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Shu F, Wang D, Sarsaiya S, Jin L, Liu K, Zhao M, Wang X, Yao Z, Chen G, Chen J. Bulbil initiation: a comprehensive review on resources, development, and utilisation, with emphasis on molecular mechanisms, advanced technologies, and future prospects. FRONTIERS IN PLANT SCIENCE 2024; 15:1343222. [PMID: 38650701 PMCID: PMC11033377 DOI: 10.3389/fpls.2024.1343222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/14/2024] [Indexed: 04/25/2024]
Abstract
Bulbil is an important asexual reproductive structure of bulbil plants. It mainly grows in leaf axils, leaf forks, tubers and the upper and near ground ends of flower stems of plants. They play a significant role in the reproduction of numerous herbaceous plant species by serving as agents of plant propagation, energy reserves, and survival mechanisms in adverse environmental conditions. Despite extensive research on bulbil-plants regarding their resources, development mechanisms, and utilisation, a comprehensive review of bulbil is lacking, hindering progress in exploiting bulbil resources. This paper provides a systematic overview of bulbil research, including bulbil-plant resources, identification of development stages and maturity of bulbils, cellular and molecular mechanisms of bulbil development, factors influencing bulbil development, gene research related to bulbil development, multi-bulbil phenomenon and its significance, medicinal value of bulbils, breeding value of bulbils, and the application of plant tissue culture technology in bulbil production. The application value of the Temporary Immersion Bioreactor System (TIBS) and Terahertz (THz) in bulbil breeding is also discussed, offering a comprehensive blueprint for further bulbil resource development. Additionally, additive, seven areas that require attention are proposed: (1) Utilization of modern network technologies, such as plant recognition apps or websites, to collect and identify bulbous plant resources efficiently and extensively; (2) Further research on cell and tissue structures that influence bulb cell development; (3) Investigation of the network regulatory relationship between genes, proteins, metabolites, and epigenetics in bulbil development; (4) Exploration of the potential utilization value of multiple sprouts, including medicinal, ecological, and horticultural applications; (5) Innovation and optimization of the plant tissue culture system for bulbils; (6) Comprehensive application research of TIBS for large-scale expansion of bulbil production; (7) To find out the common share genetics between bulbils and flowers.
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Affiliation(s)
- Fuxing Shu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
- School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Dongdong Wang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Surendra Sarsaiya
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
| | - Leilei Jin
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Kai Liu
- Bozhou Xinghe Agricultural Development Co., Ltd., Bozhou, Anhui, China
- Joint Research Center for Chinese Herbal Medicine of Anhui of Institution of Health and Medicine, Bozhou, Anhui Provence, China
| | - Mengru Zhao
- Bozhou Xinghe Agricultural Development Co., Ltd., Bozhou, Anhui, China
| | - Xin Wang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Zhaoxu Yao
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
| | - Guoguang Chen
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu, China
- School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Jishuang Chen
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
- School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
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Mehdi F, Galani S, Wickramasinghe KP, Zhao P, Lu X, Lin X, Xu C, Liu H, Li X, Liu X. Current perspectives on the regulatory mechanisms of sucrose accumulation in sugarcane. Heliyon 2024; 10:e27277. [PMID: 38463882 PMCID: PMC10923725 DOI: 10.1016/j.heliyon.2024.e27277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/12/2024] Open
Abstract
Sugars transported from leaves (source) to stems (sink) energize cell growth, elongation, and maintenance. which are regulated by a variety of genes. This review reflects progress and prospects in the regulatory mechanism for maximum sucrose accumulation, including the role of sucrose metabolizing enzymes, sugar transporters and the elucidation of post-transcriptional control of sucrose-induced regulation of translation (SIRT) in the accumulation of sucrose. The current review suggests that SIRT is emerging as a significant mechanism controlling Scbzip44 activities in response to endogenous sugar signals (via the negative feedback mechanism). Sucrose-controlled upstream open reading frame (SC-uORF) exists at the 5' leader region of Scbzip44's main ORF, which inhibits sucrose accumulation through post-transcriptional regulatory mechanisms. Sucrose transporters (SWEET1a/4a/4b/13c, TST, SUT1, SUT4 and SUT5) are crucial for sucrose translocation from source to sink. Particularly, SWEET13c was found to be a major contributor to the efflux in the transportation of stems. Tonoplast sugar transporters (TSTs), which import sucrose into the vacuole, suggest their tissue-specific role from source to sink. Sucrose cleavage has generally been linked with invertase isozymes, whereas sucrose synthase (SuSy)-catalyzed metabolism has been associated with biosynthetic processes such as UDP-Glc, cellulose, hemicellulose and other polymers. However, other two key sucrose-metabolizing enzymes, such as sucrose-6-phosphate phosphohydrolase (S6PP) and sucrose phosphate synthase (SPS) isoforms, have been linked with sucrose biosynthesis. These findings suggest that manipulation of genes, such as overexpression of SPS genes and sucrose transporter genes, silencing of the SC-uORF of Scbzip44 (removing the 5' leader region of the main ORF that is called SIRT-Insensitive) and downregulation of the invertase genes, may lead to maximum sucrose accumulation. This review provides an overview of sugarcane sucrose-regulating systems and baseline information for the development of cultivars with higher sucrose accumulation.
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Affiliation(s)
- Faisal Mehdi
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Saddia Galani
- Dr.A. Q. Khan Institute of Biotechnology and Genetic Engineering, University of Karachi, Karachi Pakistan
| | - Kamal Priyananda Wickramasinghe
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
- Sugarcane Research Institute, Uda Walawa, 70190, Sri Lanka
| | - Peifang Zhao
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Xin Lu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Xiuqin Lin
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Chaohua Xu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Hongbo Liu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Xujuan Li
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
| | - Xinlong Liu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699, China
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Xing X, Cao C, Li S, Wang H, Xu Z, Qi Y, Tong F, Jiang H, Wang X. α-naphthaleneacetic acid positively regulates soybean seed germination and seedling establishment by increasing antioxidant capacity, triacylglycerol mobilization and sucrose transport under drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107890. [PMID: 37454467 DOI: 10.1016/j.plaphy.2023.107890] [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: 03/20/2023] [Revised: 06/15/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
Drought stress is an important constraint for the germination of soybean (Glycine max [L.] Merr.) seeds and seedling establishment. A pot experiment was conducted to determine the effects of priming soybean seeds with 5 μM α-naphthaleneacetic acid (NAA) and the mechanism responsible for the induced tolerance of drought stress (soil relative water content of 55%). NAA priming inhibited drought-induced oxidative damage in seeds, and further analysis indicated that it induced an early spike in hydrogen peroxide content by the upregulation of abscisic acid-dependent GmRbohC2, resulting in an enhancement of antioxidant capacity. Moreover, NAA priming also improved the hydrolysis of triacylglycerol (TAG) to sucrose in stressed cotyledons by causing a 2- to 5-fold increase in the transcript levels of GmSDP1, GmACX2, GmMFP2, GmICL, GmMLS, GmGLI1, GmPCK1, GmFBPase1, GmSPS1 and GmSPS2. Consistently, it upregulated the expression levels of GmSUT1, GmCWINV1 and GmMST2 under drought stress, thus enhancing the transport of sucrose from cotyledons to embryonic axes, providing carbon skeletons and energy for axis growth. The seed germination percentage increased by 208.1% at 21 h after sowing, and seedling establishment percentage increased by 47.8% at 14 days after sowing. Collectively, the positive effects of NAA priming on seed germination and seedling establishment can be attributed to enhanced antioxidant ability in seeds, TAG mobilization in cotyledons and sucrose transport from cotyledons to embryonic axes under drought stress.
