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Gao G, Yan L, Cai Y, Guo Y, Jiang C, He Q, Tasnim S, Feng Z, Liu J, Zhang J, Komatsuda T, Mascher M, Yang P. Most Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley. PLANT COMMUNICATIONS 2024; 5:100828. [PMID: 38297838 PMCID: PMC11121735 DOI: 10.1016/j.xplc.2024.100828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/02/2024]
Abstract
Tibetan weedy barleys reside at the edges of qingke (hulless barley) fields in Tibet (Xizang). The spikes of these weedy barleys contain or lack a brittle rachis, with either two- or six-rowed spikes and either hulled or hulless grains at maturity. Although the brittle rachis trait of Tibetan weedy barleys is similar to that of wild barley (Hordeum vulgare ssp. spontaneum Thell.), these plants share genetic similarity with domesticated barley. The origin of Tibetan weedy barleys continues to be debated. Here, we show that most Tibetan weedy barleys originated from cross-pollinated hybridization of domesticated barleys, followed by hybrid self-pollination and recombination between Non-brittle rachis 1 (btr1) and 2 (btr2). We discovered the specific genetic ancestry of these weedy barleys in South Asian accessions. Tibetan weedy barleys exhibit lower genetic diversity than wild and Chinese landraces/cultivars and share a close relationship with qingke, genetically differing from typical eastern and western barley populations. We classified Tibetan weedy barleys into two groups, brittle rachis (BR) and non-brittle rachis (NBR); these traits align with the haplotypes of the btr1 and btr2 genes. Whereas wild barleys carry haplotype combinations of Btr1 and Btr2, each showing lower proportions in a population, the recombinant haplotype BTR2H8+BTR1H24 is predominant in the BR group. Haplotype block analysis based on whole-genome sequencing revealed two recombination breakpoints, which are present in 80.6% and 16.8% of BR accessions according to marker-assisted analysis. Hybridization events between wild and domesticated barley were rarely detected. These findings support the notion that Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley.
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Affiliation(s)
- Guangqi Gao
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Luxi Yan
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Cai
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland, Germany
| | - Congcong Jiang
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiang He
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sarah Tasnim
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jun Liu
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Zhang
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Takao Komatsuda
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland, Germany
| | - Ping Yang
- State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Wang F, Zhou Z, Liu X, Zhu L, Guo B, Lv C, Zhu J, Chen ZH, Xu R. Transcriptome and metabolome analyses reveal molecular insights into waterlogging tolerance in Barley. BMC PLANT BIOLOGY 2024; 24:385. [PMID: 38724918 PMCID: PMC11080113 DOI: 10.1186/s12870-024-05091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Waterlogging stress is one of the major abiotic stresses affecting the productivity and quality of many crops worldwide. However, the mechanisms of waterlogging tolerance are still elusive in barley. In this study, we identify key differentially expressed genes (DEGs) and differential metabolites (DM) that mediate distinct waterlogging tolerance strategies in leaf and root of two barley varieties with contrasting waterlogging tolerance under different waterlogging treatments. Transcriptome profiling revealed that the response of roots was more distinct than that of leaves in both varieties, in which the number of downregulated genes in roots was 7.41-fold higher than that in leaves of waterlogging sensitive variety after 72 h of waterlogging stress. We also found the number of waterlogging stress-induced upregulated DEGs in the waterlogging tolerant variety was higher than that of the waterlogging sensitive variety in both leaves and roots in 1 h and 72 h treatment. This suggested the waterlogging tolerant variety may respond more quickly to waterlogging stress. Meanwhile, phenylpropanoid biosynthesis pathway was identified to play critical roles in waterlogging tolerant variety by improving cell wall biogenesis and peroxidase activity through DEGs such as Peroxidase (PERs) and Cinnamoyl-CoA reductases (CCRs) to improve resistance to waterlogging. Based on metabolomic and transcriptomic analysis, we found the waterlogging tolerant variety can better alleviate the energy deficiency via higher sugar content, reduced lactate accumulation, and improved ethanol fermentation activity compared to the waterlogging sensitive variety. In summary, our results provide waterlogging tolerance strategies in barley to guide the development of elite genetic resources towards waterlogging-tolerant crop varieties.
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Affiliation(s)
- Feifei Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou University, Yangzhou, 225009, China
| | - Zhenxiang Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou University, Yangzhou, 225009, China
| | - Xiaohui Liu
- College of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, 550003, China
| | - Liang Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou University, Yangzhou, 225009, China
| | - Baojian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou University, Yangzhou, 225009, China
| | - Chao Lv
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou University, Yangzhou, 225009, China
| | - Juan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou University, Yangzhou, 225009, China
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou University, Yangzhou, 225009, China.
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Qiu CW, Ma Y, Gao ZF, Sreesaeng J, Zhang S, Liu W, Ahmed IM, Cai S, Wang Y, Zhang G, Wu F. Genome-wide profiling of genetic variations reveals the molecular basis of aluminum stress adaptation in Tibetan wild barley. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132541. [PMID: 37716271 DOI: 10.1016/j.jhazmat.2023.132541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Aluminum (Al) toxicity in acidic soil is a major factor affecting crop productivity. The extensive genetic diversity found in Tibetan wild barley germplasms offers a valuable reservoir of alleles associated with aluminum tolerance. Here, resequencing of two Al-tolerant barley genotypes (Tibetan wild barley accession XZ16 and cultivated barley Dayton) identified a total of 19,826,182 and 16,287,277 single nucleotide polymorphisms (SNPs), 1628,052 and 1386,973 insertions/deletions (InDels), 61,532 and 57,937 structural variations (SVs), 248,768 and 240,723 copy number variations (CNVs) in XZ16 and Dayton, respectively, and uncovered approximately 600 genes highly related to Al tolerance in barley. Comparative genomic analyses unveiled 71 key genes that contain unique genetic variants in XZ16 and are predominantly associated with organic acid exudation, Al sequestration, auxin response, and transcriptional regulation. Manipulation of these key genes at the genetic and transcriptional level is a promising strategy for developing optimal haplotype combinations and new barley cultivars with improved Al tolerance. This study represents the first comprehensive examination of genetic variation in Al-tolerant Tibetan wild barley through genome-wide profiling. The obtained results make the deep insight into the mechanisms underlying barley adaptation to Al toxicity, and identified the candidate genes useful for improvement of Al tolerance in barley.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Zi-Feng Gao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jakkrit Sreesaeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shuo Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Imrul Mosaddek Ahmed
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Plant Biotechnology Laboratory, Center for Viticulture & Small Fruit Research, Florida A&M University, FL 32317, USA
| | - Shengguan Cai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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Qiu CW, Ma Y, Wang QQ, Fu MM, Li C, Wang Y, Wu F. Barley HOMOCYSTEINE METHYLTRANSFERASE 2 confers drought tolerance by improving polyamine metabolism. PLANT PHYSIOLOGY 2023; 193:389-409. [PMID: 37300541 DOI: 10.1093/plphys/kiad333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
Drought stress poses a serious threat to crop production worldwide. Genes encoding homocysteine methyltransferase (HMT) have been identified in some plant species in response to abiotic stress, but its molecular mechanism in plant drought tolerance remains unclear. Here, transcriptional profiling, evolutionary bioinformatics, and population genetics were conducted to obtain insight into the involvement of HvHMT2 from Tibetan wild barley (Hordeum vulgare ssp. agriocrithon) in drought tolerance. We then performed genetic transformation coupled with physio-biochemical dissection and comparative multiomics approaches to determine the function of this protein and the underlying mechanism of HvHMT2-mediated drought tolerance. HvHMT2 expression was strongly induced by drought stress in tolerant genotypes in a natural Tibetan wild barley population and contributed to drought tolerance through S-adenosylmethionine (SAM) metabolism. Overexpression of HvHMT2 promoted HMT synthesis and efficiency of the SAM cycle, leading to enhanced drought tolerance in barley through increased endogenous spermine and less oxidative damage and growth inhibition, thus improving water status and final yield. Disruption of HvHMT2 expression led to hypersensitivity under drought treatment. Application of exogenous spermine reduced accumulation of reactive oxygen species (ROS), which was increased by exogenous mitoguazone (inhibitor of spermine biosynthesis), consistent with the association of HvHMT2-mediated spermine metabolism and ROS scavenging in drought adaptation. Our findings reveal the positive role and key molecular mechanism of HvHMT2 in drought tolerance in plants, providing a valuable gene not only for breeding drought-tolerant barley cultivars but also for facilitating breeding schemes in other crops in a changing global climate.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, P.R. China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
| | - Qing-Qing Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, P.R. China
| | - Man-Man Fu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
| | - Chengdao Li
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
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Li R, Zhang R, Yang Y, Li Y. Accumulation characteristics, driving factors, and model prediction of cadmium in soil-highland barley system on the Tibetan Plateau. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131407. [PMID: 37080024 DOI: 10.1016/j.jhazmat.2023.131407] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Cadmium (Cd) poses major human health problems due to its high toxicity and organ bioaccumulation potential. This study collected and analysed 130 pairs of representative soil-highland barley samples on the Tibetan Plateau. The total soil Cd content (Cd-soil), available soil Cd (Cd-ava), and highland barley Cd contents (Cd-barley) ranged from 0.03 to 0.46 mg kg-1, 0.006-0.185 mg kg-1, and 0.57-13.62 μg kg-1, with mean values of 0.19 ± 0.01 mg kg-1, 0.045 ± 0.003 mg kg-1, and 4.57 ± 0.17 μg kg-1, respectively. Redundancy analysis (RDA) demonstrated that geographic factors and soil properties explained 28.46% of the variation in Cd-soil and Cd-ava, and precipitation (14.6%) and pH (9.1%) were the dominant factors. The structural equation model (SEM) indicated that Cd-soil and Cd-ava were predominantly controlled by pH. Furthermore, the Cd-soil, Cd-ava, and Cd-barley with significantly different environmental conditions were more accurately predicted by conditional inference trees-multiple linear regression (CITs-MLR). When Cd-soil is more than 0.376 mg kg-1, Cd-ava obtains the most accurate predictor (R2 =0.64, P < 0.01). This study provides new scientific insight into understanding the environmental biogeochemical nexus of Cd in the complex and fragile plateau environment and evaluating food security on the Tibetan Plateau under the self-sufficiency model of highland barley.
