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Zong W, Guo X, Zhang K, Chen L, Liu YG, Guo J. Photoperiod and temperature synergistically regulate heading date and regional adaptation in rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3762-3777. [PMID: 38779909 DOI: 10.1093/jxb/erae209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Plants must accurately integrate external environmental signals with their own development to initiate flowering at the appropriate time for reproductive success. Photoperiod and temperature are key external signals that determine flowering time; both are cyclical and periodic, and they are closely related. In this review, we describe photoperiod-sensitive genes that simultaneously respond to temperature signals in rice (Oryza sativa). We introduce the mechanisms by which photoperiod and temperature synergistically regulate heading date and regional adaptation in rice. We also discuss the prospects for designing different combinations of heading date genes and other cold tolerance or thermo-tolerance genes to help rice better adapt to changes in light and temperature via molecular breeding to enhance yield in the future.
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Affiliation(s)
- Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaotong Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Kai Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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Chen S, Zhong X, Wang Z, Chen B, Huang X, Xu S, Yang X, Zhou G, Zhang T. Rice stripe mosaic virus hijacks rice heading-related gene to promote the overwintering of its insect vector. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38923382 DOI: 10.1111/jipb.13722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
Rice stripe mosaic virus (RSMV) is an emerging pathogen which significantly reduces rice yields in the southern region of China. It is transmitted by the leafhopper Recilia dorsalis, which overwinters in rice fields. Our field investigations revealed that RSMV infection causes delayed rice heading, resulting in a large number of green diseased plants remaining in winter rice fields. This creates a favorable environment for leafhoppers and viruses to overwinter, potentially contributing to the rapid spread and epidemic of the disease. Next, we explored the mechanism by which RSMV manipulates the developmental processes of the rice plant. A rice heading-related E3 ubiquitin ligase, Heading date Associated Factor 1 (HAF1), was found to be hijacked by the RSMV-encoded P6. The impairment of HAF1 function affects the ubiquitination and degradation of downstream proteins, HEADING DATE 1 and EARLY FLOWERING3, leading to a delay in rice heading. Our results provide new insights into the development regulation-based molecular interactions between virus and plant, and highlights the importance of understanding virus-vector-plant tripartite interactions for effective disease management strategies.
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Affiliation(s)
- Siping Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Xinyi Zhong
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiyi Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Xiuqin Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Sipei Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, China
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3
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Wen X, Zhong Z, Xu P, Yang Q, Wang Y, Liu L, Wu Z, Wu Y, Zhang Y, Liu Q, Zhou Z, Peng Z, He Y, Cheng S, Cao L, Zhan X, Wu W. OsCOL5 suppresses heading through modulation of Ghd7 and Ehd2, enhancing rice yield. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:162. [PMID: 38884792 DOI: 10.1007/s00122-024-04674-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/12/2024] [Indexed: 06/18/2024]
Abstract
KEY MESSAGE OsCOL5, an ortholog of Arabidopsis COL5, is involved in photoperiodic flowering and enhances rice yield through modulation of Ghd7 and Ehd2 and interactions with OsELF3-1 and OsELF3-2. Heading date, also known as flowering time, plays a crucial role in determining the adaptability and yield potential of rice (Oryza sativa L.). CONSTANS (CO)-like is one of the most critical flowering-associated gene families, members of which are evolutionarily conserved. Here, we report the molecular functional characterization of OsCOL5, an ortholog of Arabidopsis COL5, which is involved in photoperiodic flowering and influences rice yield. Structural analysis revealed that OsCOL5 is a typical member of CO-like family, containing two B-box domains and one CCT domain. Rice plants overexpressing OsCOL5 showed delayed heading and increases in plant height, main spike number, total grain number per plant, and yield per plant under both long-day (LD) and short-day (SD) conditions. Gene expression analysis indicated that OsCOL5 was primarily expressed in the leaves and stems with a diurnal rhythm expression pattern. RT-qPCR analysis of heading date genes showed that OsCOL5 suppressed flowering by up-regulating Ghd7 and down-regulating Ehd2, consequently reducing the expression of Ehd1, Hd3a, RFT1, OsMADS14, and OsMADS15. Yeast two-hybrid experiments showed direct interactions of OsCOL5 with OsELF3-1 and OsELF3-2. Further verification showed specific interactions between the zinc finger/B-box domain of OsCOL5 and the middle region of OsELF3-1 and OsELF3-2. Yeast one-hybrid assays revealed that OsCOL5 may bind to the CCACA motif. The results suggest that OsCOL5 functions as a floral repressor, playing a vital role in rice's photoperiodic flowering regulation. This gene shows potential in breeding programs aimed at improving rice yield by influencing the timing of flowering, which directly impacts crop productivity.
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Affiliation(s)
- Xiaoxia Wen
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhengzheng Zhong
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Peng Xu
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Qinqin Yang
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Yinping Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518000, China
| | - Ling Liu
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhaozhong Wu
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Yewen Wu
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Yingxin Zhang
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Qunen Liu
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Zhengping Zhou
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Zequn Peng
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shihua Cheng
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China
| | - Liyong Cao
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
| | - Xiaodeng Zhan
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
| | - Weixun Wu
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 311400, China.
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Song J, Tang L, Fan H, Xu X, Peng X, Cui Y, Wang J. Enhancing Yield and Improving Grain Quality in Japonica Rice: Targeted EHD1 Editing via CRISPR-Cas9 in Low-Latitude Adaptation. Curr Issues Mol Biol 2024; 46:3741-3751. [PMID: 38666963 PMCID: PMC11049033 DOI: 10.3390/cimb46040233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
The "Indica to Japonica" initiative in China focuses on adapting Japonica rice varieties from the northeast to the unique photoperiod and temperature conditions of lower latitudes. While breeders can select varieties for their adaptability, the sensitivity to light and temperature often complicates and prolongs the process. Addressing the challenge of cultivating high-yield, superior-quality Japonica rice over expanded latitudinal ranges swiftly, in the face of these sensitivities, is critical. Our approach harnesses the CRISPR-Cas9 technology to edit the EHD1 gene in the premium northeastern Japonica cultivars Jiyuanxiang 1 and Yinongxiang 12, which are distinguished by their exceptional grain quality-increased head rice rates, gel consistency, and reduced chalkiness and amylose content. Field trials showed that these new ehd1 mutants not only surpass the wild types in yield when grown at low latitudes but also retain the desirable traits of their progenitors. Additionally, we found that disabling Ehd1 boosts the activity of Hd3a and RFT1, postponing flowering by approximately one month in the ehd1 mutants. This research presents a viable strategy for the accelerated breeding of elite northeastern Japonica rice by integrating genomic insights with gene-editing techniques suitable for low-latitude cultivation.