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Affiliation(s)
- Xinghua Xing
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Chunxin Cao
- Jinhua Academy of Agricultural Sciences, Jinhua, 321017, China
| | - Simeng Li
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Haorang Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Zejun Xu
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Yujun Qi
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Fei Tong
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Haidong Jiang
- Key Laboratory of Crop Physiology and Ecology in Southern China, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xing Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China.
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Wang T, Wang B, Hua X, Tang H, Zhang Z, Gao R, Qi Y, Zhang Q, Wang G, Yu Z, Huang Y, Zhang Z, Mei J, Wang Y, Zhang Y, Li Y, Meng X, Wang Y, Pan H, Chen S, Li Z, Shi H, Liu X, Deng Z, Chen B, Zhang M, Gu L, Wang J, Ming R, Yao W, Zhang J. A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus. NATURE PLANTS 2023; 9:554-571. [PMID: 36997685 DOI: 10.1038/s41477-023-01378-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
A diploid genome in the Saccharum complex facilitates our understanding of evolution in the highly polyploid Saccharum genus. Here we have generated a complete, gap-free genome assembly of Erianthus rufipilus, a diploid species within the Saccharum complex. The complete assembly revealed that centromere satellite homogenization was accompanied by the insertions of Gypsy retrotransposons, which drove centromere diversification. An overall low rate of gene transcription was observed in the palaeo-duplicated chromosome EruChr05 similar to other grasses, which might be regulated by methylation patterns mediated by homologous 24 nt small RNAs, and potentially mediating the functions of many nucleotide-binding site genes. Sequencing data for 211 accessions in the Saccharum complex indicated that Saccharum probably originated in the trans-Himalayan region from a diploid ancestor (x = 10) around 1.9-2.5 million years ago. Our study provides new insights into the origin and evolution of Saccharum and accelerates translational research in cereal genetics and genomics.
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Affiliation(s)
- Tianyou Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baiyu Wang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Xiuting Hua
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ruiting Gao
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yiying Qi
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng, China
| | - Zehuai Yu
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yongji Huang
- Institute of Oceanography, Marine Biotechnology Center, Minjiang University, Fuzhou, China
| | - Zhe Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Mei
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhao Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yixing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yihan Li
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Xue Meng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongjun Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haoran Pan
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuqi Chen
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Li
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihong Shi
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinlong Liu
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianping Wang
- Department of Agronomy, University of Florida, Gainesville, FL, USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
| | - Jisen Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
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Liu H, Lin X, Li X, Luo Z, Lu X, You Q, Yang X, Xu C, Liu X, Liu J, Wu C, Wang J. Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content. BMC Genomics 2023; 24:42. [PMID: 36698074 PMCID: PMC9875459 DOI: 10.1186/s12864-023-09139-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Sucrose phosphate synthase B (SPSB) gene encoding an important rate-limiting enzyme for sucrose synthesis in sugarcane is mainly expressed on leaves, where its alleles control sucrose synthesis. In this study, genetic variation of SPSB gene represented by different haplotypes in sugarcane was investigated in hybrid clones with high and low sugar content and various accessory species. RESULTS A total of 39 haplotypes of SPSB gene with 2, 824 bp in size were identified from 18 sugarcane accessions. These haplotypes mainly distributed on Chr3B, Chr3C, and Chr3D according to the AP85-441 reference genome. Single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels) were very dense (42 bp/sequence variation) including 44 transitional and 23 transversional SNPs among the 39 haplotypes. The sequence diversity related Hd, Eta, and Pi values were all lower in clones of high sucrose content (HS) than those in clones of low sucrose content (LS). The evolutionary network analysis showed that about half SPSB haplotypes (19 out of 39) were clustered into one group, including 6 (HAP4, HAP6, HAP7, HAP9, HAP17 and HAP20) haplotypes under positive selection in comparison to HAP26 identified in Badila (S. officinarum), an ancestry noble cane species and under purification selection (except HAP19 under neutral selection) in comparison to HAP18 identified from India1 (S. spontaneum), an ancestry species with low sugar content but high stress tolerance. The average number of haplotypes under positive selection in HS clones was twice as that in LS. Most of the SNPs and InDels sequence variation sites were positively correlated with sucrose and fiber content and negatively correlated with reducing sugar. CONCLUSIONS A total of 39 haplotypes of SPSB gene were identified in this study. Haplotypes potentially associated with high sucrose synthesis efficiency were identified. The mutations of SPSB haplotypes in HS were favorable and tended to be selected and fixed. The results of this study are informative and beneficial to the molecular assisted breeding of sucrose synthesis in sugarcane in the future.
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Affiliation(s)
- Hongbo Liu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699 China ,grid.15276.370000 0004 1936 8091Agronomy Department, University of Florida, Gainesville, FL 32610 USA ,grid.15276.370000 0004 1936 8091Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, FL 32610 USA ,grid.256609.e0000 0001 2254 5798Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Guangxi 530004 Kaiyuan, China
| | - Xiuqin Lin
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699 China
| | - Xujuan Li
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699 China
| | - Ziliang Luo
- grid.15276.370000 0004 1936 8091Agronomy Department, University of Florida, Gainesville, FL 32610 USA ,grid.15276.370000 0004 1936 8091Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, FL 32610 USA
| | - Xin Lu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699 China
| | - Qian You
- grid.15276.370000 0004 1936 8091Agronomy Department, University of Florida, Gainesville, FL 32610 USA
| | - Xiping Yang
- grid.15276.370000 0004 1936 8091Agronomy Department, University of Florida, Gainesville, FL 32610 USA ,grid.256609.e0000 0001 2254 5798Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Guangxi 530004 Kaiyuan, China
| | - Chaohua Xu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699 China
| | - Xinlong Liu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699 China
| | - Jiayong Liu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699 China
| | - Caiwen Wu
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan 661699 China
| | - Jianping Wang
- grid.15276.370000 0004 1936 8091Agronomy Department, University of Florida, Gainesville, FL 32610 USA ,grid.15276.370000 0004 1936 8091Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, FL 32610 USA
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Wu Z, Chen X, Fu D, Zeng Q, Gao X, Zhang N, Wu J. Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum. BMC PLANT BIOLOGY 2022; 22:510. [PMID: 36319957 PMCID: PMC9628180 DOI: 10.1186/s12870-022-03891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Growth regulating factors (GRFs) are transcription factors that regulate diverse biological and physiological processes in plants, including growth, development, and abiotic stress. Although GRF family genes have been studied in a variety of plant species, knowledge about the identification and expression patterns of GRFs in sugarcane (Saccharum spp.) is still lacking. RESULTS In the present study, a comprehensive analysis was conducted in the genome of wild sugarcane (Saccharum spontaneum) and 10 SsGRF genes were identified and characterized. The phylogenetic relationship, gene structure, and expression profiling of these genes were analyzed entirely under both regular growth and low-nitrogen stress conditions. Phylogenetic analysis suggested that the 10 SsGRF members were categorized into six clusters. Gene structure analysis indicated that the SsGRF members in the same group were greatly conserved. Expression profiling demonstrated that most SsGRF genes were extremely expressed in immature tissues, implying their critical roles in sugarcane growth and development. Expression analysis based on transcriptome data and real-time quantitative PCR verification revealed that GRF1 and GRF3 were distinctly differentially expressed in response to low-nitrogen stress, which meant that they were additional participated in sugarcane stress tolerance. CONCLUSION Our study provides a scientific basis for the potential functional prediction of SsGRF and will be further scrutinized by examining their regulatory network in sugarcane development and abiotic stress response, and ultimately facilitating their application in cultivated sugarcane breeding.