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Affiliation(s)
- Ruxia Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ru Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Yang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghua Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
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Qiu CW, Ma Y, Liu W, Zhang S, Wang Y, Cai S, Zhang G, Chater CCC, Chen ZH, Wu F. Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley. J Adv Res 2023; 49:31-45. [PMID: 36170948 PMCID: PMC10334146 DOI: 10.1016/j.jare.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance. OBJECTIVES To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley. METHODS Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes. RESULTS Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley. CONCLUSION Our findings reveal functional genes that have been selected across barley's complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuo Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK; School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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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. FRONTIERS IN PLANT SCIENCE 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] [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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8
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Leite Dias S, Garibay-Hernández A, Brendel FL, Gabriel Chavez B, Brückner E, Mock HP, Franke J, D’Auria JC. A New Fluorescence Detection Method for Tryptophan- and Tyrosine-Derived Allelopathic Compounds in Barley and Lupin. PLANTS (BASEL, SWITZERLAND) 2023; 12:1930. [PMID: 37653847 PMCID: PMC10222917 DOI: 10.3390/plants12101930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 09/02/2023]
Abstract
Barley (Hordeum vulgare) is one of the most widely cultivated crops for feedstock and beer production, whereas lupins (Lupinus spp.) are grown as fodder and their seeds are a source of protein. Both species produce the allelopathic alkaloids gramine and hordenine. These plant-specialized metabolites may be of economic interest for crop protection, depending on their tissue distribution. However, in high concentrations they pose a health risk to humans and animals that feed on them. This study was carried out to develop and validate a new method for monitoring these alkaloids and their related metabolites using fluorescence detection. Separation was performed on an HSS T3 column using slightly acidified water-acetonitrile eluents. Calibration plots expressed linearity over the range 0.09-100 pmol/µL for gramine. The accuracy and precision ranged from 97.8 to 123.4%, <7% RSD. The method was successfully applied in a study of the natural range of abundance of gramine, hordenine and their related metabolites, AMI, tryptophan and tyramine, in 22 barley accessions and 10 lupin species. This method provides accurate and highly sensitive chromatographic separation and detection of tryptophan- and tyrosine-derived allelochemicals and is an accessible alternative to LC-MS techniques for routine screening.
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Affiliation(s)
- Sara Leite Dias
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Adriana Garibay-Hernández
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Fabian Leon Brendel
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Benjamin Gabriel Chavez
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Elena Brückner
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Hans-Peter Mock
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Jakob Franke
- Institute of Botany, Leibniz University Hannover, 30419 Hannover, Germany
| | - John Charles D’Auria
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
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9
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Zhang W, Tan C, Hu H, Pan R, Xiao Y, Ouyang K, Zhou G, Jia Y, Zhang X, Hill CB, Wang P, Chapman B, Han Y, Xu L, Xu Y, Angessa T, Luo H, Westcott S, Sharma D, Nevo E, Barrero RA, Bellgard MI, He T, Tian X, Li C. Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:46-62. [PMID: 36054248 PMCID: PMC9829399 DOI: 10.1111/pbi.13917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.
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Affiliation(s)
- Wenying Zhang
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Cong Tan
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Haifei Hu
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rui Pan
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Yuhui Xiao
- Grandomics Biotechnology Co., LtdWuhanChina
| | - Kai Ouyang
- Grandomics Biotechnology Co., LtdWuhanChina
| | - Gaofeng Zhou
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Yong Jia
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Xiao‐Qi Zhang
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Camilla Beate Hill
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Penghao Wang
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Brett Chapman
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Yong Han
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Le Xu
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Yanhao Xu
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Tefera Angessa
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Hao Luo
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Sharon Westcott
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Darshan Sharma
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaHaifaIsrael
| | - Roberto A. Barrero
- eResearch OfficeQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Matthew I. Bellgard
- eResearch OfficeQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Tianhua He
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
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10
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Exome-wide variation in a diverse barley panel reveals genetic associations with ten agronomic traits in Eastern landraces. J Genet Genomics 2022; 50:241-252. [PMID: 36566016 DOI: 10.1016/j.jgg.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Barley (Hordeum vulgare ssp. vulgare) was one of the first crops to be domesticated and is adapted to a wide range of environments. Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity. Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits, polymorphisms from East Asian varieties remain scarce. In this study, we analyzed exome polymorphisms in a panel of 274 barley varieties collected worldwide, including 137 varieties from East Asian countries and Ethiopia. We revealed the underlying population structure and conducted genome-wide association studies for ten agronomic traits. Moreover, we examined genome-wide associations for traits related to grain size such as awn length and glume length. Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties, highlighting their distinct genomic signatures relative to Western subpopulations.
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11
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Wu XT, Xiong ZP, Chen KX, Zhao GR, Feng KR, Li XH, Li XR, Tian Z, Huo FL, Wang MX, Song W. Genome-Wide Identification and Transcriptional Expression Profiles of PP2C in the Barley (Hordeum vulgare L.) Pan-Genome. Genes (Basel) 2022; 13:genes13050834. [PMID: 35627219 PMCID: PMC9140614 DOI: 10.3390/genes13050834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
The gene family protein phosphatase 2C (PP2C) is related to developmental processes and stress responses in plants. Barley (Hordeum vulgare L.) is a popular cereal crop that is primarily utilized for human consumption and nutrition. However, there is little knowledge regarding the PP2C gene family in barley. In this study, a total of 1635 PP2C genes were identified in 20 barley pan-genome accessions. Then, chromosome localization, physical and chemical feature predictions and subcellular localization were systematically analyzed. One wild barley accession (B1K-04-12) and one cultivated barley (Morex) were chosen as representatives to further analyze and compare the differences in HvPP2Cs between wild and cultivated barley. Phylogenetic analysis showed that these HvPP2Cs were divided into 12 subgroups. Additionally, gene structure, conserved domain and motif, gene duplication event detection, interaction networks and gene expression profiles were analyzed in accessions Morex and B1K-04-12. In addition, qRT-PCR experiments in Morex indicated that seven HvMorexPP2C genes were involved in the response to aluminum and low pH stresses. Finally, a series of positively selected homologous genes were identified between wild accession B1K-04-12 and another 14 cultivated materials, indicating that these genes are important during barley domestication. This work provides a global overview of the putative physiological and biological functions of PP2C genes in barley. We provide a broad framework for understanding the domestication- and evolutionary-induced changes in PP2C genes between wild and cultivated barley.
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Affiliation(s)
- Xiao-Tong Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Zhu-Pei Xiong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Kun-Xiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Guo-Rong Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Ke-Ru Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Xiu-Hua Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Xi-Ran Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Zhao Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Fu-Lin Huo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Meng-Xing Wang
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
- Correspondence: (M.-X.W.); (W.S.)
| | - Weining Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
- Correspondence: (M.-X.W.); (W.S.)
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12
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Gnutikov AA, Nosov NN, Loskutov IG, Blinova EV, Shneyer VS, Probatova NS, Rodionov AV. New Insights into the Genomic Structure of Avena L.: Comparison of the Divergence of A-Genome and One C-Genome Oat Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:1103. [PMID: 35567104 PMCID: PMC9102028 DOI: 10.3390/plants11091103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
We used next-generation sequencing analysis of the 3′-part of 18S rDNA, ITS1, and a 5′-part of the 5.8S rDNA region to understand genetic variation among seven diploid A-genome Avena species. We used 4−49 accessions per species that represented the As genome (A. atlantica, A. hirtula, and wiestii), Ac genome (A. canariensis), Ad genome (A. damascena), Al genome (A. longiglumis), and Ap genome (A. prostrata). We also took into our analysis one C-genome species, A. clauda, which previously was found to be related to A-genome species. The sequences of 169 accessions revealed 156 haplotypes of which seven haplotypes were shared by two to five species. We found 16 ribotypes that consisted of a unique sequence with a characteristic pattern of single nucleotide polymorphisms and deletions. The number of ribotypes per species varied from one in A. longiglumis to four in A. wiestii. Although most ribotypes were species-specific, we found two ribotypes shared by three species (one for A. damascena, A. hirtula, and A. wiestii, and the second for A. longiglumis, A. atlantica, and A. wiestii), and a third ribotype shared between A. atlantica and A. wiestii. A characteristic feature of the A. clauda ribotype, a diploid C-genome species, is that two different families of ribotypes have been found in this species. Some of these ribotypes are characteristic of Cc-genome species, whereas others are closely related to As-genome ribotypes. This means that A. clauda can be a hybrid between As- and C-genome oats.
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Affiliation(s)
- Alexander A. Gnutikov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Nikolai N. Nosov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Igor G. Loskutov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Elena V. Blinova
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Viktoria S. Shneyer
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Nina S. Probatova
- Laboratory of Botany, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
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13
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Transcriptome and Metabolite Insights into Domestication Process of Cultivated Barley in China. PLANTS 2022; 11:plants11020209. [PMID: 35050097 PMCID: PMC8779797 DOI: 10.3390/plants11020209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
The domestication process of cultivated barley in China remains under debate because of the controversial origins of barley. Here, we analyzed transcriptomic and non-targeted metabolic data from 29 accessions together with public resequencing data from 124 accessions to explore the domestication process of cultivated barley in China (Cb-C). These analyses revealed that both Cb-C and Tibetan wild barley (Wb-T) were the descendants of wild barley from the Near East Fertile Crescent (Wb-NE), yielding little support for a local origin of Wb-T. Wb-T was more likely an intermediate in the domestication process from Wb-NE to Cb-C. Wb-T contributed more genetically to Cb-C than Wb-NE, and was domesticated into Cb-C about 3300 years ago. These results together seem to support that Wb-T may be a feralized or hybrid form of cultivated barley from the Near East Fertile Crescent or central Asia. Additionally, the metabolite analysis revealed divergent metabolites of alkaloids and phenylpropanoids and these metabolites were specifically targeted for selection in the evolutionary stages from Wb-NE to Wb-T and from Wb-T to Cb-C. The key missense SNPs in the genes HORVU6Hr1G027650 and HORVU4Hr1G072150 might be responsible for the divergence of metabolites of alkaloids and phenylpropanoids during domestication. Our findings allow for a better understanding of the domestication process of cultivated barley in China.
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14
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Bai Y, Zhao X, Yao X, Yao Y, An L, Li X, Wang Y, Gao X, Jia Y, Guan L, Li M, Wu K, Wang Z. Genome wide association study of plant height and tiller number in hulless barley. PLoS One 2021; 16:e0260723. [PMID: 34855842 PMCID: PMC8639095 DOI: 10.1371/journal.pone.0260723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/15/2021] [Indexed: 11/18/2022] Open
Abstract
Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.
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Affiliation(s)
- Yixiong Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Xiaohong Zhao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
- Good Agricultural Practices Research Center of Traditional, Chongqing Institute of Medicinal Plant Cultivation, Chongqing, China
| | - Xiaohua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Youhua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Likun An
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Xin Li
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Yong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yatao Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Lulu Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Man Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Kunlun Wu
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
- * E-mail: (KW); (ZW)
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (KW); (ZW)
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15
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Sehar S, Adil MF, Zeeshan M, Holford P, Cao F, Wu F, Wang Y. Mechanistic Insights into Potassium-Conferred Drought Stress Tolerance in Cultivated and Tibetan Wild Barley: Differential Osmoregulation, Nutrient Retention, Secondary Metabolism and Antioxidative Defense Capacity. Int J Mol Sci 2021; 22:ijms222313100. [PMID: 34884904 PMCID: PMC8658718 DOI: 10.3390/ijms222313100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/23/2022] Open
Abstract
Keeping the significance of potassium (K) nutrition in focus, this study explores the genotypic responses of two wild Tibetan barley genotypes (drought tolerant XZ5 and drought sensitive XZ54) and one drought tolerant barley cv. Tadmor, under the exposure of polyethylene glycol-induced drought stress. The results revealed that drought and K deprivation attenuated overall plant growth in all the tested genotypes; however, XZ5 was least affected due to its ability to retain K in its tissues which could be attributed to the smallest reductions of photosynthetic parameters, relative chlorophyll contents and the lowest Na+/K+ ratios in all treatments. Our results also indicate that higher H+/K+-ATPase activity (enhancement of 1.6 and 1.3-fold for shoot; 1.4 and 2.5-fold for root), higher shoot K+ (2 and 2.3-fold) and Ca2+ content (1.5 and 1.7-fold), better maintenance of turgor pressure by osmolyte accumulation and enhanced antioxidative performance to scavenge ROS, ultimately suppress lipid peroxidation (in shoots: 4% and 35%; in roots 4% and 20% less) and bestow higher tolerance to XZ5 against drought stress in comparison with Tadmor and XZ54, respectively. Conclusively, this study adds further evidence to support the concept that Tibetan wild barley genotypes that utilize K efficiently could serve as a valuable genetic resource for the provision of genes for improved K metabolism in addition to those for combating drought stress, thereby enabling the development of elite barley lines better tolerant of abiotic stresses.
