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Gao H, Li D, Hu H, Zhou F, Yu Y, Wei Q, Liu Q, Liu M, Hu P, Chen E, Song P, Su X, Guan Y, Qiao M, Ru Z, Li C. Regulation of carbohydrate metabolism during anther development in a thermo-sensitive genic male-sterile wheat line. Plant Cell Environ 2024. [PMID: 38517937 DOI: 10.1111/pce.14888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/24/2024]
Abstract
Bainong sterility (BNS) is a thermo-sensitive genic male sterile wheat line, characterised by anther fertility transformation in response to low temperature (LT) stress during meiosis, the failure of vacuole decomposition and the absence of starch accumulation in sterile bicellular pollen. Our study demonstrates that the late microspore (LM) stage marks the transition from the anther growth to anther maturation phase, characterised by the changes in anther structure, carbohydrate metabolism and the main transport pathway of sucrose (Suc). Fructan is a main storage polysaccharide in wheat anther, and its synthesis and remobilisation are crucial for anther development. Moreover, the process of pollen amylogenesis and the fate of the large vacuole in pollen are closely intertwined with fructan synthesis and remobilisation. LT disrupts the normal physiological metabolism of BNS anthers during meiosis, particularly affecting carbohydrate metabolism, thus determining the fate of male gametophytes and pollen abortion. Disruption of fructan synthesis and remobilisation regulation serves as a decisive event that results in anther abortion. Sterile pollen exhibits common traits of pollen starvation and impaired starch accumulation due to the inhibition of apoplastic transport starting from the LM stage, which is regulated by cell wall invertase TaIVR1 and Suc transporter TaSUT1.
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Affiliation(s)
- Huanting Gao
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Dongxiao Li
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Haiyan Hu
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Feng Zhou
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Yongang Yu
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Qichao Wei
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Qili Liu
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Mingjiu Liu
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Ping Hu
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Eryong Chen
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Puwen Song
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xiaojia Su
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Yuanyuan Guan
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Mei Qiao
- College of Science and Engineering, Hebei Agricultural University, Baoding, Hebei, China
| | - Zhengang Ru
- Henan Collaborative Innovation Centre of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Chengwei Li
- Henan Engineering Research Centre of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, Henan, China
- College of Life Science, Henan Agricultural University, Zhengzhou, Henan, China
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Jia J, Xie Y, Cheng J, Kong C, Wang M, Gao L, Zhao F, Guo J, Wang K, Li G, Cui D, Hu T, Zhao G, Wang D, Ru Z, Zhang Y. Author Correction: Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression. Genome Biol 2024; 25:5. [PMID: 38167044 PMCID: PMC10763112 DOI: 10.1186/s13059-023-03154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Affiliation(s)
- Jizeng Jia
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, Henan, China.
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingfei Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuizheng Kong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meiyue Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Lifeng Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fei Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyu Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- School of Life Science, Henan University, Kaifeng, 457000, Henan, China
| | - Kai Wang
- Novogene Co. Ltd, Building 301, Jiuxianqiao North Road, Beijing, Chaoyang District, China
| | - Guangwei Li
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, Henan, China
| | - Dangqun Cui
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, Henan, China
| | - Tiezhu Hu
- Henan Institute of Science and Technology, Eastern Hualan Avenue, Xinxiang City, 453003, Henan Province, China
| | - Guangyao Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Daowen Wang
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, Henan, China.
| | - Zhengang Ru
- Henan Institute of Science and Technology, Eastern Hualan Avenue, Xinxiang City, 453003, Henan Province, China.