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Affiliation(s)
- Zilin Wu
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Xinglong Chen
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Danwen Fu
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Qiaoying Zeng
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Xiaoning Gao
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
- Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 524300, Zhanjiang, Guangdong, China
| | - Nannan Zhang
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China.
| | - Jiayun Wu
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China.
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Hua X, Shen Q, Li Y, Zhou D, Zhang Z, Akbar S, Wang Z, Zhang J. Functional characterization and analysis of transcriptional regulation of sugar transporter SWEET13c in sugarcane Saccharum spontaneum. BMC PLANT BIOLOGY 2022; 22:363. [PMID: 35869432 PMCID: PMC9308298 DOI: 10.1186/s12870-022-03749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Sugarcane is an important crop for sugar production worldwide. The Sugars Will Eventually be Exported Transporters (SWEETs) are a group of sugar transporters recently identified in sugarcane. In Saccharum spontaneum, SsSWEET13c played a role in the sucrose transportation from the source to the sink tissues, which was found to be mainly active in the mature leaf. However, the function and regulation of SWEETs in sugarcane remain elusive despite extensive studies performed on sugar metabolism. RESULTS In this study, we showed that SsSWEET13c is a member of SWEET gene family in S. spontaneum, constituting highest circadian rhythm-dependent expression. It is a functional gene that facilitates plant root elongation and increase fresh weight of Arabidopsis thaliana, when overexpressed. Furthermore, yeast one-hybrid assays indicate that 20 potential transcription factors (TFs) could bind to the SsSWEET13c promoter in S. spontaneum. We combined transcriptome data from developmental gradient leaf with distinct times during circadian cycles and stems/leaves at different growth stages. We have uncovered that 14 out of 20 TFs exhibited positive/negative gene expression patterns relative to SsSWEET13c. In the source tissues, SsSWEET13c was mainly positively regulated by SsbHLH34, SsTFIIIA-a, SsMYR2, SsRAP2.4 and SsbHLH035, while negatively regulated by SsABS5, SsTFIIIA-b and SsERF4. During the circadian rhythm, it was noticed that SsSWEET13c was more active in the morning than in the afternoon. It was likely due to the high level of sugar accumulation at night, which was negatively regulated by SsbZIP44, and positively regulated by SsbHLH34. Furthermore, in the sink tissues, SsSWEET13c was also active for sugar accumulation, which was positively regulated by SsbZIP44, SsTFIIIA-b, SsbHLH34 and SsTFIIIA-a, and negatively regulated by SsERF4, SsHB36, SsDEL1 and SsABS5. Our results were further supported by one-to-one yeast hybridization assay which verified that 12 potential TFs could bind to the promoter of SsSWEET13c. CONCLUSIONS A module of the regulatory network was proposed for the SsSWEET13c in the developmental gradient of leaf and circadian rhythm in S. spontaneum. These results provide a novel understanding of the function and regulation of SWEET13c during the sugar transport and biomass production in S. spontaneum.
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Affiliation(s)
- Xiuting Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Qiaochu Shen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yihan Li
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dong Zhou
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhe Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sehrish Akbar
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhengchao Wang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China.
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wen S, Neuhaus HE, Cheng J, Bie Z. Contributions of sugar transporters to crop yield and fruit quality. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2275-2289. [PMID: 35139196 DOI: 10.1093/jxb/erac043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/04/2022] [Indexed: 05/09/2023]
Abstract
The flux, distribution, and storage of soluble sugars regulate crop yield in terms of starch, oil, protein, and total carbohydrates, and affect the quality of many horticultural products. Sugar transporters contribute to phloem loading and unloading. The mechanisms of phloem loading have been studied in detail, but the complex and diverse mechanisms of phloem unloading and sugar storage in sink organs are less explored. Unloading and subsequent transport mechanisms for carbohydrates vary in different sink organs. Analyzing the transport and storage mechanisms of carbohydrates in important storage organs, such as cereal seeds, fruits, or stems of sugarcane, will provide information for genetic improvements to increase crop yield and fruit quality. This review discusses current research progress on sugar transporters involved in carbohydrate unloading and storage in sink organs. The roles of sugar transporters in crop yield and the accumulation of sugars are also discussed to highlight their contribution to efficient breeding.
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Affiliation(s)
- Suying Wen
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
| | - H Ekkehard Neuhaus
- Plant Physiology, University of Kaiserslautern, D-67653 Kaiserslautern, Germany
| | - Jintao Cheng
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
| | - Zhilong Bie
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University and Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
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9
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Hetero/Homo-Complexes of Sucrose Transporters May Be a Subtle Mode to Regulate Sucrose Transportation in Grape Berries. Int J Mol Sci 2021; 22:ijms222112062. [PMID: 34769493 PMCID: PMC8584533 DOI: 10.3390/ijms222112062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
The sugar distribution mechanism in fruits has been the focus of research worldwide; however, it remains unclear. In order to elucidate the relevant mechanisms in grape berries, the expression, localization, function, and regulation of three sucrose transporters were studied in three representative Vitis varieties. Both SUC11 and SUC12 expression levels were positively correlated with sugar accumulation in grape berries, whereas SUC27 showed a negative relationship. The alignment analysis and sucrose transport ability of isolated SUCs were determined to reflect coding region variations among V. vinifera, V. amurensis Ruper, and V. riparia, indicating that functional variation existed in one SUT from different varieties. Furthermore, potentially oligomerized abilities of VvSUCs colocalized in the sieve elements of the phloem as plasma membrane proteins were verified. The effects of oligomerization on transport properties were characterized in yeast. VvSUC11 and VvSUC12 are high-affinity/low-capacity types of SUTs that stimulate each other by upregulating Vmax and Km, inhibiting sucrose transport, and downregulating the Km of VvSUC27. Thus, changes in the distribution of different SUTs in the same cell govern functional regulation. The activation and inhibition of sucrose transport could be achieved in different stages and tissues of grape development to achieve an effective distribution of sugar.