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Affiliation(s)
- Shafaque Sehar
- Department of Agronomy, Zijingang Campus, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (S.S.); (M.F.A.); (M.Z.); (F.C.); (F.W.)
| | - Muhammad Faheem Adil
- Department of Agronomy, Zijingang Campus, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (S.S.); (M.F.A.); (M.Z.); (F.C.); (F.W.)
| | - Muhammad Zeeshan
- Department of Agronomy, Zijingang Campus, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (S.S.); (M.F.A.); (M.Z.); (F.C.); (F.W.)
| | - Paul Holford
- Hawkesbury Campus, School of Science and Health, University of Western Sydney, Penrith, NSW 2751, Australia;
| | - Fangbin Cao
- Department of Agronomy, Zijingang Campus, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (S.S.); (M.F.A.); (M.Z.); (F.C.); (F.W.)
| | - Feibo Wu
- Department of Agronomy, Zijingang Campus, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (S.S.); (M.F.A.); (M.Z.); (F.C.); (F.W.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Provincial Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Wang
- Department of Agronomy, Zijingang Campus, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (S.S.); (M.F.A.); (M.Z.); (F.C.); (F.W.)
- Provincial Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Correspondence:
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Cai S, Shen Q, Huang Y, Han Z, Wu D, Chen ZH, Nevo E, Zhang G. Multi-Omics Analysis Reveals the Mechanism Underlying the Edaphic Adaptation in Wild Barley at Evolution Slope (Tabigha). ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101374. [PMID: 34390227 PMCID: PMC8529432 DOI: 10.1002/advs.202101374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/27/2021] [Indexed: 06/13/2023]
Abstract
At the microsite "Evolution Slope", Tabigha, Israel, wild barley (Hordeum spontaneum) populations adapted to dry Terra Rossa soil, and its derivative abutting wild barley population adapted to moist and fungi-rich Basalt soil. However, the mechanisms underlying the edaphic adaptation remain elusive. Accordingly, whole genome bisulfite sequencing, RNA-sequencing, and metabolome analysis are performed on ten wild barley accessions inhabiting Terra Rossa and Basalt soil. A total of 121 433 differentially methylated regions (DMRs) and 10 478 DMR-genes are identified between the two wild barley populations. DMR-genes in CG context (CG-DMR-genes) are enriched in the pathways related with the fundamental processes, and DMR-genes in CHH context (CHH-DMR-genes) are mainly associated with defense response. Transcriptome and metabolome analysis reveal that the primary and secondary metabolisms are more active in Terra Rossa and Basalt wild barley populations, respectively. Multi-omics analysis indicate that sugar metabolism facilitates the adaptation of wild barley to dry Terra Rossa soil, whereas the enhancement of phenylpropanoid/phenolamide biosynthesis is beneficial for wild barley to inhabit moist and fungi pathogen-rich Basalt soil. The current results make a deep insight into edaphic adaptation of wild barley and provide elite genetic and epigenetic resources for developing barley with high abiotic stress tolerance.
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Affiliation(s)
- Shengguan Cai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qiufang Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yuqing Huang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Zhigang Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Dezhi Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 34988384, Israel
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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17
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Alseekh S, Scossa F, Wen W, Luo J, Yan J, Beleggia R, Klee HJ, Huang S, Papa R, Fernie AR. Domestication of Crop Metabolomes: Desired and Unintended Consequences. TRENDS IN PLANT SCIENCE 2021; 26:650-661. [PMID: 33653662 DOI: 10.1016/j.tplants.2021.02.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 05/02/2023]
Abstract
The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy
| | - Weiwei Wen
- Key laboratory of Horticultural Plant Biology (MOE),College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Hubei, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China; College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-, CI), 71122 Foggia, Italy
| | - Harry J Klee
- Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture - Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
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Sharif BM, Burgarella C, Cormier F, Mournet P, Causse S, Van KN, Kaoh J, Rajaonah MT, Lakshan SR, Waki J, Bhattacharjee R, Badara G, Pachakkil B, Arnau G, Chaïr H. Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata). ANNALS OF BOTANY 2020; 126:1029-1038. [PMID: 32592585 PMCID: PMC7596366 DOI: 10.1093/aob/mcaa122] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/22/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample. METHODS We characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach. KEY RESULTS Diploid genotypes were more frequent than triploids and tetraploids worldwide. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. The genetic make-up of triploids and tetraploids suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced to the Caribbean region. CONCLUSIONS Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation.
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Affiliation(s)
- Bilal Muhammad Sharif
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- University of Vienna, Department of Evolutionary Anthropology, Vienna, Austria
| | - Concetta Burgarella
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- Uppsala University, Department of Organismal Biology, Uppsala, Sweden
| | - Fabien Cormier
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Petit Bourg, Guadeloupe, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Sandrine Causse
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Kien Nguyen Van
- Plant Resources Center (PRC), An Khanh, Hoai Duc, Hanoi, Vietnam
| | - Juliane Kaoh
- Vanuatu Agricultural Research and Technical Centre (VARTC), Espiritu Santo PB, Vanuatu
| | | | | | - Jeffrey Waki
- National Agricultural Research Institute (NARI), Lae, Morobe Province, Papua New Guinea
| | - Ranjana Bhattacharjee
- International Institute of Tropical Agriculture (IITA), PMB, Ibadan, Oyo State, Nigeria
| | - Gueye Badara
- International Institute of Tropical Agriculture (IITA), PMB, Ibadan, Oyo State, Nigeria
| | - Babil Pachakkil
- Tokyo University of Agriculture (TUA), Sakuragaoka, Setagaya-ku, Tokyo, Japan
| | - Gemma Arnau
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Petit Bourg, Guadeloupe, France
| | - Hana Chaïr
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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Feng X, Liu W, Cao F, Wang Y, Zhang G, Chen ZH, Wu F. Overexpression of HvAKT1 improves drought tolerance in barley by regulating root ion homeostasis and ROS and NO signaling. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6587-6600. [PMID: 32766860 DOI: 10.1093/jxb/eraa354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 05/24/2023]
Abstract
Potassium (K+) is the major cationic inorganic nutrient utilized for osmotic regulation, cell growth, and enzyme activation in plants. Inwardly rectifying K+ channel 1 (AKT1) is the primary channel for root K+ uptake in plants, but the function of HvAKT1 in barley plants under drought stress has not been fully elucidated. In this study, we conducted evolutionary bioinformatics, biotechnological, electrophysiological, and biochemical assays to explore molecular mechanisms of HvAKT1 in response to drought in barley. The expression of HvAKT1 was significantly up-regulated by drought stress in the roots of XZ5-a drought-tolerant wild barley genotype. We isolated and functionally characterized the plasma membrane-localized HvAKT1 using Agrobacterium-mediated plant transformation and Barley stripe mosaic virus-induced gene silencing of HvAKT1 in barley. Evolutionary bioinformatics indicated that the K+ selective filter in AKT1 originated from streptophyte algae and is evolutionarily conserved in land plants. Silencing of HvAKT1 resulted in significantly decreased biomass and suppressed K+ uptake in root epidermal cells under drought treatment. Disruption of HvAKT1 decreased root H+ efflux, H+-ATPase activity, and nitric oxide (NO) synthesis, but increased hydrogen peroxide (H2O2) production in the roots under drought stress. Furthermore, we observed that overexpression of HvAKT1 improves K+ uptake and increases drought resistance in barley. Our results highlight the importance of HvAKT1 for root K+ uptake and its pleiotropic effects on root H+-ATPase, and H2O2 and NO in response to drought stress, providing new insights into the genetic basis of drought tolerance and K+ nutrition in barley.
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Affiliation(s)
- Xue Feng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
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20
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Feng X, Liu W, Dai H, Qiu Y, Zhang G, Chen ZH, Wu F. HvHOX9, a novel homeobox leucine zipper transcription factor, positively regulates aluminum tolerance in Tibetan wild barley. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6057-6073. [PMID: 32588054 DOI: 10.1093/jxb/eraa290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/20/2020] [Indexed: 05/10/2023]
Abstract
Aluminum (Al) toxicity is the primary limiting factor of crop production on acid soils. Tibetan wild barley germplasm is a valuable source of potential genes for breeding barley with acid and Al tolerance. We performed microRNA and RNA sequencing using wild (XZ16, Al-tolerant; XZ61, Al-sensitive) and cultivated (Dayton, Al-tolerant) barley. A novel homeobox-leucine zipper transcription factor, HvHOX9, was identified as a target gene of miR166b and functionally characterized. HvHOX9 was up-regulated by Al stress in XZ16 (but unchanged in XZ61 and Dayton) and was significantly induced only in root tip. Phylogenetic analysis showed that HvHOX9 is most closely related to wheat TaHOX9 and orthologues of HvHOX9 are present in the closest algal relatives of Zygnematophyceae. Barley stripe mosaic virus-induced gene silencing of HvHOX9 in XZ16 led to significantly increased Al sensitivity but did not affect its sensitivity to other metals and low pH. Disruption of HvHOX9 did not change Al concentration in the root cell sap, but led to more Al accumulation in root cell wall after Al exposure. Silencing of HvHOX9 decreased H+ influx after Al exposure. Our findings suggest that miR166b/HvHOX9 play a critical role in Al tolerance by decreasing root cell wall Al binding and increasing apoplastic pH for Al detoxification in the root.
