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Pei M, Yang P, Li J, Wang Y, Li J, Xu H, Li J. Comprehensive analysis of pepper (Capsicum annuum) RAV genes family and functional identification of CaRAV1 under chilling stress. BMC Genomics 2024; 25:731. [PMID: 39075389 PMCID: PMC11285464 DOI: 10.1186/s12864-024-10639-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/19/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Despite its known significance in plant abiotic stress responses, the role of the RAV gene family in the response of Capsicum annuum to chilling stress remains largely unexplored. RESULTS In this study, we identified and characterized six members of the CaRAV gene subfamily in pepper plants through genome-wide analysis. Subsequently, the CaRAV subfamily was classified into four branches based on homology with Arabidopsis thaliana, each exhibiting relatively conserved domains within the branch. We discovered that light response elements accounted for the majority of CaRAVs, whereas low-temperature response elements were specific to the NGA gene subfamily. After pepper plants were subjected to chilling stress, qRT‒PCR analysis revealed that CaRAV1, CaRAV2 and CaNGA1 were significantly induced in response to chilling stress, indicating that CaRAVs play a role in the response to chilling stress. Using virus-induced gene silencing (VIGS) vectors, we targeted key members of the CaRAV gene family. Under normal growth conditions, the MDA content and SOD enzyme activity of the silenced plants were slightly greater than those of the control plants, and the REC activity was significantly greater than that of the control plants. The levels of MDA and electrolyte leakage were greater in the silenced plants after they were exposed to chilling stress, and the POD and CAT enzyme activities were significantly lower than those in the control, which was particularly evident under repeated chilling stress. In addition, the relative expression of CaPOD and CaCAT was greater in V2 plants upon repeated chilling stress, especially CaCAT was significantly greater in V2 plants than in the other two silenced plants, with 3.29 and 1.10 increases within 12 and 24 h. These findings suggest that CaRAV1 and CaNGA1 positively regulate the response to chilling stress. CONCLUSIONS Silencing of key members of the CaRAV gene family results in increased susceptibility to chilling damage and reduced antioxidant enzyme activity in plants, particularly under repeated chilling stress. This study provides valuable information for understanding the classification and putative functions of RAV transcription factors in pepper plants.
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Affiliation(s)
- Minkun Pei
- College of Horticulture, Xinjiang Agriculture University, Urumqi, 830052, China
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan, 661100, China
| | - Ping Yang
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan, 661100, China
| | - Jian Li
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan, 661100, China
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, China
| | - Yanzhuang Wang
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan, 661100, China
- College of Horticulture and Forestry, Tarim University, Alar, 843300, China
| | - Juan Li
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan, 661100, China
- College of Horticulture and Forestry, Tarim University, Alar, 843300, China
| | - Hongjun Xu
- College of Horticulture, Xinjiang Agriculture University, Urumqi, 830052, China.
| | - Jie Li
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan, 661100, China.
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Wang T, Long C, Chang M, Wu Y, Su S, Wei J, Jiang S, Wang X, He J, Xing D, He Y, Ran Y, Li W. Genome-wide identification of the B3 transcription factor family in pepper (Capsicum annuum) and expression patterns during fruit ripening. Sci Rep 2024; 14:2226. [PMID: 38278802 PMCID: PMC10817905 DOI: 10.1038/s41598-023-51080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/30/2023] [Indexed: 01/28/2024] Open
Abstract
In plants, B3 transcription factors play important roles in a variety of aspects of their growth and development. While the B3 transcription factor has been extensively identified and studied in numerous species, there is limited knowledge regarding its B3 superfamily in pepper. Through the utilization of genome-wide sequence analysis, we identified a total of 106 B3 genes from pepper (Capsicum annuum), they are categorized into four subfamilies: RAV, ARF, LAV, and REM. Chromosome distribution, genetic structure, motif, and cis-acting element of the pepper B3 protein were analyzed. Conserved gene structure and motifs outside the B3 domain provided strong evidence for phylogenetic relationships, allowing potential functions to be deduced by comparison with homologous genes from Arabidopsis. According to the high-throughput transcriptome sequencing analysis, expression patterns differ during different phases of fruit development in the majority of the 106 B3 pepper genes. By using qRT-PCR analysis, similar expression patterns in fruits from various time periods were discovered. In addition, further analysis of the CaRAV4 gene showed that its expression level decreased with fruit ripening and located in the nucleus. B3 transcription factors have been genome-wide characterized in a variety of crops, but the present study is the first genome-wide analysis of the B3 superfamily in pepper. More importantly, although B3 transcription factors play key regulatory roles in fruit development, it is uncertain whether B3 transcription factors are involved in the regulation of the fruit development and ripening process in pepper and their specific regulatory mechanisms because the molecular mechanisms of the process have not been fully explained. The results of the study provide a foundation and new insights into the potential regulatory functions and molecular mechanisms of B3 genes in the development and ripening process of pepper fruits, and provide a solid theoretical foundation for the enhancement of the quality of peppers and their selection and breeding of high-yield varieties.
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Affiliation(s)
- Tao Wang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Cha Long
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Meixia Chang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Yuan Wu
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Shixian Su
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Jingjiang Wei
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China
| | - Suyan Jiang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Xiujun Wang
- College of Brewing and Food Engineering, Guizhou University, Guiyang, 550025, China
| | - Jianwen He
- Pepper Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Dan Xing
- Pepper Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Yangbo He
- Agriculture Development and Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Yaoqi Ran
- Agriculture Development and Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Wei Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China.
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China.
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China.
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Gao J, Ma G, Chen J, Gichovi B, Cao L, Liu Z, Chen L. The B3 gene family in Medicago truncatula: Genome-wide identification and the response to salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108260. [PMID: 38096733 DOI: 10.1016/j.plaphy.2023.108260] [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: 09/06/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 02/15/2024]
Abstract
The B3 family genes constitute a pivotal group of transcription factors that assume diverse roles in the growth, development, and response to both biotic and abiotic stresses in plants. Medicago truncatula is a diploid plant with a relatively small genome, adopted as a model species for legumes genetics and functional genomic research. In this study, 173 B3 genes were identified in the M. truncatula genome, and classified into seven subgroups by phylogenetic analysis. Collinearity analysis revealed that 18 MtB3 gene pairs arose from segmented replication events. Analysis of expression patterns disclosed that 61 MtB3s exhibited a spectrum of expression profiles across various tissues and in the response to salt stress, indicating their potential involvement in salt stress signaling response. Among these genes, MtB3-53 exhibited tissue-specific differential expression and demonstrated a rapid response to salt stress induction. Overexpression of MtB3-53 gene in Arabidopsis improves salt stress tolerance by increasing plant biomass and chlorophyll content, while reducing leaf cell membrane damage. Moreover, salt treatment resulted in more up-regulation of AtABF1, AtABI3, AtHKT1, AtKIN1, AtNHX1, and AtRD29A in MtB3-53 transgenic Arabidopsis plants compared to the wild type, providing evidences that MtB3-53 enhances plant salt tolerance not only by modulating ion homeostasis but also by stimulating the production of antioxidants, which leads to the alleviation of cellular damage caused by salt stress. In conclusion, this study provides a fundamental basis for future investigations into the B3 gene family and its capacity to regulate plant responses to environmental stressors.