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Liu Y, Aslam M, Yao LA, Zhang M, Wang L, Chen H, Huang Y, Qin Y, Niu X. Genomic analysis of SBP gene family in Saccharum spontaneum reveals their association with vegetative and reproductive development. BMC Genomics 2021; 22:767. [PMID: 34706643 PMCID: PMC8549313 DOI: 10.1186/s12864-021-08090-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
Background SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SBP gene family has been identified and characterized in many species, but no systematic analysis of the SBP gene family has been carried out in sugarcane. Results In the present study, a total of 50 sequences for 30 SBP genes were identified by the genome-wide analysis and designated SsSBP1 to SsSBP30 based on their chromosomal distribution. According to the phylogenetic tree, gene structure and motif features, the SsSBP genes were classified into eight groups (I to VIII). By synteny analysis, 27 homologous gene pairs existed in SsSBP genes, and 37 orthologous gene pairs between sugarcane and sorghum were found. Expression analysis in different tissues, including vegetative and reproductive organs, showed differential expression patterns of SsSBP genes, indicating their functional diversity in the various developmental processes. Additionally, 22 SsSBP genes were predicted as the potential targets of miR156. The differential expression pattern of miR156 exhibited a negative correlation of transcription levels between miR156 and the SsSBP gene in different tissues. Conclusions The sugarcane genome possesses 30 SsSBP genes, and they shared similar gene structures and motif features in their subfamily. Based on the transcriptional and qRT-PCR analysis, most SsSBP genes were found to regulate the leaf initial and female reproductive development. The present study comprehensively and systematically analyzed SBP genes in sugarcane and provided a foundation for further studies on the functional characteristics of SsSBP genes during different development processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08090-3.
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Affiliation(s)
- Yanhui Liu
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.,College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mohammad Aslam
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Li-Ang Yao
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Man Zhang
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lulu Wang
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Huihuang Chen
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youmei Huang
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuan Qin
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China. .,College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xiaoping Niu
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.
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11
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Feng X, Wang Y, Zhang N, Gao S, Wu J, Liu R, Huang Y, Zhang J, Qi Y. Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum. BMC PLANT BIOLOGY 2021; 21:395. [PMID: 34425748 PMCID: PMC8383383 DOI: 10.1186/s12870-021-03175-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/11/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND The identification and functional analysis of genes that improve tolerance to low potassium stress in S. spontaneum is crucial for breeding sugarcane cultivars with efficient potassium utilization. Calcineurin B-like (CBL) protein is a calcium sensor that interacts with specific CBL-interacting protein kinases (CIPKs) upon plants' exposure to various abiotic stresses. RESULTS In this study, nine CBL genes were identified from S. spontaneum. Phylogenetic analysis of 113 CBLs from 13 representative plants showed gene expansion and strong purifying selection in the CBL family. Analysis of CBL expression patterns revealed that SsCBL01 was the most commonly expressed gene in various tissues at different developmental stages. Expression analysis of SsCBLs under low K+ stress indicated that potassium deficiency moderately altered the transcription of SsCBLs. Subcellular localization showed that SsCBL01 is a plasma membrane protein and heterologous expression in yeast suggested that, while SsCBL01 alone could not absorb K+, it positively regulated K+ absorption mediated by the potassium transporter SsHAK1. CONCLUSIONS This study provided insights into the evolution of the CBL gene family and preliminarily demonstrated that the plasma membrane protein SsCBL01 was involved in the response to low K+ stress in S. spontaneum.
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Affiliation(s)
- Xiaomin Feng
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Yongjun Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Nannan Zhang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Shuai Gao
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Jiayun Wu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Rui Liu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Yonghong Huang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yongwen Qi
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Room 1909, Biological Engineering Building, Jianghai Avenue, Haizhu District, Guangzhou, 510316 Guangdong Province China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007 China
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12
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Li Z, Wang G, Liu X, Wang Z, Zhang M, Zhang J. Genome-wide identification and expression profiling of DREB genes in Saccharum spontaneum. BMC Genomics 2021; 22:456. [PMID: 34139993 PMCID: PMC8212459 DOI: 10.1186/s12864-021-07799-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/10/2021] [Indexed: 12/02/2022] Open
Abstract
Background The dehydration-responsive element-binding proteins (DREBs) are important transcription factors that interact with a DRE/CRT (C-repeat) sequence and involve in response to multiple abiotic stresses in plants. Modern sugarcane are hybrids from the cross between Saccharum spontaneum and Saccharum officinarum, and the high sugar content is considered to the attribution of S. officinaurm, while the stress tolerance is attributed to S. spontaneum. To understand the molecular and evolutionary characterization and gene functions of the DREBs in sugarcane, based on the recent availability of the whole genome information, the present study performed a genome-wide in silico analysis of DREB genes and transcriptome analysis in the polyploidy S. spontaneum. Results Twelve DREB1 genes and six DREB2 genes were identified in S. spontaneum genome and all proteins contained a conserved AP2/ERF domain. Eleven SsDREB1 allele genes were assumed to be originated from tandem duplications, and two of them may be derived after the split of S. spontaneum and the proximal diploid species sorghum, suggesting tandem duplication contributed to the expansion of DREB1-type genes in sugarcane. Phylogenetic analysis revealed that one DREB2 gene was lost during the evolution of sugarcane. Expression profiling showed different SsDREB genes with variable expression levels in the different tissues, indicating seven SsDREB genes were likely involved in the development and photosynthesis of S. spontaneum. Furthermore, SsDREB1F, SsDREB1L, SsDREB2D, and SsDREB2F were up-regulated under drought and cold condition, suggesting that these four genes may be involved in both dehydration and cold response in sugarcane. Conclusions These findings demonstrated the important role of DREBs not only in the stress response, but also in the development and photosynthesis of S. spontaneum. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07799-5.
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Affiliation(s)
- Zhen Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Xihui Liu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Muqing Zhang
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Jisen Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, Guangxi, China.
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13
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Saddhe AA, Manuka R, Penna S. Plant sugars: Homeostasis and transport under abiotic stress in plants. PHYSIOLOGIA PLANTARUM 2021; 171:739-755. [PMID: 33215734 DOI: 10.1111/ppl.13283] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/10/2020] [Accepted: 11/16/2020] [Indexed: 05/21/2023]
Abstract
The sessile nature of plants' life is endowed with a highly evolved defense system to adapt and survive under environmental extremes. To combat such stresses, plants have developed complex and well-coordinated molecular and metabolic networks encompassing genes, metabolites, and acclimation responses. These modulate growth, photosynthesis, osmotic maintenance, and carbohydrate homeostasis. Under a given stress condition, sugars act as key players in stress perception, signaling, and are a regulatory hub for stress-mediated gene expression ensuring responses of osmotic adjustment, scavenging of reactive oxygen species, and maintaining the cellular energy status through carbon partitioning. Several sugar transporters are known to regulate carbohydrate partitioning and key signal transduction steps involved in the perception of biotic and abiotic stresses. Sugar transporters such as SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEETs), SUCROSE TRANSPORTERS (SUTs), and MONOSACCHARIDE TRANSPORTERS (MSTs) are involved in sugar loading and unloading as well as long-distance transport (source to sink) besides orchestrating oxidative and osmotic stress tolerance. It is thus necessary to understand the structure-function relationship of these sugar transporters to fine-tune the abiotic stress-modulated responses. Advances in genomics have unraveled many sugars signaling components playing a key role in cross-talk in abiotic stress pathways. An integrated omics approach may aid in the identification and characterization of sugar transporters that could become targets for developing stress tolerance plants to mitigate climate change effects and improve crop yield. In this review, we have presented an up-to-date analysis of the sugar homeostasis under abiotic stresses as well as describe the structure and functions of sugar transporters under abiotic stresses.