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Affiliation(s)
- Jian Song
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
| | - Liqun Tang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
| | - Honghuan Fan
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
| | - Xiaozheng Xu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou 311300, China; (X.X.); (X.P.)
| | - Xinlu Peng
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou 311300, China; (X.X.); (X.P.)
| | - Yongtao Cui
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
| | - Jianjun Wang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
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Li S, Luo Y, Wei G, Zong W, Zeng W, Xiao D, Zhang H, Song Y, Hao Y, Sun K, Lei C, Guo X, Xu B, Li W, Wu Z, Liu Y, Xie X, Guo J. Improving yield-related traits by editing the promoter of the heading date gene Ehd1 in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:239. [PMID: 37930441 DOI: 10.1007/s00122-023-04489-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE We developed an efficient promoter editing method to create different weak Ehd1 alleles in elite japonica rice variety ZJ8 with slightly delayed heading and improved yield for use in breeding. Heading date is an important agronomic trait of rice (Oryza sativa) that determines the planting areas and cultivation seasons of different varieties, thus affecting final yield. Early heading date 1 (Ehd1) is a major rice integrator gene in the regulatory network of heading date whose expression level is negatively correlated with heading date and grain yield. Some elite japonica varieties such as Zhongjia 8 (ZJ8) show very early heading with poor agronomic traits when planted in South China. This problem can be addressed by downregulating the expression of Ehd1. In this study, we analyzed the cis-regulatory elements in the Ehd1 promoter region. We then used CRISPR/Cas9-mediated editing to modify the Ehd1 promoter at multiple target sites in ZJ8. We rapidly identified homozygous allelic mutations in the T2 generation via long-read sequencing. We obtained several Ehd1 promoter mutants with different degrees of lower Ehd1 expression, delayed heading date, and improved yield-related traits. We developed an efficient promoter editing method to create different weak Ehd1 alleles for breeding selection. Using this method, a series of heading date materials from elite varieties can be created to expand the planting area of rice and improve grain yields.
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Affiliation(s)
- Shengting Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanqiu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China
| | - Guangliang Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wanyong Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dongdong Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Han Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingang Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Kangli Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chen Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaotong Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Bingqun Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Weitao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zeqiang Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Yoon J, Min CW, Kim J, Baek G, Kim D, Jang JW, Gupta R, Kim ST, Cho LH. Quantitative Proteomic Analysis Deciphers the Molecular Mechanism for Endosperm Nuclear Division in Early Rice Seed Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3715. [PMID: 37960070 PMCID: PMC10650807 DOI: 10.3390/plants12213715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Understanding the molecular mechanisms underlying early seed development is important in improving the grain yield and quality of crop plants. We performed a comparative label-free quantitative proteomic analysis of developing rice seeds for the WT and osctps1-2 mutant, encoding a cytidine triphosphate synthase previously reported as the endospermless 2 (enl2) mutant in rice, harvested at 0 and 1 d after pollination (DAP) to understand the molecular mechanism of early seed development. In total, 5231 proteins were identified, of which 902 changed in abundance between 0 and 1 DAP seeds. Proteins that preferentially accumulated at 1 DAP were involved in DNA replication and pyrimidine biosynthetic pathways. Notably, an increased abundance of OsCTPS1 was observed at 1 DAP; however, no such changes were observed at the transcriptional level. We further observed that the inhibition of phosphorylation increased the stability of this protein. Furthermore, in osctps1-2, minichromosome maintenance (MCM) proteins were significantly reduced compared with those in the WT at 1 DAP, and mutations in OsMCM5 caused defects in seed development. These results highlight the molecular mechanisms underlying early seed development in rice at the post-transcriptional level.
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Affiliation(s)
- Jinmi Yoon
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea;
- Department of Biological Sciences and Bioengineering, Industry-Academia Interactive R&E Center for Bioprocess Innovation, Inha University, Incheon 22212, Republic of Korea
| | - Cheol Woo Min
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
| | - Jiyoung Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Gibeom Baek
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Dohyeon Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Jeong Woo Jang
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea;
| | - Sun Tae Kim
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Lae-Hyeon Cho
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
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7
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Grant NP, Toy JJ, Funnell-Harris DL, Sattler SE. Deleterious mutations predicted in the sorghum (Sorghum bicolor) Maturity (Ma) and Dwarf (Dw) genes from whole-genome resequencing. Sci Rep 2023; 13:16638. [PMID: 37789045 PMCID: PMC10547693 DOI: 10.1038/s41598-023-42306-8] [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: 05/10/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
In sorghum [Sorghum bicolor (L.) Moench] the Maturity (Ma1, Ma2, Ma3, Ma4, Ma5, Ma6) and Dwarf (Dw1, Dw2, Dw3, Dw4) loci, encode genes controlling flowering time and plant height, respectively, which are critical for designing sorghum ideotypes for a maturity timeframe and a harvest method. Publicly available whole-genome resequencing data from 860 sorghum accessions was analyzed in silico to identify genomic variants at 8 of these loci (Ma1, Ma2, Ma3, Ma5, Ma6, Dw1, Dw2, Dw3) to identify novel loss of function alleles and previously characterized ones in sorghum germplasm. From ~ 33 million SNPs and ~ 4.4 million InDels, 1445 gene variants were identified within these 8 genes then evaluated for predicted effect on the corresponding encoded proteins, which included newly identified mutations (4 nonsense, 15 frameshift, 28 missense). Likewise, most accessions analyzed contained predicted loss of function alleles (425 ma1, 22 ma2, 40 ma3, 74 ma5, 414 ma6, 289 dw1, 268 dw2 and 45 dw3) at multiple loci, but 146 and 463 accessions had no predicted ma or dw mutant alleles, respectively. The ma and dw alleles within these sorghum accessions represent a valuable source for manipulating flowering time and plant height to develop the full range of sorghum types: grain, sweet and forage/biomass.
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Affiliation(s)
- Nathan P Grant
- Wheat, Sorghum and Forage Research Unit, Agricultural Research Service, United States Department of Agriculture, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - John J Toy
- Wheat, Sorghum and Forage Research Unit, Agricultural Research Service, United States Department of Agriculture, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Deanna L Funnell-Harris
- Wheat, Sorghum and Forage Research Unit, Agricultural Research Service, United States Department of Agriculture, Lincoln, NE, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Scott E Sattler
- Wheat, Sorghum and Forage Research Unit, Agricultural Research Service, United States Department of Agriculture, Lincoln, NE, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
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8
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Fan X, Wang P, Qi F, Hu Y, Li S, Zhang J, Liang L, Zhang Z, Liu J, Xiong L, Xing Y. The CCT transcriptional activator Ghd2 constantly delays the heading date by upregulating CO3 in rice. J Genet Genomics 2023; 50:755-764. [PMID: 36906137 DOI: 10.1016/j.jgg.2023.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
CONSTANS, CO-like, and TOC1 (CCT) family genes play important roles in regulating heading date, which exerts a large impact on the regional and seasonal adaptation of rice. Previous studies have shown that Grain number, plant height, and heading date2 (Ghd2) exhibits a negative response to drought stress by directly upregulating Rubisco activase and exerting a negative effect on heading date. However, the target gene of Ghd2 regulating heading date is still unknown. In this study, CO3 is identified by analyzing Ghd2 ChIP-seq data. Ghd2 activates CO3 expression by binding to the CO3 promoter through its CCT domain. EMSA experiments show that the motif CCACTA in the CO3 promoter was recognized by Ghd2. A comparison of the heading dates among plants with CO3 knocked out or overexpressed and double-mutants with Ghd2 overexpressed and CO3 knocked out shows that CO3 negatively and constantly regulates flowering by repressing the transcription of Ehd1, Hd3a, and RFT1. In addition, the target genes of CO3 are explored via a comprehensive analysis of DAP-seq and RNA-seq data. Taken together, these results suggest that Ghd2 directly binds to the downstream gene CO3, and the Ghd2-CO3 module constantly delays heading date via the Ehd1-mediated pathway.
