghai China
| | - Baima Yuzheng
- Department of Obstetrics and Gynecology, The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Yongshu Huang
- Department of Obstetrics and Gynecology, The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Haikun Zhang
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoman Bi
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Chengcheng Tao
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Shujuan Lai
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Qiaoxia Luo
- The Third People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Dake Zhang
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China.,Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, China
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Pingcuo Zhaxi
- The Third People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Jianqing Zhang
- Department of Obstetrics and Gynecology, The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Changqing Zeng
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
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