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Shi C, Wang P, Wang G, Hu T, Ru Z, Feng S. Responses of root characteristics and nitrogen absorption and assimilation to different pH gradients of winter wheat at seedling stage. PLoS One 2023; 18:e0293471. [PMID: 38127853 PMCID: PMC10735037 DOI: 10.1371/journal.pone.0293471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/12/2023] [Indexed: 12/23/2023] Open
Abstract
Nitrogen (N) and rhizosphere pH are the two main factors restricting the growth of winter wheat (Triticum aestivum L.) in North China Plain. Soil nutrient availability is affected by soil acidity and alkalinity. In order to understand the effect of rhizosphere pH value on wheat nitrogen metabolism and the response of wheat growth to pH value at seedling stage, winter wheat varieties 'Aikang 58' (AK58) and 'Bainong 4199' (BN4199) were tested in hydroponics under three pH treatments (pH = 4.0, 6.5, and 9.0). The results showed that the accumulation of dry matter in root and above ground under pH 4.0 and pH 9.0 treatments was lower than that under pH 6.5 treatments, and the root/shoot ratio increased with the increase of pH value. Regardless of pH value, 'BN4199' had higher root dry weight, root length, root surface area, root activity and root tip than 'AK58'. Therefore, wheat that is tolerant to extreme pH is able to adapt to the acid-base environment by changing root characteristics. At pH 4.0, the net H+ outflow rate of wheat roots was significantly lower than that of the control group, and the net NO3- flux of wheat roots was also low. The net H+ outflow occurred at pH 6.5 and 9.0, and at the same time, the net NO3- flux of roots also increased, and both increased with the increase of pH. The activity of nitrate reductase (NR) in stem of pH 9.0 treatment was significantly higher than that of other treatments, while the activity of glutamine synthetase (GS) in root and stem of pH 6.5 treatment was significantly higher than that of other treatments. Under pH 4.0 and pH 9.0 treatments, the activities of NR and GS in 'BN4199' were higher than those in 'AK58', The root respiration of 'BN4199' was significantly higher than that of 'AK58' under pH 4.0 and pH 9.0 treatment, and 'BN4199' had higher NO3- net flux, key enzyme activity of root nitrogen metabolism and root respiration. Therefore, we believe that 'BN4199' has strong resistance ability to extreme pH stress, and high root/shoot ratio and strong root respiration can be used as important indicators for wheat variety screening adapted to the alkaline environment at the seedling stage.
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Affiliation(s)
- Chenchen Shi
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Peiyu Wang
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Guangtao Wang
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Tiezhu Hu
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Zhengang Ru
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Suwei Feng
- Henan Provincial Key Laboratory of Hybrid Wheat, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
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4
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Jia J, Zhao G, Li D, Wang K, Kong C, Deng P, Yan X, Zhang X, Lu Z, Xu S, Jiao Y, Chong K, Liu X, Cui D, Li G, Zhang Y, Du C, Wu L, Li T, Yan D, Zhan K, Chen F, Wang Z, Zhang L, Kong X, Ru Z, Wang D, Gao L. Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement. Mol Plant 2023; 16:1893-1910. [PMID: 37897037 DOI: 10.1016/j.molp.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 07/12/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.
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Affiliation(s)
- Jizeng Jia
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Wang
- Xi'An Shansheng Biosciences Co., Ltd., Xi'an 710000, China
| | - Chuizheng Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pingchuan Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 612100, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyong Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shujuan Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Chong
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dangqun Cui
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Guangwei Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chunguang Du
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Liang Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan 562000, China
| | - Tianbao Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Yan
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kehui Zhan
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Feng Chen
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Zhiyong Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhengang Ru
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China.
| | - Daowen Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Lifeng Gao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Chen X, Wu X, Zhang J, Zhang M, You J, Ru Z. Characterization of the complete mitochondrial genome of Elymus magellanicus (É.Desv.) Á.Löve (Poaceae, Pooideae). Mitochondrial DNA B Resour 2023; 8:795-798. [PMID: 37545550 PMCID: PMC10399486 DOI: 10.1080/23802359.2023.2238931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/15/2023] [Indexed: 08/08/2023] Open
Abstract
Elymus magellanicus (É.Desv.) Á.Löve is a foliage accent plant that found in South America. In this study, the mitochondrial genome of E. magellanicus was sequenced, assembled, and annotated. The complete circular mitogenome of E. magellanicus is 583,450 bp in length and the overall G + C content of mitogenome is 42.27%. It harbors 39 protein-coding genes, 64 transfer RNA genes, eight ribosomal RNA genes, and 20 simple sequence repeats. Phylogenetic analysis indicates a relatively close relationship of E. magellanicus to Hordeum vulgare subsp. Spontaneum, Aegilops speltoides, Triticum aestivum, and T. aestivum cv. Chinese Yumai.