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Affiliation(s)
- Xiaowei Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Feixiang Qi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shuangle Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jia Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Liwen Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Juhong Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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9
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Vicentini G, Biancucci M, Mineri L, Chirivì D, Giaume F, Miao Y, Kyozuka J, Brambilla V, Betti C, Fornara F. Environmental control of rice flowering time. PLANT COMMUNICATIONS 2023; 4:100610. [PMID: 37147799 PMCID: PMC10504588 DOI: 10.1016/j.xplc.2023.100610] [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: 10/02/2022] [Revised: 04/14/2023] [Accepted: 04/30/2023] [Indexed: 05/07/2023]
Abstract
Correct measurement of environmental parameters is fundamental for plant fitness and survival, as well as for timing developmental transitions, including the switch from vegetative to reproductive growth. Important parameters that affect flowering time include day length (photoperiod) and temperature. Their response pathways have been best described in Arabidopsis, which currently offers a detailed conceptual framework and serves as a comparison for other species. Rice, the focus of this review, also possesses a photoperiodic flowering pathway, but 150 million years of divergent evolution in very different environments have diversified its molecular architecture. The ambient temperature perception pathway is strongly intertwined with the photoperiod pathway and essentially converges on the same genes to modify flowering time. When observing network topologies, it is evident that the rice flowering network is centered on EARLY HEADING DATE 1, a rice-specific transcriptional regulator. Here, we summarize the most important features of the rice photoperiodic flowering network, with an emphasis on its uniqueness, and discuss its connections with hormonal, temperature perception, and stress pathways.
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Affiliation(s)
- Giulio Vicentini
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Marco Biancucci
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Lorenzo Mineri
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Daniele Chirivì
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Francesca Giaume
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Yiling Miao
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Vittoria Brambilla
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Camilla Betti
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy.
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10
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Jang MJ, Hong WJ, Park YS, Jung KH, Kim S. Genomic basis of multiphase evolution driving divergent selection of zinc-finger homeodomain genes. Nucleic Acids Res 2023; 51:7424-7437. [PMID: 37394281 PMCID: PMC10415114 DOI: 10.1093/nar/gkad489] [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: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Gene families divergently evolve and become adapted as different genes with specific structures and functions in living organisms. We performed comprehensive structural and functional analyses of Zinc-finger homeodomain genes (ZF-HDs), including Mini zinc-finger genes (MIFs) and Zinc-finger with homeodomain genes (ZHDs), displaying competitive functions each other. Intensive annotation updates for 90 plant genomes verified that most MIFs (MIF-Is) exhibited distinct motif compositions from ZHDs, although some MIFs (MIF-Zs) contained ZHD-specific motifs. Phylogenetic analyses suggested that MIF-Zs and ZHDs originated from the same ancestral gene, whereas MIF-Is emerged from a distinct progenitor. We used a gene-editing system to identify a novel function of MIF-Is in rice: regulating the surface material patterns in anthers and pollen through transcriptional regulation by interacting ZHDs. Kingdom-wide investigations determined that (i) ancestral MIFs diverged into MIF-Is and MIF-Zs in the last universal common ancestor, (ii) integration of HD into the C-terminal of MIF-Zs created ZHDs after emergence of green plants and (iii) MIF-Is and ZHDs subsequently expanded independently into specific plant lineages, with additional formation of MIF-Zs from ZHDs. Our comprehensive analysis provides genomic evidence for multiphase evolution driving divergent selection of ZF-HDs.
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Affiliation(s)
- Min-Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Young-Soo Park
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
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11
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Yoon J, Baek G, Pasriga R, Tun W, Min CW, Kim ST, Cho LH, An G. Homeobox transcription factors OsZHD1 and OsZHD2 induce inflorescence meristem activity at floral transition in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1327-1339. [PMID: 36120845 DOI: 10.1111/pce.14438] [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: 06/27/2022] [Revised: 09/04/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
Floral transition starts in the leaves when florigens respond to various environmental and developmental factors. Among several regulatory genes that are preferentially expressed in the inflorescence meristem during the floral transition, this study examines the homeobox genes OsZHD1 and OsZHD2 for their roles in regulating this transition. Although single mutations in these genes did not result in visible phenotype changes, double mutations in these genes delayed flowering. Florigen expression was not altered in the double mutants, indicating that the delay was due to a defect in florigen signaling. Morphological analysis of shoot apical meristem at the early developmental stage indicated that inflorescence meristem development was significantly delayed in the double mutants. Overexpression of ZHD2 causes early flowering because of downstream signals after the generation of florigens. Expression levels of the auxin biosynthesis genes were reduced in the mutants and the addition of indole-3-acetic acid recovered the defect in the mutants, suggesting that these homeobox genes play a role in auxin biosynthesis. A rice florigen, RICE FLOWERING LOCUS T 1, binds to the promoter regions of homeobox genes. These results indicate that florigens stimulate the expression of homeobox genes, enhancing inflorescence development in the shoot apex.
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Affiliation(s)
- Jinmi Yoon
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Gibeom Baek
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
| | - Richa Pasriga
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Win Tun
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Sun-Tae Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
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12
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Tun W, Yoon J, Vo KTX, Cho LH, Hoang TV, Peng X, Kim EJ, Win KTYS, Lee SW, Jung KH, Jeon JS, An G. Sucrose preferentially promotes expression of OsWRKY7 and OsPR10a to enhance defense response to blast fungus in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1117023. [PMID: 36778713 PMCID: PMC9911862 DOI: 10.3389/fpls.2023.1117023] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Sucrose controls various developmental and metabolic processes in plants. It also functions as a signaling molecule in the synthesis of carbohydrates, storage proteins, and anthocyanins, as well as in floral induction and defense response. We found that sucrose preferentially induced OsWRKY7, whereas other sugars (such as mannitol, glucose, fructose, galactose, and maltose) did not have the same effect. A hexokinase inhibitor mannoheptulose did not block the effect of sucrose, which is consequently thought to function directly. MG132 inhibited sucrose induction, suggesting that a repressor upstream of OsWRKY7 is degraded by the 26S proteasome pathway. The 3-kb promoter sequence of OsWRKY7 was preferentially induced by sucrose in the luciferase system. Knockout mutants of OsWRKY7 were more sensitive to the rice blast fungus Magnaporthe oryzae, whereas the overexpression of OsWRKY7 enhanced the resistance, indicating that this gene is a positive regulator in the plant defense against this pathogen. The luciferase activity driven by the OsPR10a promoter was induced by OsWRKY7 and this transcription factor bound to the promoter region of OsPR10a, suggesting that OsWRKY7 directly controls the expression of OsPR10a. We conclude that sucrose promotes the transcript level of OsWRKY7, thereby increasing the expression of OsPR10a for the defense response in rice.
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Affiliation(s)
- Win Tun
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Jinmi Yoon
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Kieu Thi Xuan Vo
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Trung Viet Hoang
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Xin Peng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Eui-Jung Kim
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Kay Tha Ye Soe Win
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Sang-Won Lee
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Gynheung An
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
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13
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Cui Y, Zhu M, Song J, Fan H, Xu X, Wu J, Guo L, Wang J. Expression dynamics of phytochrome genes for the shade-avoidance response in densely direct-seeding rice. FRONTIERS IN PLANT SCIENCE 2023; 13:1105882. [PMID: 36743577 PMCID: PMC9889870 DOI: 10.3389/fpls.2022.1105882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
Because of labor shortages or resource scarcity, direct seeding is the preferred method for rice (Oryza sativa. L) cultivation, and it necessitates direct seeding at the current density. In this study, two density of direct seeding with high and normal density were selected to identify the genes involved in shade-avoidance syndrome. Phenotypic and gene expression analysis showed that densely direct seeding (DDS) causes a set of acclimation responses that either induce shade avoidance or toleration. When compared to normal direct seeding (NDS), plants cultivated by DDS exhibit constitutive shade-avoidance syndrome (SAS), in which the accompanying solar radiation drops rapidly from the middle leaf to the base leaf during flowering. Simulation of shade causes rapid reduction in phytochrome gene expression, changes in the expression of multiple miR156 or miR172 genes and photoperiod-related genes, all of which leads to early flowering and alterations in the plant architecture. Furthermore, DDS causes senescence by downregulating the expression of chloroplast synthesis-related genes throughout almost the entire stage. Our findings revealed that DDS is linked to SAS, which can be employed to breed density-tolerant rice varieties more easily and widely.