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Affiliation(s)
- Xue Feng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Huaxin Dai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Yue Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Zhong-Hua Chen
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
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21
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Li Z, Lhundrup N, Guo G, Dol K, Chen P, Gao L, Chemi W, Zhang J, Wang J, Nyema T, Dawa D, Li H. Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley ( Hordeum Vulgare L.) in the Qinghai-Tibet Plateau. Front Genet 2020; 11:638. [PMID: 32719715 PMCID: PMC7351530 DOI: 10.3389/fgene.2020.00638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022] Open
Abstract
Barley (Hordeum vulgare L.) is one of the most important cereal crops worldwide. In the Qinghai-Tibet Plateau, six-rowed hulless (or naked) barley, called “qingke” in Chinese or “nas” in Tibetan, is produced mainly in Tibet. The complexity of the environment in the Qinghai-Tibet Plateau has provided unique opportunities for research on the breeding and adaptability of qingke barley. However, the genetic architecture of many important agronomic traits for qingke barley remains elusive. Heading date (HD), plant height (PH), and spike length (SL) are three prominent agronomic traits in barley. Here, we used genome-wide association (GWAS) mapping and GWAS with eigenvector decomposition (EigenGWAS) to detect quantitative trait loci (QTL) and selective signatures for HD, PH, and SL in a collection of 308 qingke barley accessions. The accessions were genotyped using a newly-developed, proprietary genotyping-by-sequencing (tGBS) technology, that yielded 14,970 high quality single nucleotide polymorphisms (SNPs). We found that the number of SNPs was higher in the varieties than in the landraces, which suggested that Tibetan varieties and varieties in the Tibetan area may have originated from different landraces in different areas. We have identified 62 QTLs associated with three important traits, and the observed phenotypic variation is well-explained by the identified QTLs. We mapped 114 known genes that include, but are not limited to, vernalization, and photoperiod genes. We found that 83.87% of the identified QTLs are located in the non-coding regulatory regions of annotated barley genes. Forty-eight of the QTLs are first reported here, 28 QTLs have pleotropic effects, and three QTL are located in the regions of the well-characterized genes HvVRN1, HvVRN3, and PpD-H2. EigenGWAS analysis revealed that multiple heading-date-related loci bear signatures of selection. Our results confirm that the barley panel used in this study is highly diverse, and showed a great promise for identifying the genetic basis of adaptive traits. This study should increase our understanding of complex traits in qingke barley, and should facilitate genome-assisted breeding for qingke barley improvement.
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Affiliation(s)
- Zhiyong Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Namgyal Lhundrup
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kar Dol
- Tibet Agricultural and Animal Husbandry College, Nyingchi, China
| | - Panpan Chen
- Tibet Agricultural and Animal Husbandry College, Nyingchi, China
| | - Liyun Gao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Wangmo Chemi
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiankang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tashi Nyema
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Dondrup Dawa
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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22
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Qiu CW, Liu L, Feng X, Hao PF, He X, Cao F, Wu F. Genome-Wide Identification and Characterization of Drought Stress Responsive microRNAs in Tibetan Wild Barley. Int J Mol Sci 2020; 21:E2795. [PMID: 32316632 PMCID: PMC7216285 DOI: 10.3390/ijms21082795] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 11/16/2022] Open
Abstract
Drought stress is a major obstacle to agricultural production. Tibetan wild barley with rich genetic diversity is useful for drought-tolerant improvement of cereals. MicroRNAs (miRNAs) play critical roles in controlling gene expression in response to various environment perturbations in plants. However, the genome-wide expression profiles of miRNAs and their targets in response to drought stress are largely unknown in wild barley. In this study, a polyethylene glycol (PEG) induced drought stress hydroponic experiment was performed, and the expression profiles of miRNAs from the roots of two contrasting Tibetan wild barley genotypes XZ5 (drought-tolerant) and XZ54 (drought-sensitive), and one cultivated barley Tadmor (drought-tolerant) generated by high-throughput sequencing were compared. There were 69 conserved miRNAs and 1574 novel miRNAs in the dataset of three genotypes under control and drought conditions. Among them, seven conserved miRNAs and 36 novel miRNAs showed significantly genotype-specific expression patterns in response to drought stress. And 12 miRNAs were further regarded as drought tolerant associated miRNAs in XZ5, which mostly participate in gene expression, metabolism, signaling and transportation, suggesting that they and their target genes play important roles in plant drought tolerance. This is the first comparation study on the miRNA transcriptome in the roots of two Tibetan wild barley genotypes differing in drought tolerance and one drought tolerant cultivar in response to PEG treatment. Further results revealed the candidate drought tolerant miRNAs and target genes in the miRNA regulation mechanism in wild barley under drought stress. Our findings provide valuable understandings for the functional characterization of miRNAs in drought tolerance.
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Affiliation(s)
- Cheng-Wei Qiu
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Li Liu
- Department of Applied Engineering, Zhejiang Economic and Trade Polytechnic, Hangzhou 310018, China;
| | - Xue Feng
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Peng-Fei Hao
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Xiaoyan He
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Fangbin Cao
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Feibo Wu
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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Solis CA, Yong MT, Vinarao R, Jena K, Holford P, Shabala L, Zhou M, Shabala S, Chen ZH. Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:323. [PMID: 32265970 PMCID: PMC7098918 DOI: 10.3389/fpls.2020.00323] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/05/2020] [Indexed: 05/20/2023]
Abstract
Salinity stress affects global food producing areas by limiting both crop growth and yield. Attempts to develop salinity-tolerant rice varieties have had limited success due to the complexity of the salinity tolerance trait, high variation in the stress response and a lack of available donors for candidate genes for cultivated rice. As a result, finding suitable donors of genes and traits for salinity tolerance has become a major bottleneck in breeding for salinity tolerant crops. Twenty-two wild Oryza relatives have been recognized as important genetic resources for quantitatively inherited traits such as resistance and/or tolerance to abiotic and biotic stresses. In this review, we discuss the challenges and opportunities of such an approach by critically analyzing evolutionary, ecological, genetic, and physiological aspects of Oryza species. We argue that the strategy of rice breeding for better Na+ exclusion employed for the last few decades has reached a plateau and cannot deliver any further improvement in salinity tolerance in this species. This calls for a paradigm shift in rice breeding and more efforts toward targeting mechanisms of the tissue tolerance and a better utilization of the potential of wild rice where such traits are already present. We summarize the differences in salinity stress adaptation amongst cultivated and wild Oryza relatives and identify several key traits that should be targeted in future breeding programs. This includes: (1) efficient sequestration of Na+ in mesophyll cell vacuoles, with a strong emphasis on control of tonoplast leak channels; (2) more efficient control of xylem ion loading; (3) efficient cytosolic K+ retention in both root and leaf mesophyll cells; and (4) incorporating Na+ sequestration in trichrome. We conclude that while amongst all wild relatives, O. rufipogon is arguably a best source of germplasm at the moment, genes and traits from the wild relatives, O. coarctata, O. latifolia, and O. alta, should be targeted in future genetic programs to develop salt tolerant cultivated rice.
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Affiliation(s)
- Celymar A. Solis
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Miing T. Yong
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Ricky Vinarao
- International Rice Research Institute, Metro Manila, Philippines
| | - Kshirod Jena
- International Rice Research Institute, Metro Manila, Philippines
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Lana Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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Wang Y, Zhang R, Liang Z, Li S. Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets. Genes (Basel) 2020; 11:genes11030315. [PMID: 32188014 PMCID: PMC7140798 DOI: 10.3390/genes11030315] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 01/08/2023] Open
Abstract
Since its inception, RNA sequencing (RNA-seq) has become the most effective way to study gene expression. After more than a decade of development, numerous RNA-seq datasets have been created, and the full utilization of these datasets has emerged as a major issue. In this study, we built a comprehensive database named Grape-RNA, which is focused on the collection, evaluation, treatment, and data sharing of grape RNA-seq datasets. This database contains 1529 RNA-seq samples, 112 microRNA samples from the public platform, and 485 RNA-seq in-house datasets sequenced by our lab. We classified these data into 25 conditions and provide the sample information, cleaned raw data, expression level, assembled unigenes, useful tools, and other relevant information to the users. Thus, this study provides data and tools that should be beneficial for researchers by allowing them to easily use the RNA-seq. The provided information can greatly contribute to grape breeding and genomic and biological research. This study may improve the usage of RNA-seq.
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Affiliation(s)
- Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Innovative Academy of Seed Design, the Chinese Academy of Science, Beijing 100093, China; (Y.W.); (S.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Zhang
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China;
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Innovative Academy of Seed Design, the Chinese Academy of Science, Beijing 100093, China; (Y.W.); (S.L.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Correspondence: ; Tel./Fax: 86-010-62836064
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Innovative Academy of Seed Design, the Chinese Academy of Science, Beijing 100093, China; (Y.W.); (S.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Chen J, Le XC, Zhu L. Metabolomics and transcriptomics reveal defense mechanism of rice (Oryza sativa) grains under stress of 2,2',4,4'-tetrabromodiphenyl ether. ENVIRONMENT INTERNATIONAL 2019; 133:105154. [PMID: 31521816 DOI: 10.1016/j.envint.2019.105154] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
2,2',4,4'-Tetrabromodiphenyl ether (BDE-47), a predominant polybrominated diphenyl ether (PBDE), has received extensive attention for its potential environmental impact. An integrated study of metabolomics and transcriptomics was conducted on two rice (Oryza sativa) cultivars, Lianjing-7 (LJ-7) and Yongyou-9 (YY-9), which have been identified as tolerant and sensitive cultivars to BDE-47, respectively. The objective was to investigate the molecular mechanisms of their different ability to tolerate BDE-47. Both rice plants were cultivated to maturity in soils containing three concentrations of BDE-47 (10, 20, and 50 mg/kg). Metabolomic analyses of rice grains identified 65 metabolites in LJ-7 and 45 metabolites in YY-9, including amino acids, saccharides, organic acids, fatty acids, and secondary metabolites. In the tolerant cultivar LJ-7 exposed to 50 mg/kg BDE-47, concentrations of most of the metabolites increased significantly, with α-ketoglutaric acid increased by 20-fold and stigmastanol increased by 12-fold. In the sensitive cultivar YY-9, the concentrations of most metabolites increased after the plant was exposed to 1 and 10 mg/kg BDE-47 but decreased after the plant was exposed to 50 mg/kg BDE-47. Transcriptomic data demonstrated that regulation of gene expressions was affected most in LJ-7 exposed to 50 mg/kg BDE-47 (966 genes up-regulated and 620 genes down-regulated) and in YY-9 exposed to 10 mg/kg BDE-47 (85 genes up-regulated and 291 genes down-regulated), in good accordance with the observed metabolic alternation in the two cultivars. Analyses of metabolic pathways and KEGG enrichment revealed that many biological processes, including energy consumption and biosynthesis, were perturbed in the two rice cultivars by BDE-47. A majority of metabolites and genes involved in dominating pathways of energy consumption (e.g., tricarboxylic acid cycle) and the biosynthesis (e.g., metabolism of saccharides and amino acids) were enhanced in LJ-7 by BDE-47. In contrast, energy consumption was increased while biosynthetic processes were inhibited in YY-9 by BDE-47, which could lead to the sensitivity of YY-9 to BDE-47. The combined results suggest that the different defensive abilities of these two rice cultivars in response to BDE-47 could be attributed to their differences in energy-consumption strategy and biosynthesis of nutritional components in grains. This study provides a useful reference for rice cultivation in PBDE-polluted areas.
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Affiliation(s)
- Jie Chen
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - X Chris Le
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China.
