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Han Y, Hu Q, Gong N, Yan H, Khan NU, Du Y, Sun H, Zhao Q, Peng W, Li Z, Zhang Z, Li J. Natural variation in MORE GRAINS 1 regulates grain number and grain weight in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38780111 DOI: 10.1111/jipb.13674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/14/2024] [Indexed: 05/25/2024]
Abstract
Grain yield is determined mainly by grain number and grain weight. In this study, we identified and characterized MORE GRAINS1 (MOG1), a gene associated with grain number and grain weight in rice (Oryza sativa L.), through map-based cloning. Overexpression of MOG1 increased grain yield by 18.6%-22.3% under field conditions. We determined that MOG1, a bHLH transcription factor, interacts with OsbHLH107 and directly activates the expression of LONELY GUY (LOG), which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1 (EXPLA1), positively regulating grain number per panicle and grain weight. Natural variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation, leading to functional differences. Haplotype analysis revealed that Hap-HNW, which results in a greater number and heavier grains, has undergone strong selection but has been poorly utilized in modern lowland rice breeding. In summary, the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway, thereby increasing grain number and grain weight. These findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.
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Affiliation(s)
- Yingchun Han
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qianfeng Hu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Nuo Gong
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Huimin Yan
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Najeeb Ullah Khan
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
- Rice Industrial Technology Research Institute, Guizhou University, Guiyang, 550025, China
| | - Wanxi Peng
- School of Forestry, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Junzhou Li
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
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Li JJ, Qiu XY, Dai YJ, Nyonga TM, Li CC. Genome-Wide Identification and Co-Expression Networks of WOX Gene Family in Nelumbo nucifera. PLANTS (BASEL, SWITZERLAND) 2024; 13:720. [PMID: 38475567 DOI: 10.3390/plants13050720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
WUSCHEL-related homeobox (WOX) genes are a class of plant-specific transcription factors, regulating the development of multiple tissues. However, the genomic characterizations and expression patterns of WOX genes have not been analyzed in lotus. In this study, 15 NnWOX genes were identified based on the well-annotated reference genome of lotus. According to the phylogenetic analysis, the NnWOX genes were clustered into three clades, i.e., ancient clade, intermediate clade, and WUS clade. Except for the conserved homeobox motif, we further found specific motifs of NnWOX genes in different clades and divergence gene structures, suggesting their distinct functions. In addition, two NnWOX genes in the ancient clade have conserved expression patterns and other NnWOX genes exhibit different expression patterns in lotus tissues, suggesting a low level of functional redundancy in lotus WOX genes. Furthermore, we constructed the gene co-expression networks for each NnWOX gene. Based on weighted gene co-expression network analysis (WGCNA), ten NnWOX genes and their co-expressed genes were assigned to the modules that were significantly related to the cotyledon and seed coat. We further performed RT-qPCR experiments, validating the expression levels of ten NnWOX genes in the co-expression networks. Our study reveals comprehensive genomic features of NnWOX genes in lotus, providing a solid basis for further function studies.
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Affiliation(s)
- Juan-Juan Li
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Xiao-Yan Qiu
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Yu-Jun Dai
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Tonny M Nyonga
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Chang-Chun Li
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
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Yakovleva DV, Efremova EP, Smirnov KV, Simonova VY, Konstantinov ZS, Tvorogova VE, Lutova LA. The WOX Genes from the Intermediate Clade: Influence on the Somatic Embryogenesis in Medicago truncatula. PLANTS (BASEL, SWITZERLAND) 2024; 13:223. [PMID: 38256776 PMCID: PMC10819790 DOI: 10.3390/plants13020223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
Transcription factors from the WOX family are well-known regulators of cell proliferation and differentiation in plants. Herein, we focused on several WOX genes from the intermediate clade and checked their impact on somatic embryogenesis using the model legume object Medicago truncatula. As a result, we show that MtWOX9-1 overexpression not only stimulates somatic embryogenesis in the embryogenic M. truncatula line, as it was shown previously, but can also induce somatic embryogenesis in the non-embryogenic line. Other intermediate clade WOX, including the close paralog of MtWOX9-1, as well as WOX11 homologs, did not have any significant impact on somatic embryogenesis in our in vitro cultivation system. Together, our results give new information about the diversity of the WOX family proteins and their specific functions. These data can be used for the search of new regeneration stimulators.
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Affiliation(s)
- Daria V. Yakovleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya emb, Saint Petersburg 199034, Russia; (D.V.Y.); (E.P.E.); (L.A.L.)
| | - Elena P. Efremova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya emb, Saint Petersburg 199034, Russia; (D.V.Y.); (E.P.E.); (L.A.L.)
| | - Kirill V. Smirnov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chausse 3, Pushkin, Saint Petersburg 196608, Russia;
| | - Veronika Y. Simonova
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia; (V.Y.S.); (Z.S.K.)
| | - Zakhar S. Konstantinov
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia; (V.Y.S.); (Z.S.K.)
| | - Varvara E. Tvorogova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya emb, Saint Petersburg 199034, Russia; (D.V.Y.); (E.P.E.); (L.A.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia; (V.Y.S.); (Z.S.K.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 42 Bolshaya Morskaya Street, Saint Petersburg 190000, Russia
| | - Ludmila A. Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya emb, Saint Petersburg 199034, Russia; (D.V.Y.); (E.P.E.); (L.A.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia; (V.Y.S.); (Z.S.K.)
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Zheng R, Peng Y, Chen J, Zhu X, Xie K, Ahmad S, Zhao K, Peng D, Liu ZJ, Zhou Y. The Genome-Level Survey of the WOX Gene Family in Melastoma dodecandrum Lour. Int J Mol Sci 2023; 24:17349. [PMID: 38139178 PMCID: PMC10743900 DOI: 10.3390/ijms242417349] [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: 10/15/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Though conserved in higher plants, the WOX transcription factors play crucial roles in plant growth and development of Melastoma dodecandrum Lour., which shows pioneer position in land ecosystem formation and produces nutritional fruits. Identifying the WOX family genes in M. dodecandrum is imperative for elucidating its growth and development mechanisms. However, the WOX genes in M. dodecandrum have not yet been characterized. In this study, by identification 22 WOX genes in M. dodecandrum based on current genome data, we classified family genes into three clades and nine types with homeodomains. We highlighted gene duplications of MedWOX4, which offered evidences of whole-genome duplication events. Promoter analysis illustrated that cis-regulatory elements related to light and stress responses and plant growth were enriched. Expression pattern and RT-qPCR results demonstrated that the majority of WOX genes exhibited expression in the stem. MedWOX13s displayed highest expression across various tissues. MedWOX4s displayed a specific expression in the stem. Collectively, our study provided foundations for elucidating WOX gene functions and further molecular design breeding in M. dodecandrum.
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Affiliation(s)
- Ruiyue Zheng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (S.A.); (D.P.)
| | - Yukun Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (S.A.); (D.P.)
| | - Jiemin Chen
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (S.A.); (D.P.)
| | - Xuanyi Zhu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (S.A.); (D.P.)
| | - Kai Xie
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (S.A.); (D.P.)
| | - Sagheer Ahmad
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (S.A.); (D.P.)
| | - Kai Zhao
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China;
| | - Donghui Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (S.A.); (D.P.)
| | - Zhong-Jian Liu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (S.A.); (D.P.)
| | - Yuzhen Zhou
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (S.A.); (D.P.)
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