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Affiliation(s)
- Yongtao Cui
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Minhua Zhu
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
| | - Jian Song
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Honghuan Fan
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaozheng Xu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Jiayan Wu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jianjun Wang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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14
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Wang A, Shu X, Xu D, Jiang Y, Liang J, Yi X, Zhu J, Yang F, Jiao C, Zheng A, Yin D, Li P. Understanding the Rice Fungal Pathogen Tilletia horrida from Multiple Perspectives. RICE (NEW YORK, N.Y.) 2022; 15:64. [PMID: 36522490 PMCID: PMC9755434 DOI: 10.1186/s12284-022-00612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Rice kernel smut (RKS), caused by the fungus Tilletia horrida, has become a major disease in rice-growing areas worldwide, especially since the widespread cultivation of high-yielding hybrid rice varieties. The disease causes a significant yield loss during the production of rice male sterile lines by producing masses of dark powdery teliospores. This review mainly summarizes the pathogenic differentiation, disease cycle, and infection process of the T. horrida, as well as the decoding of the T. horrida genome, functional genomics, and effector identification. We highlight the identification and characterization of virulence-related pathways and effectors of T. horrida, which could foster a better understanding of the rice-T. horrida interaction and help to elucidate its pathogenicity molecular mechanisms. The multiple effective disease control methods for RKS are also discussed, included chemical fungicides, the mining of resistant rice germplasms/genes, and the monitoring and early warning signs of this disease in field settings.
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Affiliation(s)
- Aijun Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Xinyue Shu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Deze Xu
- Food Crop Research Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Yuqi Jiang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Juan Liang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Xiaoqun Yi
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jianqing Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Feng Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Chunhai Jiao
- Food Crop Research Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Aiping Zheng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Desuo Yin
- Food Crop Research Institute, Hubei Academy of Agriculture Sciences, Wuhan, China.
| | - Ping Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China.
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15
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Xiang YH, Yu JJ, Liao B, Shan JX, Ye WW, Dong NQ, Guo T, Kan Y, Zhang H, Yang YB, Li YC, Zhao HY, Yu HX, Lu ZQ, Lin HX. An α/β hydrolase family member negatively regulates salt tolerance but promotes flowering through three distinct functions in rice. MOLECULAR PLANT 2022; 15:1908-1930. [PMID: 36303433 DOI: 10.1016/j.molp.2022.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/09/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Ongoing soil salinization drastically threatens crop growth, development, and yield worldwide. It is therefore crucial that we improve salt tolerance in rice by exploiting natural genetic variation. However, many salt-responsive genes confer undesirable phenotypes and therefore cannot be effectively applied to practical agricultural production. In this study, we identified a quantitative trait locus for salt tolerance from the African rice species Oryza glaberrima and named it as Salt Tolerance and Heading Date 1 (STH1). We found that STH1 regulates fatty acid metabolic homeostasis, probably by catalyzing the hydrolytic degradation of fatty acids, which contributes to salt tolerance. Meanwhile, we demonstrated that STH1 forms a protein complex with D3 and a vital regulatory factor in salt tolerance, OsHAL3, to regulate the protein abundance of OsHAL3 via the 26S proteasome pathway. Furthermore, we revealed that STH1 also serves as a co-activator with the floral integrator gene Heading date 1 to balance the expression of the florigen gene Heading date 3a under different circumstances, thus coordinating the regulation of salt tolerance and heading date. Notably, the allele of STH1 associated with enhanced salt tolerance and high yield is found in some African rice accessions but barely in Asian cultivars. Introgression of the STH1HP46 allele from African rice into modern rice cultivars is a desirable approach for boosting grain yield under salt stress. Collectively, our discoveries not only provide conceptual advances on the mechanisms of salt tolerance and synergetic regulation between salt tolerance and flowering time but also offer potential strategies to overcome the challenges resulted from increasingly serious soil salinization that many crops are facing.
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Affiliation(s)
- You-Huang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Jun Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ben Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Hai Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Chao Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Huai-Yu Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Xiao Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; University of the Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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16
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Sun C, He C, Zhong C, Liu S, Liu H, Luo X, Li J, Zhang Y, Guo Y, Yang B, Wang P, Deng X. Bifunctional regulators of photoperiodic flowering in short day plant rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1044790. [PMID: 36340409 PMCID: PMC9630834 DOI: 10.3389/fpls.2022.1044790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Photoperiod is acknowledged as a crucial environmental factor for plant flowering. According to different responses to photoperiod, plants were divided into short-day plants (SDPs), long-day plants (LDPs), and day-neutral plants (DNPs). The day length measurement system of SDPs is different from LDPs. Many SDPs, such as rice, have a critical threshold for day length (CDL) and can even detect changes of 15 minutes for flowering decisions. Over the last 20 years, molecular mechanisms of flowering time in SDP rice and LDP Arabidopsis have gradually clarified, which offers a chance to elucidate the differences in day length measurement between the two types of plants. In Arabidopsis, CO is a pivotal hub in integrating numerous internal and external signals for inducing photoperiodic flowering. By contrast, Hd1 in rice, the homolog of CO, promotes and prevents flowering under SD and LD, respectively. Subsequently, numerous dual function regulators, such as phytochromes, Ghd7, DHT8, OsPRR37, OsGI, OsLHY, and OsELF3, were gradually identified. This review assesses the relationship among these regulators and a proposed regulatory framework for the reversible mechanism, which will deepen our understanding of the CDL regulation mechanism and the negative response to photoperiod between SDPs and LDPs.
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Affiliation(s)
- Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Changcai He
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chao Zhong
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shihang Liu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hongying Liu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xu Luo
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuxiu Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuting Guo
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Bin Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pingrong Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
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17
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Zhang S, Deng L, Zhao L, Wu C. Genome-wide binding analysis of transcription factor Rice Indeterminate 1 reveals a complex network controlling rice floral transition. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1690-1705. [PMID: 35789063 DOI: 10.1111/jipb.13325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
RICE INDETERMINATE 1 (RID1) plays a critical role in controlling floral transition in rice (Oryza sativa). However, the molecular basis for this effect, particularly the target genes and regulatory specificity, remains largely unclear. Here, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) in young leaves at the pre-floral-transition stage to identify the target genes of RID1, identifying 2,680 genes associated with RID1 binding sites genome-wide. RID1 binding peaks were highly enriched for TTTGTC, the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1. Interestingly, CACGTG and GTGGGCCC, two previously uncharacterized indirect binding motifs, were enriched through the interactions of RID1 with the novel flowering-promoting proteins OsPIL12 and OsTCP11, respectively. Moreover, the ChIP-seq data demonstrated that RID1 bound to numerous rice heading-date genes, such as HEADING DATE 1 (HD1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1). Notably, transcriptome sequencing (RNA-seq) analysis revealed roles of RID1 in diverse developmental pathways. Genetic analysis combined with genome-wide ChIP-seq and RNA-seq results showed that RID1 directly binds to the promoter of OsERF#136 (a repressor of rice flowering) and negatively regulates its expression. Overall, our findings provide new insights into the molecular and genetic mechanisms underlying rice floral transition and characterize OsERF#136 as a previously unrecognized direct target of RID1.