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Affiliation(s)
- Jing Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Guangjing Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Junjie Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Bancy Gichovi
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Liwen Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; Academician Workstation of Agricultural High-tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Zhihao Liu
- Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, 435002, China.
| | - Liang Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; Academician Workstation of Agricultural High-tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
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Jin Y, Zeng L, Xiao M, Feng Y, Gao Z, Wei J. Exploration of the B3 transcription factor superfamily in Aquilaria sinensis reveal their involvement in seed recalcitrance and agarwood formation. PLoS One 2023; 18:e0294358. [PMID: 37972007 PMCID: PMC10653465 DOI: 10.1371/journal.pone.0294358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
The endangered tree species of the Aquilaria genus produce agarwood, a high value material produced only after wounding; however, conservation of Aquilaria seeds is difficult. The B3 transcription factor family has diverse important functions in plant development, especially in seed development, although their functions in other areas, such as stress responses, remain to be revealed. Here germination tests proved that the seeds of A. sinensis were recalcitrant seeds. To provide insights into the B3 superfamily, the members were identified and characterized by bioinformatic approaches and classified by phylogenetic analysis and domain structure. In total, 71 members were identified and classified into four subfamilies. Each subfamily not only had similar domains, but also had conserved motifs in their B3 domains. For the seed-related LAV subfamily, the B3 domain of AsLAV3 was identical to that of AsVALs but lacked a typical zf-CW domain such as VALs. AsLAV5 lacks a typical PHD-L domain present in Arabidopsis VALs. qRT-PCR expression analysis showed that the LEC2 ortholog AsLAV4 was not expressed in seeds. RAVs and REMs induced after wound treatment were also identified. These findings provide insights into the functions of B3 genes and seed recalcitrance of A. sinensis and indicate the role of B3 genes in wound response and agarwood formation.This is the first work to investigate the B3 family in A. sinensis and to provide insights of the molecular mechanism of seed recalcitrance.This will be a valuable guidance for studies of B3 genes in stress responses, secondary metabolite biosynthesis, and seed development.
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Affiliation(s)
- Yue Jin
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Zeng
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & Key Laboratory of State Administration of Traditional Chinese Medicine for Agarwood Sustainable Utilization, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Mengjun Xiao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanan Feng
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihui Gao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhe Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & Key Laboratory of State Administration of Traditional Chinese Medicine for Agarwood Sustainable Utilization, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
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5
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Ren C, Wang H, Zhou Z, Jia J, Zhang Q, Liang C, Li W, Zhang Y, Yu G. Genome-wide identification of the B3 gene family in soybean and the response to melatonin under cold stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1091907. [PMID: 36714689 PMCID: PMC9880549 DOI: 10.3389/fpls.2022.1091907] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Melatonin is a multipotent molecule that exists widely in animals and plants and plays an active regulatory role in abiotic stresses. The B3 superfamily is a ubiquitous transcription factor with a B3 functional domain in plants, which can respond temporally to abiotic stresses by activating defense compounds and plant hormones. Despite the fact that the B3 genes have been studied in a variety of plants, their role in soybean is still unknown. METHODS The regulation of melatonin on cold resistance of soybean and the response of B3 genes to cold stress were investigated by measuring biochemical indexes of soybean. Meanwhile, the genome-wide identification of B3 gene family was conducted in soybean, and B3 genes were analyzed based on phylogeny, motifs, gene structure, collinearity, and cis-regulatory elements analysis. RESULTS We found that cold stress-induced oxidative stress in soybean by producing excessive reactive oxygen species. However, exogenous melatonin treatment could increase the content of endogenous melatonin and other hormones, including IAA and ABA, and enhance the antioxidative system, such as POD activity, CAT activity, and GSH/GSSG, to scavenge ROS. Furthermore, the present study first revealed that melatonin could alleviate the response of soybean to cold stress by inducing the expression of B3 genes. In addition, we first identified 145 B3 genes in soybean that were unevenly distributed on 20 chromosomes. The B3 gene family was divided into 4 subgroups based on the phylogeny tree constructed with protein sequence and a variety of plant hormones and stress response cis-elements were discovered in the promoter region of the B3 genes, indicating that the B3 genes were involved in several aspects of the soybean stress response. Transcriptome analysis and results of qRT-PCR revealed that most GmB3 genes could be induced by cold, the expression of which was also regulated by melatonin. We also found that B3 genes responded to cold stress in plants by interacting with other transcription factors. DISCUSSION We found that melatonin regulates the response of soybean to cold stress by regulating the expression of the transcription factor B3 gene, and we identified 145 B3 genes in soybean. These findings further elucidate the potential role of the B3 gene family in soybean to resist low-temperature stress and provide valuable information for soybean functional genomics study.
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Affiliation(s)
- Chunyuan Ren
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Huamei Wang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Zhiheng Zhou
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Jingrui Jia
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Qi Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Changzhi Liang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Wanting Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Yuxian Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Gaobo Yu
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
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Guo J, Liu H, Dai K, Yuan X, Guo P, Shi W, Zhou M. Identification of Brachypodium distachyon B3 genes reveals that BdB3-54 regulates primary root growth. FRONTIERS IN PLANT SCIENCE 2022; 13:1050171. [PMID: 36438129 PMCID: PMC9686306 DOI: 10.3389/fpls.2022.1050171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
B3 is a class of plant-specific transcription factors with important roles in plant development and growth. Here, we identified 69 B3 transcription factors in Brachypodium distachyon that were unevenly distributed across all five chromosomes. The ARF, REM, LAV, and RAV subfamilies were grouped based on sequence characteristics and phylogenetic relationships. The phylogenetically related members in the B3 family shared conserved domains and gene structures. Expression profiles showed that B3 genes were widely expressed in different tissues and varied in response to different abiotic stresses. BdB3-54 protein from the REM subfamily was located in the nucleus by subcellular localization and processed transcriptional activation activity. Overexpression of BdB3-54 in Arabidopsis increased primary root length. Our study provides a basis for further research on the functions of BdB3 genes.