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26
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Ma Y, Liu M, Stiller J, Liu C. A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. BMC Genomics 2019; 20:12. [PMID: 30616511 PMCID: PMC6323845 DOI: 10.1186/s12864-018-5357-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/09/2018] [Indexed: 11/12/2022] Open
Abstract
Background It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications. Results In this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones. Conclusions We demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication. Electronic supplementary material The online version of this article (10.1186/s12864-018-5357-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanling Ma
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Miao Liu
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.,Crop Research Institute of Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jiri Stiller
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
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Zeng X, Guo Y, Xu Q, Mascher M, Guo G, Li S, Mao L, Liu Q, Xia Z, Zhou J, Yuan H, Tai S, Wang Y, Wei Z, Song L, Zha S, Li S, Tang Y, Bai L, Zhuang Z, He W, Zhao S, Fang X, Gao Q, Yin Y, Wang J, Yang H, Zhang J, Henry RJ, Stein N, Tashi N. Origin and evolution of qingke barley in Tibet. Nat Commun 2018; 9:5433. [PMID: 30575759 PMCID: PMC6303313 DOI: 10.1038/s41467-018-07920-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 12/05/2018] [Indexed: 11/09/2022] Open
Abstract
Tibetan barley (Hordeum vulgare L., qingke) is the principal cereal cultivated on the Tibetan Plateau for at least 3,500 years, but its origin and domestication remain unclear. Here, based on deep-coverage whole-genome and published exome-capture resequencing data for a total of 437 accessions, we show that contemporary qingke is derived from eastern domesticated barley and it is introduced to southern Tibet most likely via north Pakistan, India, and Nepal between 4,500 and 3,500 years ago. The low genetic diversity of qingke suggests Tibet can be excluded as a center of origin or domestication for barley. The rapid decrease in genetic diversity from eastern domesticated barley to qingke can be explained by a founder effect from 4,500 to 2,000 years ago. The haplotypes of the five key domestication genes of barley support a feral or hybridization origin for Tibetan weedy barley and reject the hypothesis of native Tibetan wild barley.
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Affiliation(s)
- Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Yu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Qijun Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Ganggang Guo
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, 999077, China
| | - Likai Mao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Qingfeng Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhanfeng Xia
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Juhong Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | | | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Zexiu Wei
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Li Song
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sang Zha
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Shiming Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yawei Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Lijun Bai
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, 610041, China
| | - Zhenhua Zhuang
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, 610041, China
| | - Weiming He
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Shancen Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jing Zhang
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
| | - Nyima Tashi
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China.
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China.
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Pourkheirandish M, Kanamori H, Wu J, Sakuma S, Blattner FR, Komatsuda T. Elucidation of the origin of 'agriocrithon' based on domestication genes questions the hypothesis that Tibet is one of the centers of barley domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:525-534. [PMID: 29469199 DOI: 10.1111/tpj.13876] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/12/2018] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
Wild barley forms a two-rowed spike with a brittle rachis whereas domesticated barley has two- or six-rowed spikes with a tough rachis. Like domesticated barley, 'agriocrithon' forms a six-rowed spike; however, the spike is brittle as in wild barley, which makes the origin of agriocrithon obscure. Haplotype analysis of the Six-rowed spike 1 (vrs1) and Non-brittle rachis 1 (btr1) and 2 (btr2) genes was conducted to infer the origin of agriocrithon barley. Some agriocrithon barley accessions (eu-agriocrithon) carried Btr1 and Btr2 haplotypes that are not found in any cultivars, implying that they are directly derived from wild barley through a mutation at the vrs1 locus. Other agriocrithon barley accessions (pseudo-agriocrithon) carried Btr1 or Btr2 from cultivated barley, thus implying that they originated from hybridization between six-rowed landraces carrying btr1Btr2 and Btr1btr2 genotypes followed by recombination to produce Btr1Btr2. All materials we collected from Tibet belong to pseudo-agriocrithon and thus do not support the Tibetan Plateau as being a center of barley domestication. Tracing the evolutionary history of these allelic variants revealed that eu-agriocrithon represents six-rowed barley lineages that were selected by early farmers, once in south-eastern Turkmenistan (vrs1.a1) and again in the eastern part of Uzbekistan (vrs1.a4).
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Affiliation(s)
- Mohammad Pourkheirandish
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
- Faculty of Science, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Shun Sakuma
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Research (IPK), Gatersleben, D-06466, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan
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29
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Wei C, Zhu L, Wen J, Yi B, Ma C, Tu J, Shen J, Fu T. Morphological, transcriptomics and biochemical characterization of new dwarf mutant of Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:97-113. [PMID: 29576090 DOI: 10.1016/j.plantsci.2018.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/16/2018] [Accepted: 01/19/2018] [Indexed: 05/08/2023]
Abstract
Plant height is a key trait of plant architecture, and is responsible for both yield and lodging resistance in Brassica napus. A dwarf mutant line (bnaC.dwf) was obtained by chemical mutagenesis of an inbred line T6. However, the molecular mechanisms and changed biological processes of the dwarf mutant remain to be determined. In this study, a comparative transcriptome analysis between bnaC.dwf and T6 plants was performed to identify genome-wide differentially expressed genes (DEGs) and possible biological processes that may explain the phenotype variations in bnaC.dwf. As a result of this analysis, 60,134,746-60,301,384 clean reads were aligned to 60,074 genes in the B. napus genome, and accounted for 60.03% of the annotated genes. In total, 819 differentially expressed genes were used for GO (Gene Ontology) term and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses with a FDR (false discovery rate) criterion of <0.001, |log2Ratio| ≥ 1. We focused on plant hormone signal transduction pathways, plant-pathogen interaction pathway, protein phosphorylation and degradation pathways and sugar metabolism pathways. Taken together, the decrease in local auxin (IAA) levels, the variation in BnTCH4, BnKAN1, BnERF109, COI1-JAZ9-MYC2, auxin response genes (BnGH3.11, BnSAUR78, and AUX/IAA19), and ABA (abscisic acid) signaling genes (BnADP5, BnSnRK2.1, BnABF3.1) partially accounted for variations of cell proliferation in internodes, shoot and root apical meristem maintenance, abiotic and biotic stress resistance, and pre-harvest sprouting. As a comprehensive consequence of the cross-talk between plant hormones, sugar metabolism, plant-pathogen interactions and protein metabolism, bnaC.dwf presents distinct phenotypes from T6. These results will be helpful for shedding light on molecular mechanisms in the dwarf mutant, and give insight into further molecular breeding of semi-dwarf B. napus.
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Affiliation(s)
- Chao Wei
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Lixia Zhu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jing Wen
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Bin Yi
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Chaozhi Ma
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxing Tu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxiong Shen
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingdong Fu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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30
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Genomic adaptation to drought in wild barley is driven by edaphic natural selection at the Tabigha Evolution Slope. Proc Natl Acad Sci U S A 2018; 115:5223-5228. [PMID: 29712833 PMCID: PMC5960308 DOI: 10.1073/pnas.1721749115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Ecological divergence at a microsite suggests adaptive evolution, and this study examined two abutting wild barley populations, each 100 m across, differentially adapted to drought tolerance on two contrasting soil types, Terra Rossa and basalt at the Tabigha Evolution Slope, Israel. We resequenced the genomes of seven and six wild barley genotypes inhabiting the Terra Rossa and basalt soils, respectively, and identified a total of 69,192,653 single-nucleotide variants (SNVs) and insertions/deletions in comparison with a reference barley genome. Comparative genomic analysis between these abutting wild barley populations involved 19,615,087 high-quality SNVs. The results revealed dramatically different selection sweep regions relevant to drought tolerance driven by edaphic natural selection within 2,577 selected genes in these regions, including key drought-responsive genes associated with ABA synthesis and degradation (such as Cytochrome P450 protein) and ABA receptor complex (such as PYL2, SNF1-related kinase). The genetic diversity of the wild barley population inhabiting Terra Rossa soil is much higher than that from the basalt soil. Additionally, we identified different sets of genes for drought adaptation in the wild barley populations from Terra Rossa soil and from wild barley populations from Evolution Canyon I at Mount Carmel. These genes are associated with abscisic acid signaling, signaling and metabolism of reactive oxygen species, detoxification and antioxidative systems, rapid osmotic adjustment, and deep root morphology. The unique mechanisms for drought adaptation of the wild barley from the Tabigha Evolution Slope may be useful for crop improvement, particularly for breeding of barley cultivars with high drought tolerance.
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31
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Dai F, Wang X, Zhang X, Chen Z, Nevo E, Jin G, Wu D, Li C, Zhang G. Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:760-770. [PMID: 28871634 PMCID: PMC5814578 DOI: 10.1111/pbi.12826] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/02/2017] [Accepted: 08/14/2017] [Indexed: 05/03/2023]
Abstract
Qingke, the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third-generation sequencer (PacBio), we de novo assembled a 4.84-Gb genome sequence of qingke, cv. Zangqing320 and anchored a 4.59-Gb sequence to seven chromosomes. Of the 46,787 annotated 'high-confidence' genes, 31 564 were validated by RNA-sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by nonredundant protein database from NCBI. As some gaps in the reference genome of Morex were covered in the reference genome of Zangqing320 by PacBio reads, we believe that the Zangqing320 genome provides the useful supplements for the Morex genome. Using the qingke genome as a reference, we conducted a genome comparison, revealing a close genetic relationship between a hulled barley (cv. Morex) and a hulless barley (cv. Zangqing320), which is strongly supported by the low-diversity regions in the two genomes. Considering the origin of Morex from its breeding pedigree, we then demonstrated a close genomic relationship between modern cultivated barley and qingke. Given this genomic relationship and the large genetic diversity between qingke and modern cultivated barley, we propose that qingke could provide elite genes for barley improvement.
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Affiliation(s)
- Fei Dai
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Xiaolei Wang
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Xiao‐Qi Zhang
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityPerthWAAustralia
| | - Zhonghua Chen
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
- School of Science and HealthWestern Sydney UniversityPenrithNSWAustralia
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaHaifaIsrael
| | - Gulei Jin
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Dezhi Wu
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Chengdao Li
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityPerthWAAustralia
| | - Guoping Zhang
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
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Pournosrat R, Kaya S, Shaaf S, Kilian B, Ozkan H. Geographical and environmental determinants of the genetic structure of wild barley in southeastern Anatolia. PLoS One 2018; 13:e0192386. [PMID: 29420597 PMCID: PMC5805283 DOI: 10.1371/journal.pone.0192386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/21/2018] [Indexed: 11/29/2022] Open
Abstract
Despite the global value of barley, compared to its wild progenitor, genetic variation in this crop has been drastically reduced due to the process of domestication, selection and improvement. In the medium term, this will negatively impact both the vulnerability and yield stability of barley against biotic and abiotic stresses under climate change. Returning to the crop wild relatives (CWR) as sources of new and beneficial alleles is a clear option for enhancing the resilience of diversity and adaptation to climate change. Southeastern Anatolia constitutes an important part of the natural distribution of wild barley in the Fertile Crescent where important crops were initially domesticated. In this study, we investigated genetic diversity in a comprehensive collection of 281 geo-referenced wild barley individuals from 92 collection sites with sample sizes ranging from 1 to 9 individuals per site, collected from southeastern Anatolia and 131 domesticated genotypes from 49 different countries using 40 EST-SSR markers. A total of 375 alleles were detected across entire collection, of which 283 were carried by domesticated genotypes and 316 alleles were present in the wild gene pool. The number of unique alleles in the wild and in the domesticated gene pool was 92 and 59, respectively. The population structure at K = 3 suggested two groups of wild barley namely G1-W consisting wild barley genotypes from the western part and G1-E comprising those mostly from the eastern part of the study area, with a sharp separation from the domesticated gene pool. The geographic and climatic factors jointly showed significant effects on the distribution of wild barley. Using a Latent Factor Mixed Model, we identified four candidate loci potentially involved in adaptation of wild barley to three environmental factors: temperature seasonality, mean temperature of driest quarter, and precipitation of coldest quarter. These loci are probably the targets of genomic regions, with potential roles against abiotic stresses.