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Affiliation(s)
- Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Deng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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Hong WJ, Kim EJ, Yoon J, Silva J, Moon S, Min CW, Cho LH, Kim ST, Park SK, Kim YJ, Jung KH. A myosin XI adaptor, TAPE, is essential for pollen tube elongation in rice. PLANT PHYSIOLOGY 2022; 190:562-575. [PMID: 35736513 PMCID: PMC9434255 DOI: 10.1093/plphys/kiac299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Pollen tube (PT) elongation is important for double fertilization in angiosperms and affects the seed-setting rate and, therefore, crop productivity. Compared to Arabidopsis (Arabidopsis thaliana L.), information on PT elongation in rice (Oryza sativa L.) is limited by the difficulty in obtaining homozygous mutants. In a screen of T-DNA insertional mutants, we identified a mutant in the Tethering protein of actomyosin transport in pollen tube elongation (TAPE) gene with an unusual segregation ratio by genotyping analysis. A CRISPR/Cas9 knockout mutant of TAPE that produced a short PT was sterile, and TAPE was expressed specifically in pollen grains. TAPE is a homolog of a myosin XI adaptor in Arabidopsis with three tetratricopeptide repeat and Phox and Bem1 protein domains. TAPE showed latrunculin B-sensitive, actin-dependent localization to the endoplasmic reticulum. Yeast two-hybrid screening and transcriptome analysis revealed that TAPE interacted with pollen-specific LIM protein 2b and elongation factor 1-alpha. Loss of TAPE affected transcription of 1,259 genes, especially genes related to cell organization, which were downregulated. In summary, TAPE encodes a myosin XI adaptor essential for rice PT elongation.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Eui-Jung Kim
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Jinmi Yoon
- Department of Plant Bioscience, Pusan National University, Miryang, 50463, Republic of Korea
| | - Jeniffer Silva
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sunok Moon
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang, 50463, Republic of Korea
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, Pusan National University, Miryang, 50463, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 50463, Republic of Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yu-Jin Kim
- Authors for correspondence: (Y.-J.K.); (K.-H.J.)
| | - Ki-Hong Jung
- Authors for correspondence: (Y.-J.K.); (K.-H.J.)
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19
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Lee SJ, Kang K, Lim JH, Paek NC. Natural alleles of CIRCADIAN CLOCK ASSOCIATED1 contribute to rice cultivation by fine-tuning flowering time. PLANT PHYSIOLOGY 2022; 190:640-656. [PMID: 35723564 PMCID: PMC9434239 DOI: 10.1093/plphys/kiac296] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The timing of flowering is a crucial factor for successful grain production at a wide range of latitudes. Domestication of rice (Oryza sativa) included selection for natural alleles of flowering-time genes that allow rice plants to adapt to broad geographic areas. Here, we describe the role of natural alleles of CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1) in cultivated rice based on analysis of single-nucleotide polymorphisms deposited in the International Rice Genebank Collection Information System database. Rice varieties harboring japonica-type OsCCA1 alleles (OsCCA1a haplotype) flowered earlier than those harboring indica-type OsCCA1 alleles (OsCCA1d haplotype). In the japonica cultivar "Dongjin", a T-DNA insertion in OsCCA1a resulted in late flowering under long-day and short-day conditions, indicating that OsCCA1 is a floral inducer. Reverse transcription quantitative PCR analysis showed that the loss of OsCCA1a function induces the expression of the floral repressors PSEUDO-RESPONSE REGULATOR 37 (OsPRR37) and Days to Heading 8 (DTH8), followed by repression of the Early heading date 1 (Ehd1)-Heading date 3a (Hd3a)-RICE FLOWERING LOCUS T 1 (RFT1) pathway. Binding affinity assays indicated that OsCCA1 binds to the promoter regions of OsPRR37 and DTH8. Naturally occurring OsCCA1 alleles are evolutionarily conserved in cultivated rice (O. sativa). Oryza rufipogon-I (Or-I) and Or-III type accessions, representing the ancestors of O. sativa indica and japonica, harbored indica- and japonica-type OsCCA1 alleles, respectively. Taken together, our results demonstrate that OsCCA1 is a likely domestication locus that has contributed to the geographic adaptation and expansion of cultivated rice.
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Affiliation(s)
| | | | - Jung-Hyun Lim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
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20
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Li X, Tian X, He M, Liu X, Li Z, Tang J, Mei E, Xu M, Liu Y, Wang Z, Guan Q, Meng W, Fang J, Zhang J, Bu Q. bZIP71 delays flowering by suppressing Ehd1 expression in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1352-1363. [PMID: 35546447 DOI: 10.1111/jipb.13275] [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: 02/27/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Flowering time is a fundamental factor determining the global distribution and final yield of rice (Oryza sativa). Although diverse flowering time genes have been reported in this crop, the transcriptional regulation of its key flowering genes are poorly understood. Here, we report that a basic leucine zipper transcription factor, bZIP71, functions as a flowering repressor. The overexpression of bZIP71 delays flowering, while the bzip71 mutant flowers early in both long-day and short-day conditions. A genetic analysis showed that the regulation of flowering by bZIP71 might be independent of Heading date 2 (Hd2), Hd4, and Hd5. Importantly, bZIP71 directly associates with the Early heading date 1 (Ehd1) promoter and represses its transcription, and genetically the function of bZIP71 is impaired in the ehd1 mutant. Moreover, bZIP71 interacts with major components of polycomb repressive complex 2 (PRC2), SET domain group protein 711 (SDG711), and Fertilization independent endosperm 2 (FIE2), through which bZIP71 regulates the H3K27me3 level of Ehd1. Taken together, we present a transcriptional regulatory mechanism in which bZIP71 enhances the H3K27me3 level of Ehd1 and transcriptionally represses its expression, which not only offers a novel insight into a flowering pathway, but also provides a valuable putative target for the genetic engineering and breeding of elite rice cultivars.