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Affiliation(s)
- Xiangdong Chen
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, P.R. China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, P.R. China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, P.R. China
| | - Xiaojun Wu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, P.R. China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, P.R. China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, P.R. China
| | - Jinlong Zhang
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, P.R. China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, P.R. China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, P.R. China
| | - Man Zhang
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, P.R. China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, P.R. China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, P.R. China
| | - Junchao You
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, P.R. China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, P.R. China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, P.R. China
| | - Zhengang Ru
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, P.R. China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, P.R. China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, P.R. China
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Zhao J, Xie Y, Kong C, Lu Z, Jia H, Ma Z, Zhang Y, Cui D, Ru Z, Wang Y, Appels R, Jia J, Zhang X. Centromere repositioning and shifts in wheat evolution. Plant Commun 2023:100556. [PMID: 36739481 PMCID: PMC10398676 DOI: 10.1016/j.xplc.2023.100556] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/07/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms. Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat. Here, we comprehensively analyzed centromeres from the de novo-assembled common wheat cultivar Aikang58 (AK58), Chinese Spring (CS), and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing, whole-genome bisulfite sequencing, RNA sequencing, assay for transposase-accessible chromatin using sequencing, and comparative genomics. We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization. Centromeric repeats of wheat (CRWs) have undergone expansion during wheat evolution, with strong interweaving between the A and B subgenomes post tetraploidization. We found that CENH3 prefers to bind with younger CRWs, as directly supported by immunocolocalization on two chromosomes (1A and 2A) of wild emmer wheat with dicentromeric regions, only one of which bound with CENH3. In a comparison of AK58 with CS, obvious centromere repositioning was detected on chromosomes 1B, 3D, and 4D. The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels. We also found that centromeric chromatin was more open than pericentromeric chromatin, with higher levels of gene expression but lower gene density. Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome. This study also showed that active wheat centromeres were genetically and epigenetically determined.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chuizheng Kong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyan Jia
- Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Zhengqiang Ma
- Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dangqun Cui
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhengang Ru
- Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yuquan Wang
- Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Rudi Appels
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083, Australia
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China.
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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Wu X, Chen X, Huang Z, Ren C, Hu T, Ru Z. De novo assembly and characterization of the complete chloroplast genome of Elymus magellanicus (É.Desv.) Á.Löve, 1984 (Poaceae, Pooideae). Mitochondrial DNA B Resour 2022; 7:1873-1875. [PMID: 36325283 PMCID: PMC9621246 DOI: 10.1080/23802359.2022.2135400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elymus magellanicus (É.Desv.) Á.Löve is a foliage accent plant that originated in South America. In this study, the complete chloroplast genome of E. magellanicus is reported. It was found to have a total size of 133,249 bp. The chloroplast genome was found to consist of two inverted repeats (IRA and IRB) of 21,421 bp each, a small single-copy region of 12,709 bp, and a large single-copy region (77,698 bp). The annotation results show the GC content of the chloroplast genome to be 38.47%, including 40 tRNA genes, 82 protein-coding genes, and 8 rRNA genes. Phylogenetic analysis of 29 species revealed that E. magellanicus is closely related to E. arenarius.
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Affiliation(s)
- Xiaojun Wu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China,Henan Key Laboratory of Hybrid Wheat, Xinxiang, China,Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Xiangdong Chen
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China,Henan Key Laboratory of Hybrid Wheat, Xinxiang, China,Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Zhongwen Huang
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China,Henan Key Laboratory of Hybrid Wheat, Xinxiang, China,Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Cuicui Ren
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China,Henan Key Laboratory of Hybrid Wheat, Xinxiang, China,Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Tiezhu Hu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China,Henan Key Laboratory of Hybrid Wheat, Xinxiang, China,Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Zhengang Ru
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China,Henan Key Laboratory of Hybrid Wheat, Xinxiang, China,Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China,CONTACT Zhengang Ru Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, Henan, China
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8
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Wang Y, Niu Z, Hu X, Wu X, Yang Z, Hao C, Zhou M, Yang S, Dong N, Liu M, Ru Z. Molecular characterization of the genome-wide BOR transporter family and their responses to boron conditions in common wheat ( Triticum aestivum L.). Front Plant Sci 2022; 13:997915. [PMID: 36275596 PMCID: PMC9583536 DOI: 10.3389/fpls.2022.997915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Boron (B) deficiency is an agricultural problem that causes significant yield losses in many countries. B transporters (BORs) are responsible for B uptake and distribution and play important roles in yield formation. A comprehensive analysis of the BOR family members in common wheat is still lacking. In the present study, to clarify the molecular characterization and response to B status, genome-wide TaBOR genes and expression patterns were investigated. Fourteen TaBOR genes were identified in common wheat by a homology search. The corresponding phylogenetic tree indicated that 14 TaBOR genes were separately classified into subfamilies of TaBOR1, TaBOR3, and TaBOR4. All TaBOR genes had 12-14 extrons and 11-13 introns. Most TaBOR proteins contained 10 conserved motifs, and motifs 1, 2, 3, 4, and 6 constituted the conserved bicarbonate (HCO3 -) domain. Fourteen TaBOR genes were mapped on 13 chromosomes mainly distributed in the first, third, fifth, and seventh homologous groups. The promoters of TaBOR genes consisted of phytohormones, light responses, and stress-related cis-elements. GO analysis indicated that TaBOR genes were enriched in terms of transmembrane transport and ion homeostasis. TaBOR genes showed diverse expression profiles in different tissues. The members of the TaBOR1 subfamily showed high expression in grains, leaves, roots, stems, and spikes, but members of the TaBOR4 subfamily were highly expressed only in spikes and grains. RT-qPCR indicated that TaBOR1-5A, TaBOR1-5B, and TaBOR1-5D were induced by low B concentrations and had much higher expression in roots than in shoots. TaBOR3-3A, TaBOR3-3B, TaBOR3-3D, TaBOR4-1A, TaBOR4-1B, TaBOR4-1D, and TaBOR3-4B were induced by low and high B concentrations and had high expression in roots and shoots. TaBOR3-4D and TaBOR3-7B were upregulated by low and high B concentrations, respectively, but had expression only in roots. Our results provide basic information on the TaBOR family, which is beneficial for elucidating the functions of TaBOR genes to overcome the problem of B deficiency.