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Affiliation(s)
- Reza Pournosrat
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Selma Kaya
- University of Çukurova, Faculty of Agriculture, Department of Field Crops, Adana, Turkey
| | - Salar Shaaf
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
- * E-mail: (HO); (BK); (SS)
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Genebank Department, Genome Diversity Group, Seeland, Germany
- * E-mail: (HO); (BK); (SS)
| | - Hakan Ozkan
- University of Çukurova, Faculty of Agriculture, Department of Field Crops, Adana, Turkey
- * E-mail: (HO); (BK); (SS)
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Shen Q, Yu J, Fu L, Wu L, Dai F, Jiang L, Wu D, Zhang G. Ionomic, metabolomic and proteomic analyses reveal molecular mechanisms of root adaption to salt stress in Tibetan wild barley. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 123:319-330. [PMID: 29289898 DOI: 10.1016/j.plaphy.2017.12.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 05/18/2023]
Abstract
In our previous study, Tibetan wild barley (Hordeum spontaneum L.) has been found to be rich in the elite accessions with strong abiotic stress tolerance, including salt stress tolerance. However, the molecular mechanism of salt tolerance underlying the wild barley remains to be elucidated. In this study, two Tibetan wild barley accessions, XZ26 (salt-tolerant) and XZ169 (salt-sensitive), were used to investigate ionomic, metabolomic and proteomic responses in roots when exposed to 0, 200 (moderate) and 400 mM (high) salinity. XZ26 showed stronger root growth and maintained higher K concentrations when compared with XZ169 under moderate salinity, while no significant difference was found between the two accessions under high salinity. A total of 574 salt-regulated proteins and 153 salt-regulated metabolites were identified in the roots of both accessions based on quantitative proteomic (iTRAQ methods) and metabolomic (GC-TOF/MS) analysis. XZ26 developed its root adaptive strategies mainly by accumulating more compatible solutes such as proline and inositol, acquiring greater antioxidant ability to cope with ROS, and consuming less energy under salt stress for producing biomass. These findings provide a better understanding of molecular responses of root adaptive strategies to salt stress in the wild barley.
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Affiliation(s)
- Qiufang Shen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Jiahua Yu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Liangbo Fu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Liyuan Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Fei Dai
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Dezhi Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
| | - Guoping Zhang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
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34
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Han Z, Zhang J, Cai S, Chen X, Quan X, Zhang G. Association mapping for total polyphenol content, total flavonoid content and antioxidant activity in barley. BMC Genomics 2018; 19:81. [PMID: 29370751 PMCID: PMC5784657 DOI: 10.1186/s12864-018-4483-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/16/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The interest has been increasing on the phenolic compounds in plants because of their nutritive function as food and the roles regulating plant growth. However, their underlying genetic mechanism in barley is still not clear. RESULTS A genome-wide association study (GWAS) was conducted for total phenolic content (TPC), total flavonoid content (FLC) and antioxidant activity (AOA) in 67 cultivated and 156 Tibetan wild barley genotypes. Most markers associated with phenolic content were different in cultivated and wild barleys. The markers bPb-0572 and bPb-4531 were identified as the major QTLs controlling phenolic compounds in Tibetan wild barley. Moreover, the marker bPb-4531 was co-located with the UDP- glycosyltransferase gene (HvUGT), which is a homolog to Arabidopsis UGTs and involved in biosynthesis of flavonoid glycosides . CONCLUSIONS GWAS is an efficient tool for exploring the genetic architecture of phenolic compounds in the cultivated and Tibetan wild barleys. The DArT markers applied in this study can be used in barley breeding for developing new barley cultivars with higher phenolics content. The candidate gene (HvUGT) provides a potential route for deep understanding of the molecular mechanism of flavonoid synthesis.
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Affiliation(s)
- Zhigang Han
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
| | - Jingjie Zhang
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
| | - Shengguan Cai
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
| | - Xiaohui Chen
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
| | - Xiaoyan Quan
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Guoping Zhang
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
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35
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Cai S, Chen G, Wang Y, Huang Y, Marchant DB, Wang Y, Yang Q, Dai F, Hills A, Franks PJ, Nevo E, Soltis DE, Soltis PS, Sessa E, Wolf PG, Xue D, Zhang G, Pogson BJ, Blatt MR, Chen ZH. Evolutionary Conservation of ABA Signaling for Stomatal Closure. PLANT PHYSIOLOGY 2017; 174:732-747. [PMID: 28232585 PMCID: PMC5462018 DOI: 10.1104/pp.16.01848] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/21/2017] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA)-driven stomatal regulation reportedly evolved after the divergence of ferns, during the early evolution of seed plants approximately 360 million years ago. This hypothesis is based on the observation that the stomata of certain fern species are unresponsive to ABA, but exhibit passive hydraulic control. However, ABA-induced stomatal closure was detected in some mosses and lycophytes. Here, we observed that a number of ABA signaling and membrane transporter protein families diversified over the evolutionary history of land plants. The aquatic ferns Azolla filiculoides and Salvinia cucullata have representatives of 23 families of proteins orthologous to those of Arabidopsis (Arabidopsis thaliana) and all other land plant species studied. Phylogenetic analysis of the key ABA signaling proteins indicates an evolutionarily conserved stomatal response to ABA. Moreover, comparative transcriptomic analysis has identified a suite of ABA-responsive genes that differentially expressed in a terrestrial fern species, Polystichum proliferum These genes encode proteins associated with ABA biosynthesis, transport, reception, transcription, signaling, and ion and sugar transport, which fit the general ABA signaling pathway constructed from Arabidopsis and Hordeum vulgare The retention of these key ABA-responsive genes could have had a profound effect on the adaptation of ferns to dry conditions. Furthermore, stomatal assays have shown the primary evidence for ABA-induced closure of stomata in two terrestrial fern species Pproliferum and Nephrolepis exaltata In summary, we report, to our knowledge, new molecular and physiological evidence for the presence of active stomatal control in ferns.
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Affiliation(s)
- Shengguan Cai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Guang Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Yuanyuan Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Yuqing Huang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - D Blaine Marchant
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Yizhou Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Qian Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Adrian Hills
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Peter J Franks
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Eviatar Nevo
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Douglas E Soltis
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Pamela S Soltis
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Emily Sessa
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Paul G Wolf
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Dawei Xue
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Barry J Pogson
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Michael R Blatt
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.)
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.)
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.)
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.)
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.)
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.)
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
| | - Zhong-Hua Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (S.C., G.C., Yu.W., Q.Y., F.D., G.Z., Z.-H.C.);
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia (S.C., Y.H., Z.-H.C.);
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S.);
- Department of Biology, University of Florida, Gainesville, Florida 32611 (D.B.M., D.E.S., P.S.S., E.S.);
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom (Yi.W., A.H., M.R.B.);
- Faculty of Agriculture and Environment, The University of Sydney, Sydney NSW 2006, Australia (P.J.F.);
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel (E.N.);
- Ecology Center and Department of Biology, Utah State University, Logan, Utah 84322 (P.G.W.);
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (D.X.); and
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton ACT 2601, Australia (P.J.B.)
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Xue D, Zhang X, Lu X, Chen G, Chen ZH. Molecular and Evolutionary Mechanisms of Cuticular Wax for Plant Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2017; 8:621. [PMID: 28503179 PMCID: PMC5408081 DOI: 10.3389/fpls.2017.00621] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/06/2017] [Indexed: 05/05/2023]
Abstract
Cuticular wax, the first protective layer of above ground tissues of many plant species, is a key evolutionary innovation in plants. Cuticular wax safeguards the evolution from certain green algae to flowering plants and the diversification of plant taxa during the eras of dry and adverse terrestrial living conditions and global climate changes. Cuticular wax plays significant roles in plant abiotic and biotic stress tolerance and has been implicated in defense mechanisms against excessive ultraviolet radiation, high temperature, bacterial and fungal pathogens, insects, high salinity, and low temperature. Drought, a major type of abiotic stress, poses huge threats to global food security and health of terrestrial ecosystem by limiting plant growth and crop productivity. The composition, biochemistry, structure, biosynthesis, and transport of plant cuticular wax have been reviewed extensively. However, the molecular and evolutionary mechanisms of cuticular wax in plants in response to drought stress are still lacking. In this review, we focus on potential mechanisms, from evolutionary, molecular, and physiological aspects, that control cuticular wax and its roles in plant drought tolerance. We also raise key research questions and propose important directions to be resolved in the future, leading to potential applications of cuticular wax for water use efficiency in agricultural and environmental sustainability.
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Affiliation(s)
- Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
- *Correspondence: Dawei Xue, Zhong-Hua Chen,
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Xueli Lu
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Guang Chen
- College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Zhong-Hua Chen
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, RichmondNSW, Australia
- *Correspondence: Dawei Xue, Zhong-Hua Chen,
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Contreras-Moreira B, Cantalapiedra CP, García-Pereira MJ, Gordon SP, Vogel JP, Igartua E, Casas AM, Vinuesa P. Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. FRONTIERS IN PLANT SCIENCE 2017; 8:184. [PMID: 28261241 PMCID: PMC5306281 DOI: 10.3389/fpls.2017.00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/30/2017] [Indexed: 05/22/2023]
Abstract
The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes. The goal was to sample their pan-genomes and classify sequences as core, if detected in all accessions, or accessory, when absent in some of them. The resulting sequence clusters were used to simulate pan-genome growth, and to compile Average Nucleotide Identity matrices that summarize intra-species variation. Although transcripts were found to under-estimate pan-genome size by at least 10%, we concluded that clusters of expressed sequences can recapitulate phylogeny and reproduce two properties observed in A. thaliana gene models: accessory loci show lower expression and higher non-synonymous substitution rates than core genes. Finally, accessory sequences were observed to preferentially encode transposon components in both species, plus disease resistance genes in cultivated barleys, and a variety of protein domains from other families that appear frequently associated with presence/absence variation in the literature. These results demonstrate that pan-genome analyses are useful to explore germplasm diversity.
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Affiliation(s)
- Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones CientíficasZaragoza, Spain; Fundación ARAIDZaragoza, Spain
| | - Carlos P Cantalapiedra
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - María J García-Pereira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | | | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | - Ernesto Igartua
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - Ana M Casas
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
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38
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Shmakov NA, Vasiliev GV, Shatskaya NV, Doroshkov AV, Gordeeva EI, Afonnikov DA, Khlestkina EK. Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq. BMC PLANT BIOLOGY 2016; 16:245. [PMID: 28105957 PMCID: PMC5123340 DOI: 10.1186/s12870-016-0926-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND Albinism in plants is characterized by lack of chlorophyll and results in photosynthesis impairment, abnormal plant development and premature death. These abnormalities are frequently encountered in interspecific crosses and tissue culture experiments. Analysis of albino mutant phenotypes with full or partial chlorophyll deficiency can shed light on genetic determinants and molecular mechanisms of albinism. Here we report analysis of RNA-seq transcription profiling of barley (Hordeum vulgare L.) near-isogenic lines, one of which is a carrier of mutant allele of the Alm gene for albino lemma and pericarp phenotype (line i:BwAlm). RESULTS 1221 genome fragments have statistically significant changes in expression levels between lines i:BwAlm and Bowman, with 148 fragments having increased expression levels in line i:BwAlm, and 1073 genome fragments, including 42 plastid operons, having decreased levels of expression in line i:BwAlm. We detected functional dissimilarity between genes with higher and lower levels of expression in i:BwAlm line. Genes with lower level of expression in the i:BwAlm line are mostly associated with photosynthesis and chlorophyll synthesis, while genes with higher expression level are functionally associated with vesicle transport. Differentially expressed genes are shown to be involved in several metabolic pathways; the largest fraction of such genes was observed for the Calvin-Benson-Bassham cycle. Finally, de novo assembly of transcriptome contains several transcripts, not annotated in current H. vulgare genome version. CONCLUSIONS Our results provide the new information about genes which could be involved in formation of albino lemma and pericarp phenotype. They demonstrate the interplay between nuclear and chloroplast genomes in this physiological process.