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Affiliation(s)
- Xiufeng Li
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
| | - Xiaojie Tian
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
| | - Mingliang He
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinxin Liu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China
| | - Jiaqi Tang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Enyang Mei
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Xu
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingxiang Liu
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenyu Wang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
| | - Qingjie Guan
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
| | - Wei Meng
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
| | - Jun Fang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China
| | - Qingyun Bu
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
- The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
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21
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Yue C, Chen Q, Hu J, Li C, Luo L, Zeng L. Genome-Wide Identification and Characterization of GARP Transcription Factor Gene Family Members Reveal Their Diverse Functions in Tea Plant ( Camellia sinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:947072. [PMID: 35845671 PMCID: PMC9280663 DOI: 10.3389/fpls.2022.947072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Golden2, ARR-B, Psr1 (GARP) proteins are plant-specific transcription factors that play vital and diverse roles in plants. However, systematic research on the GARP gene family in plants, including tea plant (Camellia sinensis), is scarce. In this study, a total of 69 GARP genes were identified and characterized from the tea plant genome based on the B-motif sequence signature. The CsGARP genes were clustered into five subfamilies: PHR1/PHL1, KAN, NIGT1/HRS1/HHO, GLK and ARR-B subfamilies. The phylogenetic relationships, gene structures, chromosomal locations, conserved motifs and regulatory cis-acting elements of the CsGARP family members were comprehensively analyzed. The expansion of CsGARP genes occurred via whole-genome duplication/segmental duplication, proximal duplication, and dispersed duplication under purifying selective pressure. The expression patterns of the CsGARP genes were systematically explored from various perspectives: in different tissues during different seasons; in different leaf color stages of tea plant; under aluminum treatment and nitrogen treatment; and in response to abiotic stresses such as cold, drought and salt and to biotic stress caused by Acaphylla theae. The results demonstrate that CsGARP family genes are ubiquitously expressed and play crucial roles in the regulation of growth and development of tea plant and the responses to environmental stimuli. Collectively, these results not only provide valuable information for further functional investigations of CsGARPs in tea plant but also contribute to broadening our knowledge of the functional diversity of GARP family genes in plants.
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Affiliation(s)
- Chuan Yue
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
| | - Qianqian Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Hu
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Congcong Li
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liyong Luo
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
| | - Liang Zeng
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
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22
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Xu Z, Li E, Xue G, Zhang C, Yang Y, Ding Y. OsHUB2 inhibits function of OsTrx1 in heading date in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1670-1680. [PMID: 35395113 DOI: 10.1111/tpj.15763] [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: 01/13/2022] [Revised: 03/15/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Heading date is one of the most pivotal agronomic traits for rice (Oryza sativa) yield and adaptation. Little is known about the crosstalk between histone ubiquitination and histone methylation in rice heading date regulation. Here, we reported HISTONE MONOUBIQUITINATION 1 (OsHUB1) and OsHUB2 are involved in heading date regulation via the Hd1 and Ehd1 pathway. Loss of OsHUB1 and OsHUB2 function resulted in early heading under long-day and short-day photoperiods. The expression of Hd3a, RFT1, and Ehd1 was induced and the transcript levels of Hd1, Ghd7, OsCCA1, OsGI, OsFKF1, and OsTOC1 were reduced under long-day conditions, whereas RFT1 and Ehd1 expression was induced in oshub2 mutants under short-day conditions. OsHUB2 interacted with OsTrx1 and repressed the gene expression of OsTrx1. OsHUB2 directly bound to Ehd1 to ubiquitinate H2B at Ehd1, and H2B ubiquitination levels were reduced in oshub2-2 and oshub2-3 mutants. OsTrx1 were highly enriched at Ehd1, and H3K4me3 levels of Ehd1 were upregulated in oshub2-2. Mutations of OsTrx1 in the oshub2-2 background rescued the early-heading phenotype of oshub2-2. The increases in Ehd1 H3K4me3 levels and transcript levels in oshub2-2 mutants were attenuated in oshub2-2 ostrx1-2 double mutants. Together, our results (i) reveal that OsHUB2 represses the function of OsTrx1 and H3K4me3 levels at Ehd1 and (ii) suggest that OsHUB2-mediated H2B ubiquitination plays critical roles together with H3K4me3 in rice heading date regulation.
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Affiliation(s)
- Zuntao Xu
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Enze Li
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Gan Xue
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Cheng Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Yachun Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Yong Ding
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
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23
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Cho LH, Yoon J, Tun W, Baek G, Peng X, Hong WJ, Mori IC, Hojo Y, Matsuura T, Kim SR, Kim ST, Kwon SW, Jung KH, Jeon JS, An G. Cytokinin increases vegetative growth period by suppressing florigen expression in rice and maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1619-1635. [PMID: 35388561 DOI: 10.1111/tpj.15760] [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: 01/28/2022] [Revised: 03/17/2022] [Accepted: 03/28/2022] [Indexed: 05/12/2023]
Abstract
Increasing the vegetative growth period of crops can increase biomass and grain yield. In rice (Oryza sativa), the concentration of trans -zeatin, an active cytokinin, was high in the leaves during vegetative growth and decreased rapidly upon induction of florigen expression, suggesting that this hormone is involved in the regulation of the vegetative phase. To elucidate whether exogenous cytokinin application influences the length of the vegetative phase, we applied 6-benzylaminopurine (BAP) to rice plants at various developmental stages. Our treatment delayed flowering time by 8-9 days when compared with mock-treated rice plants, but only at the transition stage when the flowering signals were produced. Our observations also showed that flowering in the paddy field is delayed by thidiazuron, a stable chemical that mimics the effects of cytokinin. The transcript levels of florigen genes Heading date 3a (Hd3a) and Rice Flowering locus T1 (RFT1) were significantly reduced by the treatment, but the expression of Early heading date 1 (Ehd1), a gene found directly upstream of the florigen genes, was not altered. In maize (Zea mays), similarly, BAP treatment increased the vegetative phage by inhibiting the expression of ZCN8, an ortholog of Hd3a. We showed that cytokinin treatment induced the expression of two type-A response regulators (OsRR1 and OsRR2) which interacted with Ehd1, a type-B response regulator. We also observed that cytokinin did not affect flowering time in ehd1 knockout mutants. Our study indicates that cytokinin application increases the duration of the vegetative phase by delaying the expression of florigen genes in rice and maize by inhibiting Ehd1.
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Affiliation(s)
- Lae-Hyeon Cho
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Jinmi Yoon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Win Tun
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Gibeom Baek
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
| | - Xin Peng
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
- Institute of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Woo-Jong Hong
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Izumi C Mori
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Yuko Hojo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Sung-Ryul Kim
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Sun-Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
| | - Soon-Wook Kwon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
| | - Ki-Hong Jung
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Jong-Seong Jeon
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
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24
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Zhang S, Deng L, Cheng R, Hu J, Wu CY. RID1 sets rice heading date by balancing its binding with SLR1 and SDG722. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:149-165. [PMID: 34845826 DOI: 10.1111/jipb.13196] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Rice (Oryza sativa) is a major crop that feeds billions of people, and its yield is strongly influenced by flowering time (heading date). Loss of RICE INDETERMINATE1 (RID1) function causes plants not to flower; thus, RID1 is considered a master switch among flowering-related genes. However, it remains unclear whether other proteins function together with RID1 to regulate rice floral transition. Here, we revealed that the chromatin accessibility and H3K9ac, H3K4me3, and H3K36me3 levels at Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) loci were significantly reduced in rid1 mutants. Notably, RID1 interacted with SET DOMAIN GROUP PROTEIN 722 (SDG722), a methyltransferase. We determined that SDG722 affects the global level of H3K4me2/3 and H3K36me2/3, and promotes flowering primarily through the Early heading date1-Hd3a/RFT1 pathway. We further established that rice DELLA protein SLENDER RICE1 (SLR1) interacted with RID1 to inhibit its transactivation activity, that SLR1 suppresses rice flowering, and that messenger RNA and protein levels of SLR1 gradually decrease with plant growth. Furthermore, SLR1 competed with SDG722 for interaction with RID1. Overall, our results establish that interplay between RID1, SLR1, and SDG722 feeds into rice flowering-time control.
