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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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Xu D, Dondup D, Dou T, Wang C, Zhang R, Fan C, Guo A, Lhundrup N, Ga Z, Liu M, Wu B, Gao J, Zhang J, Guo G. HvGST plays a key role in anthocyanin accumulation in colored barley. Plant J 2023; 113:47-59. [PMID: 36377282 DOI: 10.1111/tpj.16033] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Blue aleurone of barley is caused by the accumulation of delphinidin-based derivatives. Although these compounds are ideal nutrients for human health, they are undesirable contaminants in malt brewing. Therefore, the ability to add and remove this trait easily would facilitate breeding barley for different purposes. Here we identified a glutathione S-transferase gene (HvGST) that was responsible for the blue aleurone trait in Tibetan qingke barley by performing a genome-wide association study and RNA-sequencing analysis. Gene variation and expression analysis indicated that HvGST also participates in the transport and accumulation of anthocyanin in purple barley. Haplotype and the geographic distribution analyses of HvGST alleles revealed two independent natural variants responsible for the emergence of white aleurone: a 203-bp deletion causing premature termination of translation in qingke barley and two key single nucleotide polymorphisms in the promoter resulting in low transcription in Western barley. This study contributes to a better understanding of mechanisms of colored barley formation, and provides a comprehensive reference for marker-assisted barley breeding.
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Affiliation(s)
- 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, 100081, China
| | - Dawa Dondup
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Tingyu Dou
- 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, 100081, 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, 100081, China
| | - Renxu 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, 100081, China
| | - Chaofeng Fan
- 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, 100081, China
| | - Aikui 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, 100081, China
| | - Namgyal Lhundrup
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Zhuo Ga
- Agricultural and Animal Husbandry College of Tibet University, Linzhi, 860000, Tibet, China
| | - Minxuan Liu
- 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, 100081, China
| | - Bin Wu
- 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, 100081, China
| | - Jia Gao
- 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, 100081, 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, 100081, 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, 100081, China
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