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Affiliation(s)
- Jie Guo
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Hanxiao Liu
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Keli Dai
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Xiangyang Yuan
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Pingyi Guo
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Weiping Shi
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Meixue Zhou
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, Australia
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7
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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Giordani W, Gama HC, Chiorato AF, Garcia AAF, Vieira MLC. Genome-wide association studies dissect the genetic architecture of seed shape and size in common bean. G3 (BETHESDA, MD.) 2022; 12:jkac048. [PMID: 35218340 PMCID: PMC8982408 DOI: 10.1093/g3journal/jkac048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Seed weight and size are important yield components. Thus, selecting for large seeds has been a key objective in crop domestication and breeding. In common bean, seed shape is also important since it influences industrial processing and plays a vital role in determining the choices of consumers and farmers. In this study, we performed genome-wide association studies on a core collection of common bean accessions to dissect the genetic architecture and identify genomic regions associated with seed morphological traits related to weight, size, and shape. Phenotypic data were collected by high-throughput image-based approaches, and utilized to test associations with 10,362 single-nucleotide polymorphism markers using multilocus mixed models. We searched within genome-associated regions for candidate genes putatively involved in seed phenotypic variation. The collection exhibited high variability for the entire set of seed traits, and the Andean gene pool was found to produce larger, heavier seeds than the Mesoamerican gene pool. Strong pairwise correlations were verified for most seed traits. Genome-wide association studies identified marker-trait associations accounting for a considerable amount of phenotypic variation in length, width, projected area, perimeter, and circularity in 4 distinct genomic regions. Promising candidate genes were identified, e.g. those encoding an AT-hook motif nuclear-localized protein 8, type 2C protein phosphatases, and a protein Mei2-like 4 isoform, known to be associated with seed size and weight regulation. Moreover, the genes that were pinpointed are also good candidates for functional analysis to validate their influence on seed shape and size in common bean and other related crops.
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Affiliation(s)
- Willian Giordani
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Henrique Castro Gama
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | | | - Antonio Augusto Franco Garcia
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Maria Lucia Carneiro Vieira
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
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Luo J, Rouse MN, Hua L, Li H, Li B, Li T, Zhang W, Gao C, Wang Y, Dubcovsky J, Chen S. Identification and characterization of Sr22b, a new allele of the wheat stem rust resistance gene Sr22 effective against the Ug99 race group. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:554-563. [PMID: 34695276 PMCID: PMC8882774 DOI: 10.1111/pbi.13737] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/09/2021] [Accepted: 10/19/2021] [Indexed: 05/09/2023]
Abstract
Wheat stem (or black) rust, caused by Puccinia graminis f. sp. tritici (Pgt), has been historically among the most devastating global fungal diseases of wheat. The recent occurrence and spread of new virulent races such as Ug99 have prompted global efforts to identify and isolate more effective stem rust resistance (Sr) genes. Here, we report the map‐based cloning of the Ug99‐effective SrTm5 gene from diploid wheat Triticum monococcum accession PI 306540 that encodes a typical coiled‐coil nucleotide‐binding leucine‐rich repeat protein. This gene, designated as Sr22b, is a new allele of Sr22 with a rare insertion of a large (13.8‐kb) retrotransposon into its second intron. Biolistic transformation of an ~112‐kb circular bacterial artificial chromosome plasmid carrying Sr22b into the susceptible wheat variety Fielder was sufficient to confer resistance to stem rust. In a survey of 168 wheat genotypes, Sr22b was present only in cultivated T. monococcum subsp. monococcum accessions but absent in all tested tetraploid and hexaploid wheat lines. We developed a diagnostic molecular marker for Sr22b and successfully introgressed a T. monococcum chromosome segment containing this gene into hexaploid wheat to accelerate its deployment and pyramiding with other Sr genes in wheat breeding programmes. Sr22b can be a valuable component of gene pyramids or transgenic cassettes combining different resistance genes to control this devastating disease.
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Affiliation(s)
- Jing Luo
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Matthew N. Rouse
- USDA‐ARS Cereal Disease Laboratory and Department of Plant PathologyUniversity of MinnesotaSt. PaulMN55108USA
| | - Lei Hua
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Hongna Li
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Tianya Li
- College of Plant ProtectionShenyang Agricultural UniversityShenyangLiaoning110000China
| | - Wenjun Zhang
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Jorge Dubcovsky
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
| | - Shisheng Chen
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
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10
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Wang WB, Ao T, Zhang YY, Wu D, Xu W, Han B, Liu AZ. Genome-wide analysis of the B3 transcription factors reveals that RcABI3/VP1 subfamily plays important roles in seed development and oil storage in castor bean ( Ricinus communis). PLANT DIVERSITY 2022; 44:201-212. [PMID: 35505987 PMCID: PMC9043308 DOI: 10.1016/j.pld.2021.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 06/14/2023]
Abstract
The B3 transcription factors (TFs) in plants play vital roles in numerous biological processes. Although B3 genes have been broadly identified in many plants, little is known about their potential functions in mediating seed development and material accumulation. Castor bean (Ricinus communis) is a non-edible oilseed crop considered an ideal model system for seed biology research. Here, we identified a total of 61 B3 genes in the castor bean genome, which can be classified into five subfamilies, including ABI3/VP1, HSI, ARF, RAV and REM. The expression profiles revealed that RcABI3/VP1 subfamily genes are significantly up-regulated in the middle and later stages of seed development, indicating that these genes may be associated with the accumulation of storage oils. Furthermore, through yeast one-hybrid and tobacco transient expression assays, we detected that ABI3/VP1 subfamily member RcLEC2 directly regulates the transcription of RcOleosin2, which encodes an oil-body structural protein. This finding suggests that RcLEC2, as a seed-specific TF, may be involved in the regulation of storage materials accumulation. This study provides novel insights into the potential roles and molecular basis of B3 family proteins in seed development and material accumulation.
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Affiliation(s)
- Wen-Bo Wang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Ao
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Mengla, 666303, China
| | - Yan-Yu Zhang
- Northwest A&F University, Yangling, 712100, China
| | - Di Wu
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Xu
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
| | - Bing Han
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
| | - Ai-Zhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), Southwest Forestry University, Kunming, 650224, China
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11
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Rivera Pérez CA, Janz D, Schneider D, Daniel R, Polle A. Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provides Insight into N Uptake from Forest Soil. mSystems 2022; 7:e0095721. [PMID: 35089084 PMCID: PMC8725588 DOI: 10.1128/msystems.00957-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/29/2021] [Indexed: 01/05/2023] Open
Abstract
Mineral nitrogen (N) is a major nutrient showing strong fluctuations in the environment due to anthropogenic activities. The acquisition and translocation of N to forest trees are achieved mainly by highly diverse ectomycorrhizal fungi (EMF) living in symbioses with their host roots. Here, we examined colonized root tips to characterize the entire root-associated fungal community by DNA metabarcoding-Illumina sequencing of the fungal internal transcribed spacer 2 (ITS2) molecular marker and used RNA sequencing to target metabolically active fungi and the plant transcriptome after N application. The study was conducted with beech (Fagus sylvatica L.), a dominant tree species in central Europe, grown in native forest soil. We demonstrate strong enrichment of 15N from nitrate or ammonium in the ectomycorrhizal roots by stable-isotope labeling. The relative abundance of the EMF members in the fungal community was correlated with their transcriptional abundances. The fungal metatranscriptome covered Kyoto Encyclopedia of Genes and Genomes (KEGG) and Eukaryotic Orthologous Groups (KOG) categories similar to those of model fungi and did not reveal significant changes related to N metabolization but revealed species-specific transcription patterns, supporting trait stability. In contrast to the resistance of the fungal metatranscriptome, the transcriptome of the host exhibited dedicated nitrate- or ammonium-responsive changes with the upregulation of transporters and enzymes required for nitrate reduction and a drastic enhancement of glutamine synthetase transcript levels, indicating the channeling of ammonium into the pathway for plant protein biosynthesis. Our results support that naturally assembled fungal communities living in association with the tree roots buffer nutritional signals in their own metabolism but do not shield plants from high environmental N levels. IMPORTANCE Although EMF are well known for their role in supporting tree N nutrition, the molecular mechanisms underlying N flux from the soil solution into the host through the ectomycorrhizal pathway remain widely unknown. Furthermore, ammonium and nitrate availability in the soil solution is subject to frequent oscillations that create a dynamic environment for the tree roots and associated microbes during N acquisition. Therefore, it is important to understand how root-associated mycobiomes and the tree roots handle these fluctuations. We studied the responses of the symbiotic partners by screening their transcriptomes after a sudden environmental flux of nitrate or ammonium. We show that the fungi and the host respond asynchronously, with the fungi displaying resistance to increased nitrate or ammonium and the host dynamically metabolizing the supplied N sources. This study provides insights into the molecular mechanisms of the symbiotic partners operating under N enrichment in a multidimensional symbiotic system.