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Affiliation(s)
- Yuquan Wang
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Zhipeng Niu
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xigui Hu
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xiaojun Wu
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Zijun Yang
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Chenyan Hao
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Mengxue Zhou
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Shumin Yang
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Na Dong
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Mingjiu Liu
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Zhengang Ru
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, Henan, China
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
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10
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Xu X, Li X, Zhang D, Zhao J, Jiang X, Sun H, Ru Z. Identification and validation of QTLs for kernel number per spike and spike length in two founder genotypes of wheat. BMC Plant Biol 2022; 22:146. [PMID: 35346053 PMCID: PMC8962171 DOI: 10.1186/s12870-022-03544-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Kernel number per spike (KNS) and spike length (SL) are important spike-related traits in wheat variety improvement. Discovering genetic loci controlling these traits is necessary to elucidate the genetic basis of wheat yield traits and is very important for marker-assisted selection breeding. RESULTS In the present study, we used a recombinant inbred line population with 248 lines derived from the two founder genotypes of wheat, Bima4 and BainongAK58, to construct a high-density genetic map using wheat 55 K genotyping assay. The final genetic linkage map consists of 2356 bin markers (14,812 SNPs) representing all 21 wheat chromosomes, and the entire map spanned 4141.24 cM. A total of 7 and 18 QTLs were identified for KNS and SL, respectively, and they were distributed on 11 chromosomes. The allele effects of the flanking markers for 12 stable QTLs, including four QTLs for KNS and eight QTLs for SL, were estimated based on phenotyping data collected from 15 environments in a diverse wheat panel including 384 elite cultivars and breeding lines. The positive alleles at seven loci, namely, QKns.his-7D2-1, QKns.his-7D2-2, QSl.his-4A-1, QSl.his-5D1, QSl.his-4D2-2, QSl.his-5B and QSl.his-5A-2, significantly increased KNS or SL in the diverse panel, suggesting they are more universal in their effects and are valuable for gene pyramiding in breeding programs. The transmission of Bima4 allele indicated that the favorite alleles at five loci (QKns.his-7D2-1, QSl.his-5A-2, QSl.his-2D1-1, QSl.his-3A-2 and QSl.his-3B) showed a relatively high frequency or an upward trend following the continuity of generations, suggesting that they underwent rigorous selection during breeding. At two loci (QKns.his-7D2-1 and QSl.his-5A-2) that the positive effects of the Bima4 alleles have been validated in the diverse panel, two and one kompetitive allele-specific PCR (KASP) markers were further developed, respectively, and they are valuable for marker-assisted selection breeding. CONCLUSION Important chromosome regions controlling KNS and SL were identified in the founder parents. Our results are useful for knowing the molecular mechanisms of founder parents and future molecular breeding in wheat.
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Affiliation(s)
- Xin Xu
- School of Life Sciences and Basic Medicine, Xinxiang University, Xinxiang, 453003, China
| | - Xiaojun Li
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China.
| | - Dehua Zhang
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jishun Zhao
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xiaoling Jiang
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Haili Sun
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Zhengang Ru
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China.
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Wu X, Hu X, Chen X, Zhang J, Ren C, Song L, Fang F, Dong N, Hu T, Ru Z. Sequencing and characterization of the complete mitochondrial genome of Thinopyrum obtusiflorum (DC.) Banfi, 2018 (Poaceae). Mitochondrial DNA B Resour 2022; 7:539-540. [PMID: 35356795 PMCID: PMC8959512 DOI: 10.1080/23802359.2022.2054378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In this study, the mitochondrial genome of Thinopyrum obtusiflorum was sequenced, assembled, and annotated. The complete circular mitogenome of Th. obtusiflorum is 390,725 bp in length and the overall A + T content of mitogenome is 55.61%. It harbors 33 protein-coding genes (PCGs), 21 transfer RNA genes (tRNAs), six ribosomal RNA genes (rRNAs), and 20 simple sequence repeats (SSRs). Phylogenetic analysis indicates that Th. obtusiflorum is a sister to the clade including Aegilops speltoides, Triticum aestivum, and Triticum aestivum cultivar Chinese Yumai in the Triticeae.