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Affiliation(s)
- Ankush A Saddhe
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - K. K. Birla Goa Campus, Zuarinagar Goa, India
| | - Rakesh Manuka
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Suprasanna Penna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
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14
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Zhang Q, Hua X, Liu H, Yuan Y, Shi Y, Wang Z, Zhang M, Ming R, Zhang J. Evolutionary expansion and functional divergence of sugar transporters in Saccharum (S. spontaneum and S. officinarum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:884-906. [PMID: 33179305 DOI: 10.1111/tpj.15076] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 10/27/2020] [Accepted: 11/04/2020] [Indexed: 06/11/2023]
Abstract
The sugar transporter (ST) family is considered to be the most important gene family for sugar accumulation, but limited information about the ST family in the important sugar-yielding crop Saccharum is available due to its complex genetic background. Here, 105 ST genes were identified and clustered into eight subfamilies in Saccharum spontaneum. Comparative genomics revealed that tandem duplication events contributed to ST gene expansions of two subfamilies, PLT and STP, in S. spontaneum, indicating an early evolutionary step towards high sugar content in Saccharum. The analyses of expression patterns were based on four large datasets with a total of 226 RNA sequencing samples from S. spontaneum and Saccharum officinarum. The results clearly demonstrated 50 ST genes had different spatiotemporal expression patterns in leaf tissues, 10 STs were specifically expressed in the stem, and 10 STs responded to the diurnal rhythm. Heterologous expression experiments in the defective yeast strain EBY.VW4000 indicated STP13, pGlcT2, VGT3, and TMT4 are the STs with most affinity for glucose/fructose and SUT1_T1 has the highest affinity to sucrose. Furthermore, metabolomics analysis suggested STP7 is a sugar starvation-induced gene and STP13 has a function in retrieving sugar in senescent tissues. PLT11, PLT11_T1, TMT3, and TMT4 contributed to breaking the limitations of the storage sink. SUT1, SUT1_T1, PLT11, TMT4, pGlcT2, and VGT3 responded for different functions in these two Saccharum species. This study demonstrated the evolutionary expansion and functional divergence of the ST gene family and will enable the further investigation of the molecular mechanism of sugar metabolism in Saccharum.
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Affiliation(s)
- Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiuting Hua
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuan Yuan
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Yan Shi
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhengchao Wang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Muqing Zhang
- Guangxi key lab for sugarcane biology, Guangxi University, Nanning, Guangxi, 530005, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Guangxi key lab for sugarcane biology, Guangxi University, Nanning, Guangxi, 530005, China
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15
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Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum. Sci Rep 2020; 10:20536. [PMID: 33239664 PMCID: PMC7688973 DOI: 10.1038/s41598-020-77375-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/22/2020] [Indexed: 01/10/2023] Open
Abstract
Sugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes (SOC1 and SVP) may regulate vegetative development.
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Ma P, Zhang X, Chen L, Zhao Q, Zhang Q, Hua X, Wang Z, Tang H, Yu Q, Zhang M, Ming R, Zhang J. Comparative analysis of sucrose phosphate synthase (SPS) gene family between Saccharum officinarum and Saccharum spontaneum. BMC PLANT BIOLOGY 2020; 20:422. [PMID: 32928111 PMCID: PMC7488781 DOI: 10.1186/s12870-020-02599-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/13/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Saccharum officinarum and the high stress tolerance species Saccharum spontaneum, generating one of the most complex genomes among all crops. The genomics of sugarcane SPS remains under-studied despite its profound impact on sugar yield. RESULTS In the present study, 8 and 6 gene sequences for SPS were identified from the BAC libraries of S. officinarum and S. spontaneum, respectively. Phylogenetic analysis showed that SPSD was newly evolved in the lineage of Poaceae species with recently duplicated genes emerging from the SPSA clade. Molecular evolution analysis based on Ka/Ks ratios suggested that polyploidy reduced the selection pressure of SPS genes in Saccharum species. To explore the potential gene functions, the SPS expression patterns were analyzed based on RNA-seq and proteome dataset, and the sugar content was detected using metabolomics analysis. All the SPS members presented the trend of increasing expression in the sink-source transition along the developmental gradient of leaves, suggesting that the SPSs are involved in the photosynthesis in both Saccharum species as their function in dicots. Moreover, SPSs showed the higher expression in S. spontaneum and presented expressional preference between stem (SPSA) and leaf (SPSB) tissue, speculating they might be involved in the differentia of carbohydrate metabolism in these two Saccharum species, which required further verification from experiments. CONCLUSIONS SPSA and SPSB genes presented relatively high expression and differential expression patterns between the two Saccharum species, indicating these two SPSs are important in the formation of regulatory networks and sucrose traits in the two Saccharum species. SPSB was suggested to be a major contributor to the sugar accumulation because it presented the highest expressional level and its expression positively correlated with sugar content. The recently duplicated SPSD2 presented divergent expression levels between the two Saccharum species and the relative protein content levels were highest in stem, supporting the neofunctionalization of the SPSD subfamily in Saccharum.
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Affiliation(s)
- Panpan Ma
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lanping Chen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qian Zhao
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiuting Hua
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhengchao Wang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qingyi Yu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX 75252 USA
| | - Muqing Zhang
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi China
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Li Z, Hua X, Zhong W, Yuan Y, Wang Y, Wang Z, Ming R, Zhang J. Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in the Autopolyploid Saccharum spontaneum. PLANT & CELL PHYSIOLOGY 2020; 61:616-630. [PMID: 31830269 DOI: 10.1093/pcp/pcz227] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 12/08/2019] [Indexed: 05/19/2023]
Abstract
WRKY is one of the largest transcription factor families in plants and plays important roles in the regulation of developmental and physiological processes. To date, the WRKY gene family has not been identified in Saccharum species because of its complex polyploid genome. In this study, a total of 294 sequences for 154 SsWRKY genes were identified in the polyploid Saccharum spontaneum genome and then named on the basis of their chromosome locations, including 13 (8.4%) genes with four alleles, 29 (18.8%) genes with three alleles and 41 (26.6%) genes with two alleles. Among them, 73.8% and 16.0% of the SsWRKY genes originated from segmental duplications and tandem duplications, respectively. The WRKY members exhibited conserved gene structures and amino acid sequences among the allelic haplotypes, which were accompanied by variations in intron sizes. Phylogenetic and collinearity analyses revealed that 27 SsWRKYs originated after the split of sorghum and Saccharum, resulting in a significantly higher number of WRKYs in sugarcane than in the proximal diploid species sorghum. The analysis of RNA-seq data revealed that SsWRKYs' expression profiles in 46 different samples including different developmental stages revealed distinct temporal and spatial patterns with 52 genes expressed in all tissues, four genes not expressed in any tissues and 21 SsWRKY genes likely to be involved in photosynthesis. The comprehensive analysis of SsWRKYs' expression will provide an important and valuable foundation for further investigation of the regulatory mechanisms of WRKYs in physiological roles in sugarcane S. spontaneum.