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Affiliation(s)
- Carmen Alicia Rivera Pérez
- Forest Botany and Tree Physiology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Dennis Janz
- Forest Botany and Tree Physiology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
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12
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Kang SH, Lee WH, Sim JS, Thaku N, Chang S, Hong JP, Oh TJ. De novo Transcriptome Assembly of Senna occidentalis Sheds Light on the Anthraquinone Biosynthesis Pathway. FRONTIERS IN PLANT SCIENCE 2022; 12:773553. [PMID: 35046973 PMCID: PMC8761625 DOI: 10.3389/fpls.2021.773553] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Senna occidentalis is an annual leguminous herb that is rich in anthraquinones, which have various pharmacological activities. However, little is known about the genetics of S. occidentalis, particularly its anthraquinone biosynthesis pathway. To broaden our understanding of the key genes and regulatory mechanisms involved in the anthraquinone biosynthesis pathway, we used short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) to perform a spatial and temporal transcriptomic analysis of S. occidentalis. This generated 121,592 RNA-Seq unigenes and 38,440 Iso-Seq unigenes. Comprehensive functional annotation and classification of these datasets using public databases identified unigene sequences related to major secondary metabolite biosynthesis pathways and critical transcription factor families (bHLH, WRKY, MYB, and bZIP). A tissue-specific differential expression analysis of S. occidentalis and measurement of the amount of anthraquinones revealed that anthraquinone accumulation was related to the gene expression levels in the different tissues. In addition, the amounts and types of anthraquinones produced differ between S. occidentalis and S. tora. In conclusion, these results provide a broader understanding of the anthraquinone metabolic pathway in S. occidentalis.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Woo-Haeng Lee
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, South Korea
| | - Joon-Soo Sim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Niha Thaku
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, South Korea
| | - Saemin Chang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Jong-Pil Hong
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, South Korea
- Genome-Based BioIT Convergence Institute, Asan, South Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, South Korea
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13
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Medicago ABI3 Splicing Isoforms Regulate the Expression of Different Gene Clusters to Orchestrate Seed Maturation. PLANTS 2021; 10:plants10081710. [PMID: 34451755 PMCID: PMC8398556 DOI: 10.3390/plants10081710] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022]
Abstract
Seed maturation comprises important developmental processes, such as seed filling and the acquisition of seed germination capacity, desiccation tolerance, longevity, and dormancy. The molecular regulation of these processes is tightly controlled by the LAFL transcription factors, among which ABSCISIC ACID INSENSITIVE 3 (ABI3) was shown to be involved in most of these seed maturation processes. Here, we studied the ABI3 gene from Medicago truncatula, a model legume plant for seed studies. With the transcriptomes of two loss-of-function Medicago abi3 mutants, we were able to show that many gene classes were impacted by the abi3 mutation at different stages of early, middle, and late seed maturation. We also discovered three MtABI3 expression isoforms, which present contrasting expression patterns during seed development. Moreover, by ectopically expressing these isoforms in Medicago hairy roots generated from the abi3 mutant line background, we showed that each isoform regulated specific gene clusters, suggesting divergent molecular functions. Furthermore, we complemented the Arabidopsis abi3 mutant with each of the three MtABI3 isoforms and concluded that all isoforms were capable of restoring seed viability and desiccation tolerance phenotypes even if not all isoforms complemented the seed color phenotype. Taken together, our results allow a better understanding of the ABI3 network in Medicago during seed development, as well as the discovery of commonly regulated genes from the three MtABI3 isoforms, which can give us new insights into how desiccation tolerance and seed viability are regulated.
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14
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Ruan CC, Chen Z, Hu FC, Fan W, Wang XH, Guo LJ, Fan HY, Luo ZW, Zhang ZL. Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.). BMC Genomics 2021; 22:561. [PMID: 34289810 PMCID: PMC8296579 DOI: 10.1186/s12864-021-07854-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The B3 superfamily (B3s) represents a class of large plant-specific transcription factors, which play diverse roles in plant growth and development process including flowering induction. However, identification and functional surveys of B3 superfamily have not been reported in ethylene-induced pineapple flowering (Ananas comosus). RESULTS 57 B3 genes containing B3 domain were identified and phylogenetically classified into five subfamilies. Chromosomal localization analysis revealed that 54 of 57 AcB3s were located on 21 Linkage Groups (LG). Collinearity analysis demonstrated that the segmental duplication was the main event in the evolution of B3 gene superfamily, and most of them were under purifying selection. The analysis of cis-element composition suggested that most of these genes may have function in response to abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR analysis of 40 AcB3s containing ethylene responsive elements exhibited that the expression levels of 35 genes were up-regulated within 1 d after ethephon treatment and some were highly expressed in flower bud differentiation period in stem apex, such as Aco012003, Aco019552 and Aco014401. CONCLUSION This study provides a basic information of AcB3s and clues for involvement of some AcB3s in ethylene-induced flowering in pineapple.
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Affiliation(s)
- Cheng Cheng Ruan
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhe Chen
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Fu Chu Hu
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Wei Fan
- College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, China
| | - Xiang He Wang
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Li Jun Guo
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Hong Yan Fan
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhi Wen Luo
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhi Li Zhang
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou, 571100, China.