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Affiliation(s)
- Xiaojun Wu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Xigui Hu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Xiangdong Chen
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Jinlong Zhang
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Cuicui Ren
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Lintong Song
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Fang Fang
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Na Dong
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Tiezhu Hu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Zhengang Ru
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
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12
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Wang Z, Zhao G, Yang Q, Gao L, Liu C, Ru Z, Wang D, Jia J, Cui D. Helitron and CACTA DNA transposons actively reshape the common bread wheat - AK58 genome. Genomics 2022; 114:110288. [DOI: 10.1016/j.ygeno.2022.110288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 12/01/2021] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
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Song P, Zhang L, Wu L, Hu H, Liu Q, Li D, Hu P, Zhou F, Bu R, Wei Q, Yu Y, Guan Y, Chen E, Su X, Huang Z, Qiao M, Ru Z, Li C. A Ricin B-Like Lectin Protein Physically Interacts with TaPFT and Is Involved in Resistance to Fusarium Head Blight in Wheat. Phytopathology 2021; 111:2309-2316. [PMID: 34058858 DOI: 10.1094/phyto-11-20-0506-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fusarium head blight (FHB), mainly caused by Fusarium graminearum, has become one of the most serious diseases that damage wheat. The TaPFT (pore-forming toxin-like) and TaHRC (histidine-rich calcium-binding protein) genes at the quantitative trait locus Fhb1 were identified to confer resistance to FHB in the wheat cultivar Sumai 3. In this study, a wheat ricin B-like lectin gene (designated TaRBL) that interacted with TaPFT was isolated by a yeast two-hybrid screen of a wheat cDNA library. A yeast two-hybrid and bimolecular fluorescence complementation study further verified that TaRBL interacted with TaPFT but not with TaHRC. Gene expression studies showed that upon F. graminearum infection, TaRBL expression was upregulated in resistant cultivars but downregulated in susceptible cultivars. Furthermore, knockdown of TaRBL expression by barley stripe mosaic virus-induced gene silencing significantly reduced the resistance of wheat to FHB in both the resistant cultivar Sumai 3 and the susceptible cultivar Jimai 22. Thus, we conclude that TaRBL encodes a ricin B-like lectin protein that interacts with TaPFT and is involved in resistance to FHB in wheat.
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Affiliation(s)
- Puwen Song
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Lufan Zhang
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Liuliu Wu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Haiyan Hu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Qili Liu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Dongxiao Li
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ping Hu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Feng Zhou
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ruifang Bu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Qichao Wei
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yongang Yu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yuanyuan Guan
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Eryong Chen
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiaojia Su
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zhongwen Huang
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Mei Qiao
- College of Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Zhengang Ru
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Chengwei Li
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
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Jia J, Xie Y, Cheng J, Kong C, Wang M, Gao L, Zhao F, Guo J, Wang K, Li G, Cui D, Hu T, Zhao G, Wang D, Ru Z, Zhang Y. Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression. Genome Biol 2021; 22:26. [PMID: 33419466 PMCID: PMC7792079 DOI: 10.1186/s13059-020-02225-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. RESULTS We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely cultivated allohexaploid wheat variety in China carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity. CONCLUSIONS The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.
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Affiliation(s)
- Jizeng Jia
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, Henan, China.
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingfei Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuizheng Kong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meiyue Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Lifeng Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fei Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyu Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- Henan University, School of Life Science, Kaifeng, 457000, Henan, China
| | - Kai Wang
- Novogene Co. Ltd, Building 301, Jiuxianqiao North Road, Chaoyang District, Beijing, China
| | - Guangwei Li
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, Henan, China
| | - Dangqun Cui
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, Henan, China
| | - Tiezhu Hu
- Henan Institute of Science and Technology, Eastern Hualan Avenue, Xinxiang City, 453003, Henan Province, China
| | - Guangyao Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Daowen Wang
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, Henan, China.
| | - Zhengang Ru
- Henan Institute of Science and Technology, Eastern Hualan Avenue, Xinxiang City, 453003, Henan Province, China.