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Affiliation(s)
- Zhen Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiuting Hua
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiming Zhong
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Yuan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi 530004, China
| | - Yongjun Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Ray Ming
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi 530004, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jisen Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi 530004, China
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Cai M, Lin J, Li Z, Lin Z, Ma Y, Wang Y, Ming R. Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane. PLoS One 2020; 15:e0227716. [PMID: 31945094 PMCID: PMC6964845 DOI: 10.1371/journal.pone.0227716] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022] Open
Abstract
Dof transcription factors plant-specific and associates with growth and development in plants. We conducted comprehensive and systematic analyses of Dof transcription factors in sugarcane, and identified 29 SsDof transcription factors in sugarcane genome. Those SsDof genes were divided into five groups, with similar gene structures and conserved motifs within the same groups. Segmental duplications are predominant in the evolution of Dof in sugarcane. Cis-element analysis suggested that the functions of SsDofs were involved in growth and development, hormones and abiotic stresses responses in sugarcane. Expression patterns indicated that SsDof7, SsDof23 and SsDof24 had a comparatively high expression in all detected tissues, indicating these genes are crucial in sugarcane growth and development. Moreover, we examined the transcription levels of SsDofs under four plant hormone treatments, SsDof7-3 and SsDof7-4 were down-regulated after ABA treatment, while SsDof7-1 and SsDof7-2 were induced after the same treatment, indicating different alleles may play different roles in response to plant hormones. We also analyzed SsDofs' expression profiling under four abiotic stresses, SsDof5 and SsDof28 significantly responded to these four stresses, indicating they are associate with abiotic stresses responses. Collectively, our results yielded allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane, and their cis-elements could be crucial for sugarcane improvement.
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Affiliation(s)
- Mingxing Cai
- College of Life Sciences, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jishan Lin
- College of Life Sciences, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zeyun Li
- College of Life Sciences, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhicong Lin
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yaying Ma
- College of Life Sciences, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yibin Wang
- College of Life Sciences, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ray Ming
- College of Life Sciences, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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Feng X, Wang Y, Zhang N, Wu Z, Zeng Q, Wu J, Wu X, Wang L, Zhang J, Qi Y. Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K + stress in Saccharum. BMC PLANT BIOLOGY 2020; 20:20. [PMID: 31931714 PMCID: PMC6958797 DOI: 10.1186/s12870-019-2227-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/30/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plant genomes contain a large number of HAK/KUP/KT transporters, which play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance, root morphogenesis and plant development. Potassium deficiency in the soil of a sugarcane planting area is serious. However, the HAK/KUP/KT gene family remains to be characterized in sugarcane (Saccharum). RESULTS In this study, 30 HAK/KUP/KT genes were identified in Saccharum spontaneum. Phylogenetics, duplication events, gene structures and expression patterns were analyzed. Phylogenetic analysis of the HAK/KUP/KT genes from 15 representative plants showed that this gene family is divided into four groups (clades I-IV). Both ancient whole-genome duplication (WGD) and recent gene duplication contributed to the expansion of the HAK/KUP/KT gene family. Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that purifying selection was the main force driving the evolution of HAK/KUP/KT genes. The divergence time of the HAK/KUP/KT gene family was estimated to range from 134.8 to 233.7 Mya based on Ks analysis, suggesting that it is an ancient gene family in plants. Gene structure analysis showed that the HAK/KUP/KT genes were accompanied by intron gain/loss in the process of evolution. RNA-seq data analysis demonstrated that the HAK/KUP/KT genes from clades II and III were mainly constitutively expressed in various tissues, while most genes from clades I and IV had no or very low expression in the tested tissues at different developmental stages. The expression of SsHAK1 and SsHAK21 was upregulated in response to low-K+ stress. Yeast functional complementation analysis revealed that SsHAK1 and SsHAK21 could rescue K+ uptake in a yeast mutant. CONCLUSIONS This study provided insights into the evolutionary history of HAK/KUP/KT genes. HAK7/9/18 were mainly expressed in the upper photosynthetic zone and mature zone of the stem. HAK7/9/18/25 were regulated by sunlight. SsHAK1 and SsHAK21 played important roles in mediating potassium acquisition under limited K+ supply. Our results provide valuable information and key candidate genes for further studies on the function of HAK/KUP/KT genes in Saccharum.
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Affiliation(s)
- Xiaomin Feng
- Guangdong Key Lab of Sugarcane Improvement & Biorefinery, Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, 510316 China
- Guangzhou Guansheng Breeding Research Institute, Guangzhou, 511453 China
| | - Yongjun Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Nannan Zhang
- Guangdong Key Lab of Sugarcane Improvement & Biorefinery, Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, 510316 China
- Guangzhou Guansheng Breeding Research Institute, Guangzhou, 511453 China
| | - Zilin Wu
- Guangdong Key Lab of Sugarcane Improvement & Biorefinery, Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, 510316 China
- Guangzhou Guansheng Breeding Research Institute, Guangzhou, 511453 China
| | - Qiaoying Zeng
- Guangdong Key Lab of Sugarcane Improvement & Biorefinery, Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, 510316 China
- Guangzhou Guansheng Breeding Research Institute, Guangzhou, 511453 China
| | - Jiayun Wu
- Guangdong Key Lab of Sugarcane Improvement & Biorefinery, Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, 510316 China
- Guangzhou Guansheng Breeding Research Institute, Guangzhou, 511453 China
| | - Xiaobin Wu
- Guangdong Key Lab of Sugarcane Improvement & Biorefinery, Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, 510316 China
- Guangzhou Guansheng Breeding Research Institute, Guangzhou, 511453 China
| | - Lei Wang
- Guangdong Key Lab of Sugarcane Improvement & Biorefinery, Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, 510316 China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yongwen Qi
- Guangdong Key Lab of Sugarcane Improvement & Biorefinery, Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, 510316 China
- Guangzhou Guansheng Breeding Research Institute, Guangzhou, 511453 China
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20
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Wang Y, Hua X, Xu J, Chen Z, Fan T, Zeng Z, Wang H, Hour AL, Yu Q, Ming R, Zhang J. Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum. BMC Genomics 2019; 20:83. [PMID: 30678642 PMCID: PMC6345045 DOI: 10.1186/s12864-019-5437-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/08/2019] [Indexed: 12/19/2022] Open
Abstract
Background Sugarcane served as the model plant for discovery of the C4 photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynthesis. In plants, the magnesium transporter (MGT) family is composed of a number of membrane proteins, which play crucial roles in maintaining Mg homeostasis. However, to date there is no information available on the genomics of MGTs in sugarcane due to the complexity of the Saccharum genome. Results Here, we identified 10 MGTs from the Saccharum spontaneum genome. Phylogenetic analysis of MGTs suggested that the MGTs contained at least 5 last common ancestors before the origin of angiosperms. Gene structure analysis suggested that MGTs family of dicotyledon may be accompanied by intron loss and pseudoexon phenomena during evolution. The pairwise synonymous substitution rates corresponding to a divergence time ranged from 142.3 to 236.6 Mya, demonstrating that the MGTs are an ancient gene family in plants. Both the phylogeny and Ks analyses indicated that SsMGT1/SsMGT2 originated from the recent ρWGD, and SsMGT7/SsMGT8 originated from the recent σ WGD. These 4 recently duplicated genes were shown low expression levels and assumed to be functionally redundant. MGT6, MGT9 and MGT10 weredominant genes in the MGT family and werepredicted to be located inthe chloroplast. Of the 3 dominant MGTs, SsMGT6 expression levels were found to be induced in the light period, while SsMGT9 and SsMTG10 displayed high expression levels in the dark period. These results suggested that SsMGT6 may have a function complementary to SsMGT9 and SsMTG10 that follows thecircadian clock for MGT in the leaf tissues of S. spontaneum. MGT3, MGT7 and MGT10 had higher expression levels Insaccharum officinarum than in S. spontaneum, suggesting their functional divergence after the split of S. spontaneum and S. officinarum. Conclusions This study of gene evolution and expression of MGTs in S. spontaneum provided basis for the comprehensive genomic study of the entire MGT genes family in Saccharum. The results are valuable for further functional analyses of MGT genes and utilization of the MGTs for Saccharum genetic improvement. Electronic supplementary material The online version of this article (10.1186/s12864-019-5437-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yongjun Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Resources and Environment, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
| | - Xiuting Hua
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Resources and Environment, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
| | - Jingsheng Xu
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
| | - Zhichang Chen
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tianqu Fan
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Resources and Environment, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhaohui Zeng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Resources and Environment, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hengbo Wang
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
| | - Ai-Ling Hour
- Department of Life Science, Fu-Jen Catholic University, Xinzhuang Dist., Taibei, 242, Taiwan
| | - Qingyi Yu
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX, 75252, USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Resources and Environment, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Resources and Environment, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China.