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15
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Liu Z, Ge XX, Wu XM, Xu Q, Atkinson RG, Guo WW. Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis. BMC Genomics 2020; 21:305. [PMID: 32299363 PMCID: PMC7161213 DOI: 10.1186/s12864-020-6715-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/03/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogenesis, little is known about the B3 superfamily in citrus, and which members might be involved in SE. RESULTS Genome-wide sequence analysis identified 72 (CsB3) and 69 (CgB3) putative B3 superfamily members in the genomes of sweet orange (Citrus sinensis, polyembryonic) and pummelo (C. grandis, monoembryonic), respectively. Genome duplication analysis indicated that segmental and tandem duplication events contributed to the expansion of the B3 superfamily in citrus, and that the B3 superfamily evolved under the effect of purifying selection. Phylogenetic relationships were well supported by conserved gene structure and motifs outside the B3 domain, which allowed possible functions to be inferred by comparison with homologous genes from Arabidopsis. Expression analysis identified 23 B3 superfamily members that were expressed during SE in citrus and 17 that may play functional roles at late SE stages. Eight B3 genes were identified that were specific to the genome of polyembryonic sweet orange compared to monoembryonic pummelo. Of these eight B3 genes, CsARF19 was found to be specifically expressed at higher levels in embryogenic callus (EC), implying its possible involvement in EC initiation. CONCLUSIONS This study provides a genome-wide analysis of the citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, and identifies specific family members that may be associated with SE.
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Affiliation(s)
- Zheng Liu
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064 China
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiao-Xia Ge
- Center of Applied Biotechnology, Wuhan University of Bioengineering, Wuhan, 430415 China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
| | - Ross G. Atkinson
- The New Zealand Institute for Plant & Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
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16
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Ahmad B, Zhang S, Yao J, Rahman MU, Hanif M, Zhu Y, Wang X. Genomic Organization of the B3-Domain Transcription Factor Family in Grapevine ( Vitis vinifera L.) and Expression during Seed Development in Seedless and Seeded Cultivars. Int J Mol Sci 2019; 20:ijms20184553. [PMID: 31540007 PMCID: PMC6770561 DOI: 10.3390/ijms20184553] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/03/2019] [Accepted: 09/11/2019] [Indexed: 12/22/2022] Open
Abstract
Members of the plant-specific B3-domain transcription factor family have important and varied functions, especially with respect to vegetative and reproductive growth. Although B3 genes have been studied in many other plants, there is limited information on the genomic organization and expression of B3 genes in grapevine (Vitis vinifera L.). In this study, we identified 50 B3 genes in the grapevine genome and analyzed these genes in terms of chromosomal location and syntenic relationships, intron–exon organization, and promoter cis-element content. We also analyzed the presumed proteins in terms of domain structure and phylogenetic relationships. Based on the results, we classified these genes into five subfamilies. The syntenic relationships suggest that approximately half of the genes resulted from genome duplication, contributing to the expansion of the B3 family in grapevine. The analysis of cis-element composition suggested that most of these genes may function in response to hormones, light, and stress. We also analyzed expression of members of the B3 family in various structures of grapevine plants, including the seed during seed development. Many B3 genes were expressed preferentially in one or more structures of the developed plant, suggesting specific roles in growth and development. Furthermore, several of the genes were expressed differentially in early developing seeds from representative seeded and seedless cultivars, suggesting a role in seed development or abortion. The results of this study provide a foundation for functional analysis of B3 genes and new resources for future molecular breeding of grapevine.
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Affiliation(s)
- Bilal Ahmad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Xianyang 712100, China.
| | - Songlin Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Xianyang 712100, China.
| | - Jin Yao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Xianyang 712100, China.
| | - Mati Ur Rahman
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Xianyang 712100, China.
| | - Muhammad Hanif
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Xianyang 712100, China.
| | - Yanxun Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Xianyang 712100, China.
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Xianyang 712100, China.
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17
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A comprehensive analysis of the B3 superfamily identifies tissue-specific and stress-responsive genes in chickpea ( Cicer arietinum L.). 3 Biotech 2019; 9:346. [PMID: 31497464 DOI: 10.1007/s13205-019-1875-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
Abstract
The aim of this study was to provide a comprehensive analysis of the plant-specific B3 domain-containing transcription factors (TFs) in chickpea. Scanning of the chickpea genome resulted in the identification of 51 B3 domain-containing TFs that were located on seven out of eight chickpea chromosomes. Based on the presence of additional domains other than the B3 domain, the candidates were classified into four subfamilies, i.e., ARF (24), REM (19), LAV (6) and RAV (2). Phylogenetic analysis classified them into four groups in which members of the same group had similar intron-exon organization and motif composition. Genome duplication analysis of the candidate B3 genes revealed an event of segmental duplication that was instrumental in the expansion of the B3 gene family. Ka/Ks analysis showed that the B3 gene family was under purifying selection. Further, chickpea B3 genes showed maximum orthology with Medicago followed by soybean and Arabidopsis. Promoter analyses of the B3 genes led to the identification of several tissue-specific and stress-responsive cis-regulatory elements. Expression profiling of the candidate B3 genes using publicly available RNA-seq data of several chickpea tissues indicated their putative role in plant development and abiotic stress response. These findings were further validated by real-time expression analysis. Overall, this study provides a comprehensive analysis of the B3 domain-containing proteins in chickpea that would aid in devising strategies for crop manipulation in chickpea.
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18
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Xia F, Sun T, Yang S, Wang X, Chao J, Li X, Hu J, Cui M, Liu G, Wang D, Sun Y. Insight into the B3Transcription Factor Superfamily and Expression Profiling of B3 Genes in Axillary Buds after Topping in Tobacco( Nicotiana tabacum L.). Genes (Basel) 2019; 10:E164. [PMID: 30791672 PMCID: PMC6409620 DOI: 10.3390/genes10020164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 12/11/2022] Open
Abstract
Members of the plant-specific B3 transcription factor superfamily play important roles in various growth and developmental processes in plants. Even though there are many valuable studies on B3 genes in other species, little is known about the B3 superfamily in tobacco. We identified 114 B3 proteins from tobacco using comparative genome analysis. These proteins were classified into four subfamilies based on their phylogenetic relationships, and include the ARF, RAV, LAV, and REM subfamilies. The chromosomal locations, gene structures, conserved protein motifs, and sub-cellular localizations of the tobacco B3 proteins were analyzed. The patterns of exon-intron numbers and arrangement and the protein structures of the tobacco B3 proteins were in general agreement with their phylogenetic relationships. The expression patterns of 114 B3 genes revealed that many B3 genes show tissue-specific expression. The expression levels of B3 genes in axillary buds after topping showed that the REM genes are mainly up-regulated in response to topping, while the ARF genes are down-regulated after topping.
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Affiliation(s)
- Fei Xia
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Tingting Sun
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.
| | - Shuangjuan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
| | - Xiao Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Jiangtao Chao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
| | - Xiaoxu Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Junhua Hu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Mengmeng Cui
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
| | - Guanshan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
| | - Dawei Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
| | - Yuhe Sun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao 266101, China.