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Affiliation(s)
- Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Deng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Cheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chang-Yin Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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25
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Chen R, Deng Y, Ding Y, Guo J, Qiu J, Wang B, Wang C, Xie Y, Zhang Z, Chen J, Chen L, Chu C, He G, He Z, Huang X, Xing Y, Yang S, Xie D, Liu Y, Li J. Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2022. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Affiliation(s)
- Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bing Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changsheng Wang
- National Center for Gene Research, Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihua Zhang
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Daoxin Xie
- MOE Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Yoon J, Jeong HJ, Baek G, Yang J, Peng X, Tun W, Kim ST, An G, Cho LH. A VIN3-like Protein OsVIL1 Is Involved in Grain Yield and Biomass in Rice. PLANTS (BASEL, SWITZERLAND) 2021; 11:83. [PMID: 35009085 PMCID: PMC8747509 DOI: 10.3390/plants11010083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/23/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
In chromatin remodeling, the post-translational modification of histone proteins is mediated by multimeric protein complexes. VERNALIZATION INSENSITIVE3 (VIN3) forms a complex with Polycomb Repressive Complex 2 (PRC2), which mediates the trimethylation of H3K27 to repress target gene expression. In rice, four genes (OsVIL1-OsVIL4) encoding the VIN3-like proteins are expressed ubiquitously in various tissues. Null mutants of osvil2 display pleiotropic phenotypes such as altered flowering time, floral organ defects, and reduced tiller size. In contrast, osvil1 mutants did not show significant phenotypes except in fertilization compared with the wild type. However, transgenic plants overexpressing OsVIL1 showed phenotypes of increased biomass and grain yield. Cross-sections of the basal region of elongating stems revealed that the increased biomass was mediated by inducing cell proliferation in the meristem. Chromatin immunoprecipitation assay indicated that OsVIL1 repressed expression of cytokinin oxidase/dehydrogenase gene (OsCKX2) by binding to the promoter and genic regions of OsCKX2. We also observed that OsVIL1 modified the levels of H3K27me3 in the OsCKX2 chromatin. Because OsCKX2 encodes an enzyme that degrades active cytokinin, we conclude that OsVIL1 functions in the regulation of endogenous active cytokinin levels, thereby increasing plant height and productivity.
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Affiliation(s)
- Jinmi Yoon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea; (J.Y.); (G.B.); (S.-T.K.)
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (H.-J.J.); (J.Y.); (X.P.); (W.T.)
| | - Hee-Joong Jeong
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (H.-J.J.); (J.Y.); (X.P.); (W.T.)
| | - Gibeom Baek
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea; (J.Y.); (G.B.); (S.-T.K.)
| | - Jungil Yang
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (H.-J.J.); (J.Y.); (X.P.); (W.T.)
| | - Xin Peng
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (H.-J.J.); (J.Y.); (X.P.); (W.T.)
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Win Tun
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (H.-J.J.); (J.Y.); (X.P.); (W.T.)
| | - Sun-Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea; (J.Y.); (G.B.); (S.-T.K.)
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (H.-J.J.); (J.Y.); (X.P.); (W.T.)
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea; (J.Y.); (G.B.); (S.-T.K.)
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Yoon J, Cho L, Kim S, Tun W, Peng X, Pasriga R, Moon S, Hong W, Ji H, Jung K, Jeon J, An G. CTP synthase is essential for early endosperm development by regulating nuclei spacing. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2177-2191. [PMID: 34058048 PMCID: PMC8541778 DOI: 10.1111/pbi.13644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/04/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Cereal grain endosperms are an important source of human nutrition. Nuclear division in early endosperm development plays a major role in determining seed size; however, this development is not well understood. We identified the rice mutant endospermless 2 (enl2), which shows defects in the early stages of endosperm development. These phenotypes arise from mutations in OsCTPS1 that encodes a cytidine triphosphate synthase (CTPS). Both wild-type and mutant endosperms were normal at 8 h after pollination (HAP). In contrast, at 24 HAP, enl2 endosperm had approximately 10-16 clumped nuclei while wild-type nuclei had increased in number and migrated to the endosperm periphery. Staining of microtubules in endosperm at 24 HAP revealed that wild-type nuclei were evenly distributed by microtubules while the enl2-2 nuclei were tightly packed due to their reduction in microtubule association. In addition, OsCTPS1 interacts with tubulins; thus, these observations suggest that OsCTPS1 may be involved in microtubule formation. OsCTPS1 transiently formed macromolecular structures in the endosperm during early developmental stages, further supporting the idea that OsCTPS1 may function as a structural component during endosperm development. Finally, overexpression of OsCTPS1 increased seed weight by promoting endosperm nuclear division, suggesting that this trait could be used to increase grain yield.
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Affiliation(s)
- Jinmi Yoon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Lae‐Hyeon Cho
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Sung‐Ryul Kim
- Gene Identification and Validation GroupGenetic Design and Validation UnitInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Win Tun
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Xin Peng
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
| | - Richa Pasriga
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Sunok Moon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Woo‐Jong Hong
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Hyeonso Ji
- National Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Ki‐Hong Jung
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Jong‐Seong Jeon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
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Transcriptome analysis of flowering regulation by sowing date in Japonica Rice (Oryza sativa L.). Sci Rep 2021; 11:15026. [PMID: 34294838 PMCID: PMC8298600 DOI: 10.1038/s41598-021-94552-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/12/2021] [Indexed: 11/08/2022] Open
Abstract
Hybrid japonica cultivars, such as the Yongyou series, have shown high yield potential in the field in both the early and late growing seasons. Moreover, understanding the responses of rice flowering dates to temperature and light is critical for improving yield performance. However, few studies have analyzed flowering genes in high-yielding japonica cultivars. Based on the five sowing date experiments from 2019 to 2020, select the sensitive cultivar Yongyou 538 and the insensitive cultivar Ninggeng 4 and take their flag leaves and panicles for transcriptome analysis. The results showed that compared with sowing date 1 (6/16), after the sowing date was postponed (sowing date 5, 7/9), 4480 and 890 differentially expressed genes (DEGs) were detected in the leaves and panicles in Ninggeng 4, 9275 and 2475 DEGs were detected in the leaves and panicles in Yongyou 538, respectively. KEGG pathway analysis showed that both Ninggeng 4 and Yongyou 538 regulated rice flowering through the plant circadian rhythm and plant hormone signal transduction pathways. Gene expression analysis showed that Os01g0566050 (OsELF3-2), Os01g0182600 (OsGI), Os11g0547000 (OsFKF1), Os06g0275000 (Hd1), and Os09g0513500 (FT-1) were expressed higher and Os02g0771100 (COP1-1) was expressed lower in Yongyou 538 compared with Ninggeng 4 as the climate conditions changed, which may be the key genes that regulate the flowering process with the change of temperature and light resources in sensitive cultivar Yongyou 538 in the late season.