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Hu W, Hua X, Zhang Q, Wang J, Shen Q, Zhang X, Wang K, Yu Q, Lin YR, Ming R, Zhang J. New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics. BMC PLANT BIOLOGY 2018; 18:270. [PMID: 30404601 PMCID: PMC6222987 DOI: 10.1186/s12870-018-1495-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/22/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND The SWEET (Sugars Will Eventually be Exported Transporters) gene family is a recently identified group of sugar transporters that play an indispensable role in sugar efflux, phloem loading, plant-pathogen interaction, nectar secretion, and reproductive tissue development. However, little information on Saccharum SWEET is available for this crop with a complex genetic background. RESULTS In this study, 22 SWEET genes were identified from Saccharum spontaneum Bacterial Artificial Chromosome libraries sequences. Phylogenetic analyses of SWEETs from 11 representative plant species showed that gene expansions of the SWEET family were mainly caused by the recent gene duplication in dicot plants, while these gene expansions were attributed to the ancient whole genome duplication (WGD) in monocot plant species. Gene expression profiles were obtained from RNA-seq analysis. SWEET1a and SWEET2s had higher expression levels in the transitional zone and maturing zone than in the other analyzed zones. SWEET1b was mainly expressed in the leaf tissues and the mature zone of the leaf of both S. spontaneum and S. officinarum, and displayed a peak in the morning and was undetectable in both sclerenchyma and parenchyma cells from the mature stalks of S. officinarum. SsSWEET4a\4b had higher expression levels than SWEET4c and were mainly expressed in the stems of seedlings and mature plants. SWEET13s are recently duplicated genes, and the expression of SWEET13s dramatically increased from the maturing to mature zones. SWEET16b's expression was not detected in S. officinarum, but displayed a rhythmic diurnal expression pattern. CONCLUSIONS Our study revealed the gene evolutionary history of SWEETs in Saccharum and SWEET1b was found to be a sucrose starvation-induced gene involved in the sugar transportation in the high photosynthetic zones. SWEET13c was identified as the key player in the efflux of sugar transportation in mature photosynthetic tissues. SWEET4a\4b were found to be mainly involved in sugar transportation in the stalk. SWEET1a\2a\4a\4b\13a\16b were suggested to be the genes contributing to the differences in sugar contents between S. spontaneum and S. officinarum. Our results are valuable for further functional analysis of SWEET genes and utilization of the SWEET genes for genetic improvement of Saccharum for biofuel production.
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Affiliation(s)
- Weichang Hu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiuting Hua
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianping Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Agronomy Department, University of Florida, Gainesville, FL 32610 USA
| | - Qiaochu Shen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Kai Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qingyi Yu
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX 75252 USA
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, 100 Taiwan
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Li W, Sun K, Ren Z, Song C, Pei X, Liu Y, Wang Z, He K, Zhang F, Zhou X, Ma X, Yang D. Molecular Evolution and Stress and Phytohormone Responsiveness of SUT Genes in Gossypium hirsutum. Front Genet 2018; 9:494. [PMID: 30405700 PMCID: PMC6205988 DOI: 10.3389/fgene.2018.00494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 10/04/2018] [Indexed: 11/13/2022] Open
Abstract
Sucrose transporters (SUTs) play key roles in allocating the translocation of assimilates from source to sink tissues. Although the characteristics and biological roles of SUTs have been intensively investigated in higher plants, this gene family has not been functionally characterized in cotton. In this study, we performed a comprehensive analysis of SUT genes in the tetraploid cotton Gossypium hirsutum. A total of 18 G. hirsutum SUT genes were identified and classified into three groups based on their evolutionary relationships. Up to eight SUT genes in G. hirsutum were placed in the dicot-specific SUT1 group, while four and six SUT genes were, respectively, clustered into SUT4 and SUT2 groups together with members from both dicot and monocot species. The G. hirsutum SUT genes within the same group displayed similar exon/intron characteristics, and homologous genes in G. hirsutum At and Dt subgenomes, G. arboreum, and G. raimondii exhibited one-to-one relationships. Additionally, the duplicated genes in the diploid and polyploid cotton species have evolved through purifying selection, suggesting the strong conservation of SUT loci in these species. Expression analysis in different tissues indicated that SUT genes might play significant roles in cotton fiber elongation. Moreover, analyses of cis-acting regulatory elements in promoter regions and expression profiling under different abiotic stress and exogenous phytohormone treatments implied that SUT genes, especially GhSUT6A/D, might participate in plant responses to diverse abiotic stresses and phytohormones. Our findings provide valuable information for future studies on the evolution and function of SUT genes in cotton.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kuan Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhongying Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Xiaoyu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yangai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhenyu Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kunlun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaojian Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Daigang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
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23
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Dong G, Shen J, Zhang Q, Wang J, Yu Q, Ming R, Wang K, Zhang J. Development and Applications of Chromosome-Specific Cytogenetic BAC-FISH Probes in S. spontaneum. FRONTIERS IN PLANT SCIENCE 2018; 9:218. [PMID: 29535742 PMCID: PMC5834487 DOI: 10.3389/fpls.2018.00218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Saccharum spontaneum is a major Saccharum species that contributed to the origin of modern sugarcane cultivars, and due to a high degree of polyploidy is considered to be a plant species with one of the most complex genetics. Fluorescence in situ hybridization (FISH) is a powerful and widely used tool in genome studies. Here, we demonstrated that FISH based on bacterial artificial chromosome (BAC) clones can be used as a specific cytological marker to identify S. spontaneum individual chromosomes and study the relationship between S. spontaneum and other related species. We screened low-copy BACs as probes from the sequences of a high coverage of S. spontaneum BAC library based on BLAST search of the sorghum genome. In total, we isolated 49 positive BAC clones, and identified 27 BAC clones that can give specific signals on the S. spontaneum chromosomes. Of the 27 BAC probes, 18 were confirmed to be able to discriminate the eight basic chromosomes of S. spontaneum. Moreover, BAC-24, BAC-66, BAC-78, BAC-69, BAC-71, BAC-73, and BAC-77 probes were used to construct physical maps of chromosome 1 and chromosome 2 of S. spontaneum, which indicated synteny in Sb01 between S. spontaneum and sorghum. Furthermore, we found that BAC-14 and BAC-19 probes, corresponding to the sorghum chromosomes 2 and 8, respectively, localized to different arms of the same S. spontaneum chromosome, suggesting that there was an inter-chromosomal rearrangement event between S. spontaneum and sorghum. Our study provides the first set of chromosome-specific cytogenetic markers in Saccharum and is critical for future advances in cytogenetics and genome sequencing studies in Saccharum.