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19
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Lepiniec L, Devic M, Roscoe TJ, Bouyer D, Zhou DX, Boulard C, Baud S, Dubreucq B. Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development. PLANT REPRODUCTION 2018; 31:291-307. [PMID: 29797091 DOI: 10.1007/s00497-018-0337-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/10/2018] [Indexed: 05/20/2023]
Abstract
The LAFL (i.e. LEC1, ABI3, FUS3, and LEC2) master transcriptional regulators interact to form different complexes that induce embryo development and maturation, and inhibit seed germination and vegetative growth in Arabidopsis. Orthologous genes involved in similar regulatory processes have been described in various angiosperms including important crop species. Consistent with a prominent role of the LAFL regulators in triggering and maintaining embryonic cell fate, their expression appears finely tuned in different tissues during seed development and tightly repressed in vegetative tissues by a surprisingly high number of genetic and epigenetic factors. Partial functional redundancies and intricate feedback regulations of the LAFL have hampered the elucidation of the underpinning molecular mechanisms. Nevertheless, genetic, genomic, cellular, molecular, and biochemical analyses implemented during the last years have greatly improved our knowledge of the LALF network. Here we summarize and discuss recent progress, together with current issues required to gain a comprehensive insight into the network, including the emerging function of LEC1 and possibly LEC2 as pioneer transcription factors.
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Affiliation(s)
- L Lepiniec
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France.
| | - M Devic
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - T J Roscoe
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - D Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - D-X Zhou
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Sud 11, Université Paris-Saclay, 91405, Orsay, France
| | - C Boulard
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - S Baud
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - B Dubreucq
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
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Hanano A, Almousally I, Shaban M, Murphy DJ. Arabidopsis plants exposed to dioxin result in a WRINKLED seed phenotype due to 20S proteasomal degradation of WRI1. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1781-1794. [PMID: 29394403 DOI: 10.1093/jxb/ery027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dioxins are highly toxic persistent organic pollutants bioaccumulated by both plants and animals that cause severe developmental abnormalities in humans. We investigated the effects of dioxins on seed development in Arabidopsis. Plants were exposed to various concentrations of the most toxic congener of dioxins, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and the effects on seed development were analysed in-depth at transcriptome, proteome and metabolome levels. Exposure to dioxin led to generalized effects on vegetative tissues plus a specific set of perturbations to seed development. Mature seeds from TCDD-treated plants had a characteristic 'wrinkled' phenotype, due to a two-thirds reduction in storage oil content. Transcriptional analysis of a panel of genes related to lipid and carbohydrate metabolism was consistent with the observed biochemical phenotypes. There were increases in WRI1 and LEC1 expression but decreases in ABI3 and FUS3 expression, which is puzzling in view of the low seed oil phenotype. This anomaly was explained by increased expression of 20S proteasome components that resulted in a substantial degradation of WRI1 protein, despite the up-regulation of the WRI1 gene. Our findings reveal novel effects of dioxins that lead to altered gene regulation patterns that profoundly affect seed development in Arabidopsis.
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Affiliation(s)
- Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), Damascus, Syria
| | - Ibrahem Almousally
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), Damascus, Syria
| | - Mouhnad Shaban
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), Damascus, Syria
| | - Denis J Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, UK
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Sharma N, Dang TM, Singh N, Ruzicic S, Mueller-Roeber B, Baumann U, Heuer S. Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice. RICE (NEW YORK, N.Y.) 2018; 11:2. [PMID: 29313187 PMCID: PMC5758481 DOI: 10.1186/s12284-017-0192-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/12/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown. RESULTS Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression. CONCLUSION This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance.
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Affiliation(s)
- Niharika Sharma
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Trang Minh Dang
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Intrexon Corp, California, USA
| | - Namrata Singh
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | | | | | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Sigrid Heuer
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia.
- International Rice Research Institute (IRRI), Los Banos, Philippines.
- Rothamsted Research, Plant Science Department, Hertfordshire, Harpenden, AL5 2JQ, UK.
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Almeida DSM, Gramacho KP, Cardoso THS, Micheli F, Alvim FC, Pirovani CP. Cacao Phylloplane: The First Battlefield against Moniliophthora perniciosa, Which Causes Witches' Broom Disease. PHYTOPATHOLOGY 2017; 107:864-871. [PMID: 28430024 DOI: 10.1094/phyto-06-16-0226-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The phylloplane is the first contact surface between Theobroma cacao and the fungus Moniliophthora perniciosa, which causes witches' broom disease (WBD). We evaluated the index of short glandular trichomes (SGT) in the cacao phylloplane and the effect of irrigation on the disease index of cacao genotypes with or without resistance to WBD, and identified proteins present in the phylloplane. The resistant genotype CCN51 and susceptible Catongo presented a mean index of 1,600 and 700 SGT cm-2, respectively. The disease index in plants under drip irrigation was reduced by approximately 30% compared with plants under sprinkler irrigation prior to inoculation. Leaf water wash (LWW) of the cacao inhibited the germination of spores by up to 98%. Proteins from the LWW of CCN51 were analyzed by two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by tandem mass spectrometry. The gel showed 71 spots and identified a total of 42 proteins (28 from the plant and 14 from bacteria). Proteins related to defense and synthesis of defense metabolites and involved in nucleic acid metabolism were identified. The results support the hypothesis that the proteins and water-soluble compounds secreted to the cacao phylloplane participate in the defense against pathogens. They also suggest that SGT can contribute to the resistance of cacao.
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Affiliation(s)
- D S M Almeida
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - K P Gramacho
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - T H S Cardoso
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - F Micheli
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - F C Alvim
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - C P Pirovani
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
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Fatihi A, Boulard C, Bouyer D, Baud S, Dubreucq B, Lepiniec L. Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 250:198-204. [PMID: 27457996 DOI: 10.1016/j.plantsci.2016.06.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 05/11/2023]
Abstract
Increasing yield and quality of seed storage compounds in a sustainable way is a key challenge for our societies. Genome-wide analyses conducted in both monocot and dicot angiosperms emphasized drastic transcriptional switches that occur during seed development. In Arabidopsis thaliana, a reference species, genetic and molecular analyses have demonstrated the key role of LAFL (LEC1, ABI3, FUS3, and LEC2) transcription factors (TFs), in controlling gene expression programs essential to accomplish seed maturation and the accumulation of storage compounds. Here, we summarize recent progress obtained in the characterization of these LAFL proteins, their regulation, partners and target genes. Moreover, we illustrate how these evolutionary conserved TFs can be used to engineer new crops with altered seed compositions and point out the current limitations. Last, we discuss about the interest of investigating further the environmental and epigenetic regulation of this network for the coming years.