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Affiliation(s)
- Nickolay A. Shmakov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | | | | | - Dmitry A. Afonnikov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Elena K. Khlestkina
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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Shen Q, Fu L, Dai F, Jiang L, Zhang G, Wu D. Multi-omics analysis reveals molecular mechanisms of shoot adaption to salt stress in Tibetan wild barley. BMC Genomics 2016; 17:889. [PMID: 27821058 PMCID: PMC5100661 DOI: 10.1186/s12864-016-3242-9] [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: 07/22/2016] [Accepted: 11/01/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Tibetan wild barley (Hordeum spontaneum L.) has been confirmed to contain elite accessions in tolerance to abiotic stresses, including salinity. However, molecular mechanisms underlying genotypic difference of salt tolerance in wild barley are unknown. RESULTS In this study, two Tibetan wild barley accessions (XZ26 and XZ169), differing greatly in salt tolerance, were used to determine changes of ionomic, metabolomic and proteomic profiles in the shoots exposed to salt stress at seedling stage. Compared with XZ169, XZ26 showed better shoot growth and less Na accumulation after 7 days treatments. Salt stress caused significant reduction in concentrations of sucrose and metabolites involved in glycolysis pathway in XZ169, and elevated level of tricarboxylic acid (TCA) cycle, as reflected by up-accumulation of citric acid, aconitic acid and succinic acid, especially under high salinity, but not in XZ26. Correspondingly, proteomic analysis further proved the findings from the metabolomic study. CONCLUSION XZ26 maintained a lower Na concentration in the shoots and developed superior shoot adaptive strategies to salt stress. The current result provides possible utilization of Tibetan wild barley in developing barley cultivars for salt tolerance.
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Affiliation(s)
- Qiufang Shen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Liangbo Fu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Fei Dai
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Guoping Zhang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Dezhi Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
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40
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Molecular evidence of RNA polymerase II gene reveals the origin of worldwide cultivated barley. Sci Rep 2016; 6:36122. [PMID: 27786300 PMCID: PMC5081693 DOI: 10.1038/srep36122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/11/2016] [Indexed: 12/12/2022] Open
Abstract
The origin and domestication of cultivated barley have long been under debate. A population-based resequencing and phylogenetic analysis of the single copy of RPB2 gene was used to address barley domestication, to explore genetic differentiation of barley populations on the worldwide scale, and to understand gene-pool exchanges during the spread and subsequent development of barley cultivation. Our results revealed significant genetic differentiation among three geographically distinct wild barley populations. Differences in haplotype composition among populations from different geographical regions revealed that modern cultivated barley originated from two major wild barley populations: one from the Near East Fertile Crescent and the other from the Tibetan Plateau, supporting polyphyletic origin of cultivated barley. The results of haplotype frequencies supported multiple domestications coupled with widespread introgression events that generated genetic admixture between divergent barley gene pools. Our results not only provide important insight into the domestication and evolution of cultivated barley, but also enhance our understanding of introgression and distinct selection pressures in different environments on shaping the genetic diversity of worldwide barley populations, thus further facilitating the effective use of the wild barley germplasm.
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Wang X, Wu D, Yang Q, Zeng J, Jin G, Chen ZH, Zhang G, Dai F. Identification of Mild Freezing Shock Response Pathways in Barley Based on Transcriptome Profiling. FRONTIERS IN PLANT SCIENCE 2016; 7:106. [PMID: 26904070 PMCID: PMC4744895 DOI: 10.3389/fpls.2016.00106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/20/2016] [Indexed: 05/19/2023]
Abstract
Low temperature is a major abiotic stress affecting crop growth and productivity. A better understanding of low temperature tolerance mechanisms is imperative for developing the crop cultivars with improved tolerance. We herein performed an Illumina RNA-sequencing experiment using two barley genotypes differing in freezing tolerance (Nure, tolerant and Tremois, sensitive), to determine the transcriptome profiling and genotypic difference under mild freezing shock treatment after a very short acclimation for gene induction. A total of 6474 differentially expressed genes, almost evenly distributed on the seven chromosomes, were identified. The key DEGs could be classified into six signaling pathways, i.e., Ca(2+) signaling, PtdOH signaling, CBFs pathway, ABA pathway, jasmonate pathway, and amylohydrolysis pathway. Expression values of DEGs in multiple signaling pathways were analyzed and a hypothetical model of mild freezing shock tolerance mechanism was proposed. Expression and sequence profile of HvCBFs cluster within Frost resistance-H2, a major quantitative trait locus on 5H being closely related to low temperature tolerance in barley, were further illustrated, considering the crucial role of HvCBFs on freezing tolerance. It may be concluded that multiple signaling pathways are activated in concert when barley is exposed to mild freezing shock. The pathway network we presented may provide a platform for further exploring the functions of genes involved in low temperature tolerance in barley.
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Affiliation(s)
| | | | | | | | | | | | | | - Fei Dai
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, Zhejiang UniversityHangzhou, China
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Cai S, Han Z, Huang Y, Hu H, Dai F, Zhang G. Identification of Quantitative Trait Loci for the Phenolic Acid Contents and Their Association with Agronomic Traits in Tibetan Wild Barley. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:980-987. [PMID: 26757245 DOI: 10.1021/acs.jafc.5b05441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Phenolic acids have been of considerable interest in human nutrition because of their strong antioxidative properties. However, even in a widely grown crop, such as barley, their genetic architecture is still unclear. In this study, genetic control of two main phenolic acids, ferulic acid (FA) and p-coumaric acid (p-CA), and their associations with agronomic traits were investigated among 134 Tibetan wild barley accessions. A genome-wide association study (GWAS) identified three DArT markers (bpb-2723, bpb-7199, and bpb-7273) associated with p-CA content and one marker (bpb-3653) associated with FA content in 2 consecutive years. The contents of the two phenolic acids were positively correlated with some agronomic traits, such as the first internode length, plant height, and some grain color parameters, and negatively correlated with the thousand-grain weight (TGW). This study provides DNA markers for barley breeding programs to improve the contents of phenolic acids.
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Affiliation(s)
- Shengguan Cai
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Zhigang Han
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Yuqing Huang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Hongliang Hu
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Fei Dai
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Guoping Zhang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
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43
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He X, Zeng J, Cao F, Ahmed IM, Zhang G, Vincze E, Wu F. HvEXPB7, a novel β-expansin gene revealed by the root hair transcriptome of Tibetan wild barley, improves root hair growth under drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:7405-19. [PMID: 26417018 PMCID: PMC4765802 DOI: 10.1093/jxb/erv436] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Tibetan wild barley is a treasure trove of useful genes for crop improvement including abiotic stress tolerance, like drought. Root hair of single-celled structures plays an important role in water and nutrition uptake. Polyethylene-glycol-induced drought stress hydroponic/petri-dish experiments were performed, where root hair morphology and transcriptional characteristics of two contrasting Tibetan wild barley genotypes (drought-tolerant XZ5 and drought-sensitive XZ54) and drought-tolerant cv. Tadmor were compared. Drought-induced root hair growth was only observed in XZ5. Thirty-six drought tolerance-associated genes were identified in XZ5, including 16 genes specifically highly expressed in XZ5 but not Tadmor under drought. The full length cDNA of a novel β-expansin gene (HvEXPB7), being the unique root hair development related gene in the identified genes, was cloned. The sequence comparison indicated that HvEXPB7 carried both DPBB_1 and Pollon_allerg_1 domains. HvEXPB7 is predominantly expressed in roots. Subcellular localization verified that HvEXPB7 is located in the plasma membrane. Barley stripe mosaic virus induced gene silencing (BSMV-VIGS) of HvEXPB7 led to severely suppressed root hairs both under control and drought conditions, and significantly reduced K uptake. These findings highlight and confer the significance of HvEXPB7 in root hair growth under drought stress in XZ5, and provide a novel insight into the genetic basis for drought tolerance in Tibetan wild barley.
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Affiliation(s)
- Xiaoyan He
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Jianbin Zeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Imrul Mosaddek Ahmed
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
| | - Eva Vincze
- Department of Molecular Biology and Genetics, University of Aarhus, Fosøgsvej 1, DK-4200 Slagelse, Denmark
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, PR China
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44
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Pourkheirandish M, Hensel G, Kilian B, Senthil N, Chen G, Sameri M, Azhaguvel P, Sakuma S, Dhanagond S, Sharma R, Mascher M, Himmelbach A, Gottwald S, Nair SK, Tagiri A, Yukuhiro F, Nagamura Y, Kanamori H, Matsumoto T, Willcox G, Middleton CP, Wicker T, Walther A, Waugh R, Fincher GB, Stein N, Kumlehn J, Sato K, Komatsuda T. Evolution of the Grain Dispersal System in Barley. Cell 2015; 162:527-39. [PMID: 26232223 DOI: 10.1016/j.cell.2015.07.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/13/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
Abstract
About 12,000 years ago in the Near East, humans began the transition from hunter-gathering to agriculture-based societies. Barley was a founder crop in this process, and the most important steps in its domestication were mutations in two adjacent, dominant, and complementary genes, through which grains were retained on the inflorescence at maturity, enabling effective harvesting. Independent recessive mutations in each of these genes caused cell wall thickening in a highly specific grain "disarticulation zone," converting the brittle floral axis (the rachis) of the wild-type into a tough, non-brittle form that promoted grain retention. By tracing the evolutionary history of allelic variation in both genes, we conclude that spatially and temporally independent selections of germplasm with a non-brittle rachis were made during the domestication of barley by farmers in the southern and northern regions of the Levant, actions that made a major contribution to the emergence of early agrarian societies.
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Affiliation(s)
| | - Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Natesan Senthil
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Guoxiong Chen
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Mohammad Sameri
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Perumal Azhaguvel
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Shun Sakuma
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Sidram Dhanagond
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Rajiv Sharma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Sven Gottwald
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Sudha K Nair
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Akemi Tagiri
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Fumiko Yukuhiro
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Yoshiaki Nagamura
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - George Willcox
- Archéorient CNRS UMR 5133, Université de Lyon II, Jalés, Berrias 07460, France
| | | | - Thomas Wicker
- Institute of Plant Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Alexander Walther
- Department of Earth Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Robbie Waugh
- University of Dundee, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Geoffrey B Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Glen Osmond, SA 5066, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 710-0046 Kurashiki, Japan
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan.