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
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15
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Li X, Xu X, Liu W, Li X, Yang X, Ru Z, Li L. Dissection of Superior Alleles for Yield-Related Traits and Their Distribution in Important Cultivars of Wheat by Association Mapping. Front Plant Sci 2020; 11:175. [PMID: 32194592 PMCID: PMC7061769 DOI: 10.3389/fpls.2020.00175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/05/2020] [Indexed: 05/18/2023]
Abstract
Uncovering the genetic basis of yield-related traits is important for molecular improvement of wheat cultivars. In this study, a genome-wide association study was conducted using the wheat 55K genotyping assay and a diverse panel of 384 wheat genotypes. The accessions used included 18 founder parents and 15 widely grown cultivars with annual maximum acreages of over 667,000 ha, and the remaining materials were elite cultivars and breeding lines from several major wheat ecological areas of China. Field trials were conducted in five major wheat ecological regions of China over three consecutive years. A total of 460 significant loci were detected for eight yield-related traits. Forty-five superior alleles distributed over 31 loci for which differences in phenotypic values grouped by single nucleotide polymorphism (SNP) reached significant levels (P < 0.05) in nine or more environments, were detected; some of these loci were previously reported. Eleven of the 31 superior allele loci on chromosomes 4A, 5A, 3B, 5B, 6B, 7B, 5D, and 7D had pleiotropic effects. For example, AX-95152512 on 5D was simultaneously related to increased grain weight per spike (GWS) and decreased plant height (PH); AX-109860828 on 5B simultaneously led to a high 1,000-kernel weight (TKW) and short PH; and AX-111600193 on 4A was simultaneously linked to a high TKW and GWS, and short PH. The favorable alleles in each accession ranged from 2 to 30 with an average of 16 at the thirty-one loci in the population, and six accessions (Zhengzhou683, Suzhou7829, Longchun7, Ningmai6, Yunmai35 and Zhen7630) contained more than 27 favorable alleles. A significant association between the number of favorable alleles and yield was observed (r = 0.799, p < 0.0001), suggesting that pyramiding multiple QTL with marker-assisted selection may effectively increase yield of wheat. Furthermore, distribution of superior alleles in founder parents and widely grown cultivars was also discussed here. This study is useful for marker-assisted selection for yield improvement and dissecting the genetic mechanism of important cultivars in wheat.
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Affiliation(s)
- Xiaojun Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Provincial Key Laboratory of Hybrid Wheat, Xinxiang, China
| | - Xin Xu
- Department of Life Sciences and Technology, Xinxiang University, Xinxiang, China
| | - Weihua Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinming Yang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengang Ru
- School of Life Science and Technology, Henan Institute of Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Provincial Key Laboratory of Hybrid Wheat, Xinxiang, China
| | - Lihui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Guan Y, Li G, Chu Z, Ru Z, Jiang X, Wen Z, Zhang G, Wang Y, Zhang Y, Wei W. Transcriptome analysis reveals important candidate genes involved in grain-size formation at the stage of grain enlargement in common wheat cultivar "Bainong 4199". PLoS One 2019; 14:e0214149. [PMID: 30908531 PMCID: PMC6433227 DOI: 10.1371/journal.pone.0214149] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/07/2019] [Indexed: 12/19/2022] Open
Abstract
Grain-size is one of the yield components, and the first 14 days after pollination (DAP) is a crucial stage for wheat grain-size formation. To understand the mechanism of grain-size formation at the whole gene expression level and to identify the candidate genes related to grain pattern formation, cDNA libraries from immature grains of 5 DAP and 14 DAP were constructed. According to transcriptome analysis, a total of 12,555 new genes and 9,358 differentially expressed genes (DEGs) were obtained. In DEGs, 2,876, 3,357 and 3,125 genes were located on A, B and D subgenome respectively. 9,937 (79.15%) new genes and 9,059 (96.80%) DEGs were successfully annotated. For DEGs, 4,453 were up-regulated and 4,905 were down-regulated at 14 DAP. The Gene Ontology (GO) database indicated that most of the grain-size-related genes were in the same cluster. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis showed that 130, 129 and 20 DEGs were respectively involved in starch and sucrose metabolism, plant hormone signal transduction and ubiquitin-mediated proteolysis. Expression levels of 8 randomly selected genes were confirmed by qRT-PCR, which was consistent with the transcriptome data. The present database will help us understand the molecular mechanisms underlying early grain development and provide the foundation for increasing grain-size and yield in wheat breeding programs.