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Affiliation(s)
- Abdelhak Fatihi
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
| | - Céline Boulard
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Daniel Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris cedex 05, France
| | - Sébastien Baud
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Bertrand Dubreucq
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Loïc Lepiniec
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
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24
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Grimault A, Gendrot G, Chaignon S, Gilard F, Tcherkez G, Thévenin J, Dubreucq B, Depège-Fargeix N, Rogowsky PM. Role of B3 domain transcription factors of the AFL family in maize kernel filling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:116-25. [PMID: 26025525 DOI: 10.1016/j.plantsci.2015.03.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 05/20/2023]
Abstract
In the dicot Arabidopsis thaliana, the B3 transcription factors, ABA-INSENSITIVE 3 (ABI3), FUSCA 3 (FUS3) and LEAFY COTYLEDON 2 (LEC2) are key regulators of seed maturation. This raises the question of the role of ABI3/FUS3/LEC2 (AFL) proteins in cereals, where not only the embryo but also the persistent endosperm accumulates reserve substances. Among the five ZmAFL genes identified in the maize genome, ZmAFL2 and ZmAFL3/ZmVp1 closely resemble FUS3 and ABI3, respectively, in terms of their sequences, domain structure and gene activity profiles. Of the three genes that fall into the LEC2 phylogenetic sub-clade, ZmAFL5 and ZmAFL6 have constitutive gene activity, whereas ZmAFL4, like LEC2, has preferential gene activity in pollen and seed, although its seed gene activity is restricted to the endosperm during reserve accumulation. Knock down of ZmAFL4 gene activity perturbs carbon metabolism and reduces starch content in the developing endosperm at 20 DAP. ZmAFL4 and ZmAFL3/ZmVp1 trans-activate a maize oleosin promoter in a heterologous moss system. In conclusion our results suggest, based on gene activity profiles, that the functions of FUS3 and ABI3 could be conserved between dicot and monocot species. In contrast, LEC2 function may have partially diverged in cereals where our findings provide first evidence of the specialization of ZmAFL4 for roles in the endosperm.
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Affiliation(s)
- Aurélie Grimault
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Ghislaine Gendrot
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Sandrine Chaignon
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Françoise Gilard
- CNRS, UMR 9213, Institute of Plant Sciences Paris-Saclay, F-91405 Orsay, France
| | - Guillaume Tcherkez
- CNRS, UMR 9213, Institute of Plant Sciences Paris-Saclay, F-91405 Orsay, France
| | - Johanne Thévenin
- INRA, UMR 1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Bertrand Dubreucq
- INRA, UMR 1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Nathalie Depège-Fargeix
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Peter M Rogowsky
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France.
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25
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Liu Y, Yuan J, Ma H, Song J, Wang L, Weng Q. Characterization and functional analysis of a B3 domain factor from Zea mays. J Appl Genet 2015; 56:427-438. [PMID: 25953393 DOI: 10.1007/s13353-015-0287-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 11/26/2022]
Abstract
In this study, we isolated a full-length cDNA and named ZmBDF from zea mays. ZmBDF encoded a protein of 356 amino acids and phylogenetic analysis showed that it belongs to a closely related subgroup with B3 domain factors in plants. The transcript level of ZmBDF could be induced by ABA, MeJA, salt or drought treatments. To further investigated the function of ZmBDF, ZmBDF over-expression transgenic lines were got by transforming it into Arabidopsis thaliana. ZmBDF over-expression transgenic plants in Arabidopsis could increase drought and salt tolerant in germination assay. Under drought condition, net photosynthetic rates (PN), stomatal conductance (gs), and internal leaf CO2 concentration (Ci) were less affected in transgenic plants compared with wild type. Besides, the chlorophyll a and chlorophyll b (chl a/chl b) ratio decreased in WT plants than the transgenic plants and total carotenoid content show opposite trends. Moreover, transgenic plants could also reduce the stomatal density and changed the stomatal shape. Taken together, our data suggested that ZmBDF could improve stress tolerance to drought and salt in maize.
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Affiliation(s)
- Yinghui Liu
- Hebei North University, Zhangjikou, Heibei, China, 075000.
| | - Jincheng Yuan
- Hebei North University, Zhangjikou, Heibei, China, 075000
| | - Halian Ma
- Hebei North University, Zhangjikou, Heibei, China, 075000
| | - Jinhui Song
- Hebei North University, Zhangjikou, Heibei, China, 075000
| | - Lingyun Wang
- Hebei North University, Zhangjikou, Heibei, China, 075000
| | - Qiaoyun Weng
- Hebei North University, Zhangjikou, Heibei, China, 075000
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26
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Deng W, Casao MC, Wang P, Sato K, Hayes PM, Finnegan EJ, Trevaskis B. Direct links between the vernalization response and other key traits of cereal crops. Nat Commun 2015; 6:5882. [PMID: 25562483 DOI: 10.1038/ncomms6882] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 11/17/2014] [Indexed: 11/09/2022] Open
Abstract
Transcription of the vernalization1 gene (VRN1) is induced by prolonged cold (vernalization) to trigger flowering of cereal crops, such as wheat and barley. VRN1 encodes a MADS box transcription factor that promotes flowering by regulating the expression of other genes. Here we use transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to identify direct targets of VRN1. Over 500 genomic regions were identified as potential VRN1-binding targets by ChIP-seq. VRN1 binds the promoter of flowering locus T-like 1, a promoter of flowering in vernalized plants. VRN1 also targets vernalization2 and ODDSOC2, repressors of flowering that are downregulated in vernalized plants. RNA-seq identified additional VRN1 targets that might play roles in triggering flowering. Other targets of VRN1 include genes that play central roles in low-temperature-induced freezing tolerance, spike architecture and hormone metabolism. This provides evidence for direct regulatory links between the vernalization response pathway and other important traits in cereal crops.
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Affiliation(s)
- Weiwei Deng
- CSIRO, Agriculture, Canberra, Australian Capital Territory 2601, Australia
| | - M Cristina Casao
- CSIRO, Agriculture, Canberra, Australian Capital Territory 2601, Australia
| | - Penghao Wang
- CSIRO, Agriculture, Canberra, Australian Capital Territory 2601, Australia
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon 97331, USA
| | - E Jean Finnegan
- CSIRO, Agriculture, Canberra, Australian Capital Territory 2601, Australia
| | - Ben Trevaskis
- CSIRO, Agriculture, Canberra, Australian Capital Territory 2601, Australia
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27
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Mittal A, Gampala SSL, Ritchie GL, Payton P, Burke JJ, Rock CD. Related to ABA-Insensitive3(ABI3)/Viviparous1 and AtABI5 transcription factor coexpression in cotton enhances drought stress adaptation. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:578-89. [PMID: 24483851 PMCID: PMC4043863 DOI: 10.1111/pbi.12162] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 11/24/2013] [Accepted: 12/02/2013] [Indexed: 05/18/2023]
Abstract
Drought tolerance is an important trait being pursued by the agbiotech industry. Abscisic acid (ABA) is a stress hormone that mediates a multitude of processes in growth and development, water use efficiency (WUE) and gene expression during seed development and in response to environmental stresses. Arabidopsis B3-domain transcription factor Related to ABA-Insensitive3 (ABI3)/Viviparous1 (namely AtRAV2) and basic leucine zipper (bZIPs) AtABI5 or AtABF3 transactivated ABA-inducible promoter:GUS reporter expression in a maize mesophyll protoplast transient assay and showed synergies in reporter transactivation when coexpressed. Transgenic cotton (Gossypium hirsutum) expressing AtRAV1/2 and/or AtABI5 showed resistance to imposed drought stress under field and greenhouse conditions and exhibited improved photosynthesis and WUEs associated with absorption through larger root system and greater leaf area. We observed synergy for root biomass accumulation in the greenhouse, intrinsic WUE in the field and drought tolerance in stacked AtRAV and AtABI5 double-transgenic cotton. We assessed AtABI5 and AtRAV1/2 involvement in drought stress adaptations through reactive oxygen species scavenging and osmotic adjustment by marker gene expression in cotton. Deficit irrigation-grown AtRAV1/2 and AtABI5 transgenics had 'less-stressed' molecular and physiological phenotypes under drought, likely due to improved photoassimilation and root and shoot sink strengths and enhanced expression of endogenous GhRAV and genes for antioxidant and osmolyte biosynthesis. Overexpression of bZIP and RAV TFs could impact sustainable cotton agriculture and potentially other crops under limited irrigation conditions.