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Shi T, Dimitrov I, Zhang Y, Tax FE, Yi J, Gou X, Li J. Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication. PLANT MOLECULAR BIOLOGY 2015; 89:253-261. [PMID: 26362289 DOI: 10.1007/s11103-015-0366-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/21/2015] [Indexed: 06/05/2023]
Abstract
Traits related to grain and reproductive organs in grass crops have been under continuous directional selection during domestication. Barley is one of the oldest domesticated crops in human history. Thus genes associated with the grain and reproductive organs in barley may show evidence of dramatic evolutionary change. To understand how artificial selection contributes to protein evolution of biased genes in different barley organs, we used Digital Gene Expression analysis of six barley organs (grain, pistil, anther, leaf, stem and root) to identify genes with biased expression in specific organs. Pairwise comparisons of orthologs between barley and Brachypodium distachyon, as well as between highland and lowland barley cultivars mutually indicated that grain and pistil biased genes show relatively higher protein evolutionary rates compared with the median of all orthologs and other organ biased genes. Lineage-specific protein evolutionary rates estimation showed similar patterns with elevated protein evolution in barley grain and pistil biased genes, yet protein sequences generally evolve much faster in the lowland barley cultivar. Further functional annotations revealed that some of these grain and pistil biased genes with rapid protein evolution are related to nutrient biosynthesis and cell cycle/division. Our analyses provide insights into how domestication differentially shaped the evolution of genes specific to different organs of a crop species, and implications for future functional studies of domestication genes.
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Affiliation(s)
- Tao Shi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Ivan Dimitrov
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Yinling Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Frans E Tax
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jing Yi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Dockter C, Hansson M. Improving barley culm robustness for secured crop yield in a changing climate. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3499-509. [PMID: 25614659 DOI: 10.1093/jxb/eru521] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The Green Revolution combined advancements in breeding and agricultural practice, and provided food security to millions of people. Daily food supply is still a major issue in many parts of the world and is further challenged by future climate change. Fortunately, life science research is currently making huge progress, and the development of future crop plants will be explored. Today, plant breeding typically follows one gene per trait. However, new scientific achievements have revealed that many of these traits depend on different genes and complex interactions of proteins reacting to various external stimuli. These findings open up new possibilities for breeding where variations in several genes can be combined to enhance productivity and quality. In this review we present an overview of genes determining plant architecture in barley, with a special focus on culm length. Many genes are currently known only through their mutant phenotypes, but emerging genomic sequence information will accelerate their identification. More than 1000 different short-culm barley mutants have been isolated and classified in different phenotypic groups according to culm length and additional pleiotropic characters. Some mutants have been connected to deficiencies in biosynthesis and reception of brassinosteroids and gibberellic acids. Still other mutants are unlikely to be connected to these hormones. The genes and corresponding mutations are of potential interest for development of stiff-straw crop plants tolerant to lodging, which occurs in extreme weather conditions with strong winds and heavy precipitation.
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Affiliation(s)
- Christoph Dockter
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK- Copenhagen V, Denmark.
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, SE-22362 Lund, Sweden
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Wang X, Zhang X, Cai S, Ye L, Zhou M, Chen Z, Zhang G, Dai F. Genetic diversity and QTL mapping of thermostability of limit dextrinase in barley. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3778-3783. [PMID: 25816850 DOI: 10.1021/acs.jafc.5b00190] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Limit dextrinase (LD) is an essential amylolytic enzyme for the complete degradation of starch, and it is closely associated with malt quality. A survey of 51 cultivated barley and 40 Tibetan wild barley genotypes showed a wide genetic diversity of LD activity and LD thermostability. Compared with cultivated barley, Tibetan wild barley showed lower LD activity and higher LD thermostability. A doubled haploid population composed of 496 DArT and 28 microsatellite markers was used for mapping Quantitative Trait Loci (QTLs). Parental line Yerong showed low LD activity and high LD thermostability, but Franklin exhibited high LD activity and low LD thermostability. Three QTLs associated with thermostable LD were identified. The major QTL is close to the LD gene on chromosome 7H. The two minor QTLs colocalized with previously reported QTLs determining malt-extract and diastatic power on chromosomes 1H and 2H, respectively. These QTLs may be useful for a better understanding of the genetic control of LD activity and LD thermostability in barley.
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Affiliation(s)
- Xiaolei Wang
- †Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Xuelei Zhang
- †Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- †Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Lingzhen Ye
- †Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Meixue Zhou
- §Tasmanian Institute of Agriculture, University of Tasmania, P.O. Box 46, Kings Meadows, TAS 7249, Australia
| | - Zhonghua Chen
- ‡School of Science and Health, University of Western Sydney, Penrith, NSW 2751, Australia
| | - Guoping Zhang
- †Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Fei Dai
- †Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
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Zeng X, Long H, Wang Z, Zhao S, Tang Y, Huang Z, Wang Y, Xu Q, Mao L, Deng G, Yao X, Li X, Bai L, Yuan H, Pan Z, Liu R, Chen X, WangMu Q, Chen M, Yu L, Liang J, DunZhu D, Zheng Y, Yu S, LuoBu Z, Guang X, Li J, Deng C, Hu W, Chen C, TaBa X, Gao L, Lv X, Abu YB, Fang X, Nevo E, Yu M, Wang J, Tashi N. The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau. Proc Natl Acad Sci U S A 2015; 112:1095-100. [PMID: 25583503 PMCID: PMC4313863 DOI: 10.1073/pnas.1423628112] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called "Qingke" in Chinese and "Ne" in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.
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Affiliation(s)
- Xingquan Zeng
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Zhuo Wang
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yawei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | | | - Yulin Wang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | - Qijun Xu
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | - Likai Mao
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | | | - Xiangfeng Li
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lijun Bai
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | - Hongjun Yuan
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Renjian Liu
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | - Xin Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - QiMei WangMu
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | - Ming Chen
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | - Lili Yu
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - DaWa DunZhu
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | - Yuan Zheng
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | - Shuiyang Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - ZhaXi LuoBu
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | | | - Jiang Li
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | - Cao Deng
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | - Wushu Hu
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | | | - XiongNu TaBa
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | - Liyun Gao
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China
| | - Xiaodan Lv
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | - Yuval Ben Abu
- Projects and Physics Section, Sapir Academic College, D.N. Hof Ashkelon 79165, Israel
| | | | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel;
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China;
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark; and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21441, Saudi Arabia
| | - Nyima Tashi
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
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Wang Y, Ren X, Sun D, Sun G. Origin of worldwide cultivated barley revealed by NAM-1 gene and grain protein content. FRONTIERS IN PLANT SCIENCE 2015; 6:803. [PMID: 26483818 PMCID: PMC4588695 DOI: 10.3389/fpls.2015.00803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 09/15/2015] [Indexed: 05/02/2023]
Abstract
The origin, evolution, and distribution of cultivated barley provides powerful insights into the historic origin and early spread of agrarian culture. Here, population-based genetic diversity and phylogenetic analyses were performed to determine the evolution and origin of barley and how domestication and subsequent introgression have affected the genetic diversity and changes in cultivated barley on a worldwide scale. A set of worldwide cultivated and wild barleys from Asia and Tibet of China were analyzed using the sequences for NAM-1 gene and gene-associated traits-grain protein content (GPC). Our results showed Tibetan wild barley distinctly diverged from Near Eastern barley, and confirmed that Tibet is one of the origin and domestication centers for cultivated barley, and in turn supported a polyphyletic origin of domesticated barley. Comparison of haplotype composition among geographic regions revealed gene flow between Eastern and Western barley populations, suggesting that the Silk Road might have played a crucial role in the spread of genes. The GPC in the 118 cultivated and 93 wild barley accessions ranged from 6.73 to 12.35% with a mean of 9.43%. Overall, wild barley had higher averaged GPC (10.44%) than cultivated barley. Two unique haplotypes (Hap2 and Hap7) caused by a base mutations (at position 544) in the coding region of the NAM-1 gene might have a significant impact on the GPC. Single nucleotide polymorphisms and haplotypes of NAM-1 associated with GPC in barley could provide a useful method for screening GPC in barley germplasm. The Tibetan wild accessions with lower GPC could be useful for malt barley breeding.
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Affiliation(s)
- Yonggang Wang
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Dongfa Sun, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China, ; Genlou Sun, Department of Biology, Saint Mary’s University, 923 Robie Street, Halifax, NS B3H 3C3, Canada,
| | - Genlou Sun
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- Department of Biology, Saint Mary’s University, HalifaxNS, Canada
- *Correspondence: Dongfa Sun, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China, ; Genlou Sun, Department of Biology, Saint Mary’s University, 923 Robie Street, Halifax, NS B3H 3C3, Canada,
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50
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Liu X, Mak M, Babla M, Wang F, Chen G, Veljanoski F, Wang G, Shabala S, Zhou M, Chen ZH. Linking stomatal traits and expression of slow anion channel genes HvSLAH1 and HvSLAC1 with grain yield for increasing salinity tolerance in barley. FRONTIERS IN PLANT SCIENCE 2014; 5:634. [PMID: 25505473 PMCID: PMC4243495 DOI: 10.3389/fpls.2014.00634] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/26/2014] [Indexed: 05/20/2023]
Abstract
Soil salinity is an environmental and agricultural problem in many parts of the world. One of the keys to breeding barley for adaptation to salinity lies in a better understanding of the genetic control of stomatal regulation. We have employed a range of physiological (stomata assay, gas exchange, phylogenetic analysis, QTL analysis), and molecular techniques (RT-PCR and qPCR) to investigate stomatal behavior and genotypic variation in barley cultivars and a genetic population in four experimental trials. A set of relatively efficient and reliable methods were developed for the characterization of stomatal behavior of a large number of varieties and genetic lines. Furthermore, we found a large genetic variation of gas exchange and stomatal traits in barley in response to salinity stress. Salt-tolerant cultivar CM72 showed significantly larger stomatal aperture under 200 mM NaCl treatment than that of salt-sensitive cultivar Gairdner. Stomatal traits such as aperture width/length were found to significantly correlate with grain yield under salt treatment. Phenotypic characterization and QTL analysis of a segregating double haploid population of the CM72/Gairdner resulted in the identification of significant stomatal traits-related QTLs for salt tolerance. Moreover, expression analysis of the slow anion channel genes HvSLAH1 and HvSLAC1 demonstrated that their up-regulation is linked to higher barley grain yield in the field.
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Affiliation(s)
- Xiaohui Liu
- School of Science and Health, University of Western SydneyPenrith, NSW, Australia
- School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
| | - Michelle Mak
- School of Science and Health, University of Western SydneyPenrith, NSW, Australia
| | - Mohammad Babla
- School of Science and Health, University of Western SydneyPenrith, NSW, Australia
| | - Feifei Wang
- School of Land and Food, University of TasmaniaHobart, TAS, Australia
| | - Guang Chen
- College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Filip Veljanoski
- School of Science and Health, University of Western SydneyPenrith, NSW, Australia
| | - Gang Wang
- School of Environmental Science and Engineering, Tianjin UniversityTianjin, China
| | - Sergey Shabala
- School of Land and Food, University of TasmaniaHobart, TAS, Australia
| | - Meixue Zhou
- School of Land and Food, University of TasmaniaHobart, TAS, Australia
| | - Zhong-Hua Chen
- School of Science and Health, University of Western SydneyPenrith, NSW, Australia
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