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Affiliation(s)
- Guangrui Dong
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiao Shen
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qing Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianping Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Qingyi Yu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Ray Ming
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Texas A&M AgriLife Research Center, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX, United States
| | - Kai Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jisen Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Normal University, Fuzhou, China
- *Correspondence: Jisen Zhang,
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24
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Rippin M, Becker B, Holzinger A. Enhanced Desiccation Tolerance in Mature Cultures of the Streptophytic Green Alga Zygnema circumcarinatum Revealed by Transcriptomics. PLANT & CELL PHYSIOLOGY 2017; 58:2067-2084. [PMID: 29036673 PMCID: PMC5722205 DOI: 10.1093/pcp/pcx136] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/05/2017] [Indexed: 05/20/2023]
Abstract
Desiccation tolerance is commonly regarded as one of the key features for the colonization of terrestrial habitats by green algae and the evolution of land plants. Extensive studies, focused mostly on physiology, have been carried out assessing the desiccation tolerance and resilience of the streptophytic genera Klebsormidium and Zygnema. Here we present transcriptomic analyses of Zygnema circumcarinatum exposed to desiccation stress. Cultures of Z. circumcarinatum grown in liquid medium or on agar plates were desiccated at ∼86% relative air humidity until the effective quantum yield of PSII [Y(II)] ceased. In general, the response to dehydration was much more pronounced in Z. circumcarinatum cultured in liquid medium for 1 month compared with filaments grown on agar plates for 7 and 12 months. Culture on solid medium enables the alga to acclimate to dehydration much better and an increase in desiccation tolerance was clearly correlated to increased culture age. Moreover, gene expression analysis revealed that photosynthesis was strongly repressed upon desiccation treatment in the liquid culture while only minor effects were detected in filaments cultured on agar plates for 7 months. Otherwise, both samples showed induction of stress protection mechanisms such as reactive oxygen species scavenging (early light-induced proteins, glutathione metabolism) and DNA repair as well as the expression of chaperones and aquaporins. Additionally, Z. circumcarinatum cultured in liquid medium upregulated sucrose-synthesizing enzymes and strongly induced membrane modifications in response to desiccation stress. These results corroborate the previously described hardening and associated desiccation tolerance in Zygnema in response to seasonal fluctuations in water availability.
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Affiliation(s)
- Martin Rippin
- University of Cologne, Cologne Biocentre, Botanical Institute, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Burkhard Becker
- University of Cologne, Cologne Biocentre, Botanical Institute, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Functional Plant Biology, Sternwartestrasse 15, 6020 Innsbruck, Austria
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25
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ElSayed AI, Lehrer A, Ebrahim M, Mohamed AH, Komor E. Assessment of sucrose transporters, metabolites and sucrose phosphate synthase in different sugarcane tissues. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:703-712. [PMID: 28878508 PMCID: PMC5567715 DOI: 10.1007/s12298-017-0454-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/28/2017] [Accepted: 05/25/2017] [Indexed: 05/29/2023]
Abstract
The expression of sucrose-phosphate synthase II (SPSII) and sucrose transporters ShSUT1A and ShSUT4 were determined by RT-PCR and qRT-PCR in the sink and source leaves and in rind and pith of mature internodes of four high-yielding Hawaiian sugarcane cultivars. Expression of SPSII, ShSUT1A, and ShSUT4 was lower in pith than in rind, except in one cultivar, but else quite similar in the cultivars. The strong expression of transporter ShSUT4 in the rind of the internodes may hint to a special role of ShSUT4 in the rind. ShSUT4-expression in the sink and source leaves was similar in all four cultivars, whereas large differences were found for the expression of ShSUT1A and SPSII between the source and sink leaves and between the cultivars. The levels of sucrose precursors were doubled in source leaves compared to sink leaves, whereas they were higher in immature internode compared to mature internode. The role of sucrose transporters and SPSII in leaves and internodes is discussed, but the large differences, which were observed in the transcript levels of SPSII and sucrose transporters between some cultivars, although all the cultivars were similarly high-yielding cultivars, show that SPSII and SUT transcript levels cannot be used as indicators of high-yield cultivars.
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Affiliation(s)
- Abdelaleim Ismail ElSayed
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, 44519 Egypt
- Plant Physiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Axel Lehrer
- Hawaii Agriculture Research Center, Kunia, HI USA
| | - Mohsen Ebrahim
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Azza H. Mohamed
- Biochemistry Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Ewald Komor
- Plant Physiology, University of Bayreuth, 95440 Bayreuth, Germany
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26
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Chen Y, Zhang Q, Hu W, Zhang X, Wang L, Hua X, Yu Q, Ming R, Zhang J. Evolution and expression of the fructokinase gene family in Saccharum. BMC Genomics 2017; 18:197. [PMID: 28222695 PMCID: PMC5319016 DOI: 10.1186/s12864-017-3535-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 02/02/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity. RESULTS In this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S. spontaneum. Phylogenetic analysis based on representative monocotyledon and dicotyledon plant species suggested that the FRK gene family is ancient and its evolutionary history can be traced in duplicated descending order: SsFRK4, SsFRK6/SsFRK7,SsFRK5, SsFRK3 and SsFRK1/SsFRK2. Among the close orthologs, the number and position of exons in FRKs were conserved; in contrast, the size of introns varied among the paralogous FRKs in Saccharum. Genomic constraints were analyzed within the gene alleles and between S. spontaneum and Sorghum bicolor, and gene expression analysis was performed under drought stress and with exogenous applications of plant hormones. FRK1, which was under strong functional constraint selection, was conserved among the gene allelic haplotypes, and displayed dominant expression levels among the gene families in the control conditions, suggesting that FRK1 plays a major role in the phosphorylation of fructose. FRK3 and FRK5 were dramatically induced under drought stress, and FRK5 was also found to increase its expression levels in the mature stage of Saccharum. Similarly, FRK3 and FRK5 were induced in response to drought stress in Saccharum. FRK2 and FRK7 displayed lower expression levels than the other FRK family members; FRK2 was under strong genomic selection constraints whereas FRK7 was under neutral selection. FRK7 may have become functionally redundant in Saccharum through pseudogenization. FRK4 and FRK6 shared the most similar expression pattern: FRK4 was revealed to have higher expression levels in mature tissues than in premature tissues of Saccharum, and FRK6 presented a slight increase under drought stress. CONCLUSIONS Our study presents a comprehensive genomic study of the entire FRK gene family in Saccharum, providing the foundations for approaches to characterize the molecular mechanism regulated by the SsFRK family in sugarcane.
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Affiliation(s)
- Yihong Chen
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117 China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weichang Hu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liming Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiuting Hua
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117 China
| | - Qingyi Yu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX 75252 USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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