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Affiliation(s)
- Yuanyuan Guan
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Gan Li
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Zongli Chu
- Xinyang Agriculture and Forestry University, Xinyang, China
| | - Zhengang Ru
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Xiaoling Jiang
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Zhaopu Wen
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Guang Zhang
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Yuquan Wang
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Yang Zhang
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Wenhui Wei
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
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17
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Keeble-Gagnère G, Rigault P, Tibbits J, Pasam R, Hayden M, Forrest K, Frenkel Z, Korol A, Huang BE, Cavanagh C, Taylor J, Abrouk M, Sharpe A, Konkin D, Sourdille P, Darrier B, Choulet F, Bernard A, Rochfort S, Dimech A, Watson-Haigh N, Baumann U, Eckermann P, Fleury D, Juhasz A, Boisvert S, Nolin MA, Doležel J, Šimková H, Toegelová H, Šafář J, Luo MC, Câmara F, Pfeifer M, Isdale D, Nyström-Persson J, IWGSC, Koo DH, Tinning M, Cui D, Ru Z, Appels R. Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. Genome Biol 2018; 19:112. [PMID: 30115128 PMCID: PMC6097218 DOI: 10.1186/s13059-018-1475-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 07/09/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. RESULTS Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. CONCLUSIONS Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
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Affiliation(s)
- Gabriel Keeble-Gagnère
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Philippe Rigault
- GYDLE, 1135 Grande Allée Ouest, Suite 220, Québec, QC G1S 1E7 Canada
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Josquin Tibbits
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Raj Pasam
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Matthew Hayden
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - B. Emma Huang
- CSIRO-Plant Industry, Black Mountain, Canberra, ACT 2601 Australia
| | - Colin Cavanagh
- CSIRO-Plant Industry, Black Mountain, Canberra, ACT 2601 Australia
| | - Jen Taylor
- CSIRO-Plant Industry, Black Mountain, Canberra, ACT 2601 Australia
| | - Michael Abrouk
- King Abdullah University of Science and Technology, Desert Agriculture Initiative, Thuwal, Saudi Arabia
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Andrew Sharpe
- Global Institute of Food Security, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK Canada
| | - David Konkin
- National Research Council of Canada, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK Canada
| | - Pierre Sourdille
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Benoît Darrier
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Frédéric Choulet
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Aurélien Bernard
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Simone Rochfort
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Adam Dimech
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Nathan Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Paul Eckermann
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Delphine Fleury
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Angela Juhasz
- Veterinary and Agriculture, Murdoch University, 90 South St, Murdoch, Western Australia 6150 Australia
| | | | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Ming-Cheng Luo
- UC Davis Plant Sciences, Plant Genetics and Bioinformatics, 258A Hunt Hall, Davis, CA 95616 USA
| | - Francisco Câmara
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), 88 Dr. Aiguader, 08003 Barcelona, Spain
| | - Matthias Pfeifer
- Plant Genome and Systems Biology, Helmholtz Center, Munich, 85764 Neuherberg, Germany
| | - Don Isdale
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Johan Nyström-Persson
- Level Five Co. Ltd. GYB Akihabara, Kanda-Sudacho 2-25, Chiyoda-ku, Tokyo, 101-0041 Japan
| | - IWGSC
- International Wheat Genome Sequencing Consortium, 2841 NE Marywood Ct, Lee’s Summit, MO 64086 USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Matthew Tinning
- Australian Genome Research Facility, Suite 219, 55 Flemington Road, North Melbourne, VIC 3051 Australia
| | - Dangqun Cui
- Henan Agricultural University, Zhengzhou, China
| | - Zhengang Ru
- Henan Institute of Science and Technology, Zhengzhou, China
| | - Rudi Appels
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
- Veterinary and Agriculture, Murdoch University, 90 South St, Murdoch, Western Australia 6150 Australia
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Hu H, He J, Zhao J, Ou X, Li H, Ru Z. Low pH stress responsive transcriptome of seedling roots in wheat (Triticum aestivum L.). Genes Genomics 2018; 40:1199-1211. [PMID: 30315523 DOI: 10.1007/s13258-018-0680-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/28/2018] [Indexed: 12/22/2022]
Abstract
Soil acidification is one of major problems limiting crop growth and especially becoming increasingly serious in China owing to excessive use of nitrogen fertilizer. Only the STOP1 of Arabidopsis was identified clearly sensitive to proton rhizotoxicity and the molecular mechanism for proton toxicity tolerance of plants is still poorly understood. The main objective of this study was to investigate the transcriptomic change in plants under the low pH stress. The low pH as a single factor was employed to induce the response of the wheat seedling roots. Wheat cDNA microarray was used to identify differentially expressed genes (DEGs). A total of 1057 DEGs were identified, of which 761 genes were up-regulated and 296 were down-regulated. The greater percentage of up-regulated genes involved in developmental processes, immune system processes, multi-organism processes, positive regulation of biological processes and metabolic processes of the biological processes. The more proportion of down-regulation genes belong to the molecular function category including transporter activity, antioxidant activity and molecular transducer activity and to the extracellular region of the cellular components category. Moreover, most genes among 41 genes involved in ion binding, 17 WAKY transcription factor genes and 17 genes related to transport activity were up-regulated. KEGG analysis showed that the jasmonate signal transduction and flavonoid biosynthesis might play important roles in response to the low pH stress in wheat seedling roots. Based on the data, it is can be deduced that WRKY transcription factors might play a critical role in the transcriptional regulation, and the alkalifying of the rhizosphere might be the earliest response process to low pH stress in wheat seedling roots. These results provide a basis to reveal the molecular mechanism of proton toxicity tolerance in plants.