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Affiliation(s)
- Amandeep Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock TX 79409-3131
| | | | - Glen L. Ritchie
- Department of Plant and Soil Science, Texas Tech University, Lubbock TX 79409-2122
| | - Paxton Payton
- USDA-ARS Plant Stress and Germplasm Lab, Lubbock, TX 79415
| | - John J. Burke
- USDA-ARS Plant Stress and Germplasm Lab, Lubbock, TX 79415
| | - Christopher D. Rock
- Department of Biological Sciences, Texas Tech University, Lubbock TX 79409-3131
- The author responsible for distribution of materials integral to the findings presented in this article is: (). Ph. (806) 742-3722 x271; fax (806) 742-2963
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Cheng F, Wu J, Wang X. Genome triplication drove the diversification of Brassica plants. HORTICULTURE RESEARCH 2014; 1:14024. [PMID: 26504539 PMCID: PMC4596316 DOI: 10.1038/hortres.2014.24] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 05/20/2023]
Abstract
The genus Brassica belongs to the plant family Brassicaceae, which includes many important crop species that are used as oilseed, condiments, or vegetables throughout the world. Brassica plants comprise many diverse species, and each species contains rich morphotypes showing extreme traits. Brassica species experienced an extra whole genome triplication (WGT) event compared with the model plant Arabidopsis thaliana. Whole genome sequencing of the Brassica species Brassica rapa, Brassica oleracea and others demonstrated that WGT plays an important role in the speciation and morphotype diversification of Brassica plants. Comparative genomic analysis based on the genome sequences of B. rapa and A. thaliana clearly identified the WGT event and further demonstrated that the translocated Proto-Calepine Karyotype (tPCK, n=7) was the diploid ancestor of the three subgenomes in B. rapa. Following WGT, subsequent extensive genome fractionation, block reshuffling and chromosome reduction accompanied by paleocentromere descent from the three tPCK subgenomes during the rediploidization process produced stable diploid species. Genomic rearrangement of the diploid species and their hybridization then contributed to Brassica speciation. The subgenome dominance effect and biased gene retention, such as the over-retention of auxin-related genes after WGT, promoted functional gene evolution and thus propelled the expansion of rich morphotypes in the Brassica species. In conclusion, the WGT event initiated subsequent genomic and gene-level evolution, which further drove Brassica speciation and created rich morphotypes in each species.
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Affiliation(s)
- Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Kim HU, Jung SJ, Lee KR, Kim EH, Lee SM, Roh KH, Kim JB. Ectopic overexpression of castor bean LEAFY COTYLEDON2 (LEC2) in Arabidopsis triggers the expression of genes that encode regulators of seed maturation and oil body proteins in vegetative tissues. FEBS Open Bio 2013; 4:25-32. [PMID: 24363987 PMCID: PMC3863707 DOI: 10.1016/j.fob.2013.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 12/27/2022] Open
Abstract
The LEAFY COTYLEDON2 (LEC2) gene plays critically important regulatory roles during both early and late embryonic development. Here, we report the identification of the LEC2 gene from the castor bean plant (Ricinus communis), and characterize the effects of its overexpression on gene regulation and lipid metabolism in transgenic Arabidopsis plants. LEC2 exists as a single-copy gene in castor bean, is expressed predominantly in embryos, and encodes a protein with a conserved B3 domain, but different N- and C-terminal domains to those found in LEC2 from Arabidopsis. Ectopic overexpression of LEC2 from castor bean under the control of the cauliflower mosaic virus (CaMV) 35S promoter in Arabidopsis plants induces the accumulation of transcripts that encodes five major transcription factors (the LEAFY COTYLEDON1 (LEC1), LEAFY COTYLEDON1-LIKE (L1L), FUSCA3 (FUS3), and ABSCISIC ACID INSENSITIVE 3 (ABI3) transcripts for seed maturation, and WRINKELED1 (WRI1) transcripts for fatty acid biosynthesis), as well as OLEOSIN transcripts for the formation of oil bodies in vegetative tissues. Transgenic Arabidopsis plants that express the LEC2 gene from castor bean show a range of dose-dependent morphological phenotypes and effects on the expression of LEC2-regulated genes during seedling establishment and vegetative growth. Expression of castor bean LEC2 in Arabidopsis increased the expression of fatty acid elongase 1 (FAE1) and induced the accumulation of triacylglycerols, especially those containing the seed-specific fatty acid, eicosenoic acid (20:1Δ11), in vegetative tissues. Castor bean LEC2 is single copy and shows seed-specific expression. Over-expression of castor LEC2 induces genes involved in seed maturation in leaves. Castor LEC2 induces the accumulation of triacylglycerols and 20:1 fatty acids in leaves. Ectopic expression of castor LEC2 in Arabidopsis affects plant growth.
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Key Words
- ABI3-VP1, abscisic acid-insensitive 3-viviparous 1
- CaMV, cauliflower mosaic virus
- Castor bean
- DHA, docosahexaenoic acid
- DIG, digoxigenin
- Eicosenoic acid
- FAE1, fatty acid elongase 1
- GC, gas chromatography
- LEAFY COTYLEDON2
- ORF, open reading frame
- RT-PCR, reverse transcription polymerase chain reaction
- SSC, sodium chloride-sodium citrate
- Seed maturation
- TAG, triacylglycerol
- TF, transcription factor
- TLC, thin-layer chromatography
- Transcription factor
- Triacylglycerol
- cDNA, complementary DNA
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Affiliation(s)
- Hyun Uk Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Su-Jin Jung
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Kyeong-Ryeol Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Eun Ha Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Sang-Min Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Kyung Hee Roh
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Jong-Bum Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
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