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Affiliation(s)
- Haiyan Hu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China.
- Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, Henan, China.
- Henan Engineering Research Center of Crop Genome Editing, Xinxiang, 453003, Henan, China.
| | - Jie He
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Junjie Zhao
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Xingqi Ou
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
- Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, Henan, China
| | - Hongmin Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
- Henan Engineering Research Center of Crop Genome Editing, Xinxiang, 453003, Henan, China
| | - Zhengang Ru
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China.
- Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, Henan, China.
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Li X, Jiang X, Chen X, Song J, Ren C, Xiao Y, Gao X, Ru Z. Molecular cytogenetic identification of a novel wheat-Agropyron elongatum chromosome translocation line with powdery mildew resistance. PLoS One 2017; 12:e0184462. [PMID: 28886152 PMCID: PMC5590951 DOI: 10.1371/journal.pone.0184462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/24/2017] [Indexed: 11/27/2022] Open
Abstract
Agropyron elongatum (Host.) Neviski (synonym, Thinopyrum ponticum Podp., 2n = 70) has been used extensively as a valuable source for wheat breeding. Numerous chromosome fragments containing valuable genes have been successfully translocated into wheat from A. elongatum. However, reports on the transfer of powdery mildew resistance from A. elongatum to wheat are rare. In this study, a novel wheat-A. elongatum translocation line, 11-20-1, developed and selected from the progenies of a sequential cross between wheat varieties (Lankaoaizaoba, Keyu 818 and BainongAK 58) and A. elongatum, was evaluated for disease resistance and characterized using molecular cytogenetic methods. Cytological observations indicated that 11-20-1 had 42 chromosomes and formed 21 bivalents at meiotic metaphase I. Genomic in situ hybridization analysis using whole genomic DNA from A. elongatum as a probe showed that the short arms of a pair of wheat chromosomes were replaced by a pair of A. elongatum chromosome arms. Fluorescence in situ hybridization, using wheat D chromosome specific sequence pAs1 as a probe, suggested that the replaced chromosome arms of 11-20-1 were 5DS. This was further confirmed by wheat SSR markers specific for 5DS. EST-SSR and EST-STS multiple loci markers confirmed that the introduced A. elongatum chromosome arms belonged to homoeologous group 5. Therefore, it was deduced that 11-20-1 was a wheat-A. elongatum T5DL∙5AgS translocation line. Both resistance observation and molecular marker analyses using two specific markers (BE443538 and CD452608) of A. elongatum in a F2 population from a cross between line 11-20-1 and a susceptible cultivar Yannong 19 verified that the A. elongatum chromosomes were responsible for the powdery mildew resistance. This work suggests that 11-20-1 likely contains a novel resistance gene against powdery mildew. We expect this line to be useful for the genetic improvement of wheat.
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Affiliation(s)
- Xiaojun Li
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xiaoling Jiang
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xiangdong Chen
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Jie Song
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Cuicui Ren
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Yajuan Xiao
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xiaohui Gao
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Zhengang Ru
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, Henan, China
- * E-mail:
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20
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Gao Q, Xue X, Wu Y, Ru Z. [Effects of sowing times on the spike differentiation of different wheat varieties under the climate of warm winter]. Ying Yong Sheng Tai Xue Bao 2003; 14:1627-31. [PMID: 14986353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Spike differentiation processes and freezing damage of three wheat varieties were studied by sowing in different stages. The results showed that under the condition of weather changing warm, the time of entering each stage of spike differentiation of wheat of strong spring variety was earlier than that of wheat of spring variety and semi-winter variety. Sowing times had more effects on durative time of the elongation stage, single-prism stage and two-prism stage of the spike differentiation. Under sowing early, the stronger the springness of wheat was, the quicker it developed, the higher spike differentiation phases it reached before winter, and the more serious freezing damage it suffered in wintering. According to this, the semi-winter varieties of wheat should be adopted first and arranged in pairs with spring varieties in wheat production, and the sowing times should not be too early as the weather becoming warm.
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Affiliation(s)
- Qinglu Gao
- Henan Vocational Technical Teachers' College, Xinxiang 453003, China.
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