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Peng M, Gan F, Yang F, Pan C, Lin X, Fan X, Chen K, Gao P. Nuclear factor OsNF-YB4 promotes flowering by negatively regulating the floral repressor gene Ghd7 in rice. Biochem Biophys Res Commun 2021; 571:32-37. [PMID: 34303193 DOI: 10.1016/j.bbrc.2021.07.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/24/2022]
Abstract
Flowering time or heading date is a critical agronomic trait of rice and is regulated by numerous genes, including several genes encoding nuclear factor YB (NF-YB) in rice, NF-YB11 is one of the genes well known to be involved in the process, delaying flowering under long-day (LD) conditions but promoting flowering under short-day (SD) conditions. In this study, we identified another NF-YB gene, OsNF-YB4. Overexpression of OsNF-YB4 promoted rice flowering under both natural long-day (NLD) and natural short-day (NSD) conditions, whereas suppression or loss-of-function of this gene delayed flowering. The transcription of OsNF-YB4 exhibited an obvious circadian pattern and was induced by light under both LD and SD conditions. Expression analyses of flowering regulators in the photoperiodic flowering pathway demonstrated that up-regulation of OsNF-YB4 resulted in down-regulation of floral repressor Grain number, plant height and heading date 7 (Ghd7), and thus activating the Early heading date 1 (Ehd1)-mediated flowering pathway. Besides, OsNF-YB4 was observed to bind to the specific CCAAT-box regions in the Ghd7 promoter in vitro and interact with GHD7 in yeast. All these evidences support that OsNF-YB4 functions as a flowering promoter by negatively regulating the expression of floral repressor Ghd7 in rice photoperiodic flowering-time regulatory network.
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Affiliation(s)
- Meifang Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China; Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, PR China
| | - Feng Gan
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, PR China
| | - Feng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China
| | - Chunmei Pan
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, PR China
| | - Xiaomin Lin
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, PR China
| | - Xiaoli Fan
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, PR China
| | - Kegui Chen
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, PR China.
| | - Ping Gao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China.
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Leuendorf JE, Schmülling T. Meeting at the DNA: Specifying Cytokinin Responses through Transcription Factor Complex Formation. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10071458. [PMID: 34371661 PMCID: PMC8309282 DOI: 10.3390/plants10071458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 05/10/2023]
Abstract
Cytokinin is a plant hormone regulating numerous biological processes. Its diverse functions are realized through the expression control of specific target genes. The transcription of the immediate early cytokinin target genes is regulated by type-B response regulator proteins (RRBs), which are transcription factors (TFs) of the Myb family. RRB activity is controlled by phosphorylation and protein degradation. Here, we focus on another step of regulation, the interaction of RRBs among each other or with other TFs to form active or repressive TF complexes. Several examples in Arabidopsis thaliana illustrate that RRBs form homodimers or complexes with other TFs to specify the cytokinin response. This increases the variability of the output response and provides opportunities of crosstalk between the cytokinin signaling pathway and other cellular signaling pathways. We propose that a targeted approach is required to uncover the full extent and impact of RRB interaction with other TFs.
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Cui D, Tang C, Lu H, Li J, Ma X, A X, Han B, Yang Y, Dong C, Zhang F, Dai L, Han L. Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment. RICE (NEW YORK, N.Y.) 2021; 14:54. [PMID: 34131824 PMCID: PMC8206287 DOI: 10.1186/s12284-021-00497-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing. RESULTS The genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. CONCLUSIONS Our findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.
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Affiliation(s)
- Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Cuifeng Tang
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Jinmei Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Xinxiang A
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Yayun Yang
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Chao Dong
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Feifei Zhang
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Luyuan Dai
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
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Kim EJ, Hong WJ, Tun W, An G, Kim ST, Kim YJ, Jung KH. Interaction of OsRopGEF3 Protein With OsRac3 to Regulate Root Hair Elongation and Reactive Oxygen Species Formation in Rice ( Oryza sativa). FRONTIERS IN PLANT SCIENCE 2021; 12:661352. [PMID: 34113363 PMCID: PMC8185220 DOI: 10.3389/fpls.2021.661352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
Root hairs are tip-growing cells that emerge from the root epidermis and play a role in water and nutrient uptake. One of the key signaling steps for polar cell elongation is the formation of Rho-GTP by accelerating the intrinsic exchange activity of the Rho-of-plant (ROP) or the Rac GTPase protein; this step is activated through the interaction with the plant Rho guanine nucleotide exchange factor (RopGEFs). The molecular players involved in root hair growth in rice are largely unknown. Here, we performed the functional analysis of OsRopGEF3, which is highly expressed in the root hair tissues among the OsRopGEF family genes in rice. To reveal the role of OsRopGEF3, we analyzed the phenotype of loss-of-function mutants of OsRopGEF3, which were generated using the CRISPR-Cas9 system. The mutants had reduced root hair length and increased root hair width. In addition, we confirmed that reactive oxygen species (ROS) were highly reduced in the root hairs of the osropgef3 mutant. The pairwise yeast two-hybrid experiments between OsRopGEF3 and OsROP/Rac proteins in rice revealed that the OsRopGEF3 protein interacts with OsRac3. This interaction and colocalization at the same subcellular organelles were again verified in tobacco leaf cells and rice root protoplasts via bimolecular functional complementation (BiFC) assay. Furthermore, among the three respiratory burst oxidase homolog (OsRBOH) genes that are highly expressed in rice root hair cells, we found that OsRBOH5 can interact with OsRac3. Our results demonstrate an interaction network model wherein OsRopGEF3 converts the GDP of OsRac3 into GTP, and OsRac3-GTP then interacts with the N-terminal of OsRBOH5 to produce ROS, thereby suggesting OsRopGEF3 as a key regulating factor in rice root hair growth.
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Affiliation(s)
- Eui-Jung Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Win Tun
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Sun-Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, and Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
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Zhou S, Zhu S, Cui S, Hou H, Wu H, Hao B, Cai L, Xu Z, Liu L, Jiang L, Wang H, Wan J. Transcriptional and post-transcriptional regulation of heading date in rice. THE NEW PHYTOLOGIST 2021; 230:943-956. [PMID: 33341945 PMCID: PMC8048436 DOI: 10.1111/nph.17158] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/15/2020] [Indexed: 05/04/2023]
Abstract
Rice is a facultative short day (SD) plant. In addition to serving as a model plant for molecular genetic studies of monocots, rice is a staple crop for about half of the world's population. Heading date is a critical agronomic trait, and many genes controlling heading date have been cloned over the last 2 decades. The mechanism of flowering in rice from recognition of day length by leaves to floral activation in the shoot apical meristem has been extensively studied. In this review, we summarise current progress on transcriptional and post-transcriptional regulation of heading date in rice, with emphasis on post-translational modifications of key regulators, including Heading date 1 (Hd1), Early heading date 1 (Ehd1), Grain number, plant height, and heading date7 (Ghd7). The contribution of heading date genes to heterosis and the expansion of rice cultivation areas from low-latitude to high-latitude regions are also discussed. To overcome the limitations of diverse genetic backgrounds used in heading date studies and to gain a clearer understanding of flowering in rice, we propose a systematic collection of genetic resources in a common genetic background. Strategies in breeding adapted cultivars by rational design are also discussed.
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Affiliation(s)
- Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Song Cui
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haigang Hou
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haoqin Wu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Benyuan Hao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Liang Cai
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Zhuang Xu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Linglong Liu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
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Choi J, Lee W, An G, Kim SR. OsCBE1, a Substrate Receptor of Cullin4-Based E3 Ubiquitin Ligase, Functions as a Regulator of Abiotic Stress Response and Productivity in Rice. Int J Mol Sci 2021; 22:ijms22052487. [PMID: 33801226 PMCID: PMC7957871 DOI: 10.3390/ijms22052487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 01/03/2023] Open
Abstract
Ubiquitination is an important environmental stress response, and E3 ubiquitin ligases play a major role in the process. T-DNA insertion mutants of rice, Oscbe1-1, and Oscbe1-2, were identified through the screening of cold stress tolerance at seedling stage. Oscbe1 mutants showed a significantly higher cold stress tolerance in the fresh weight, chlorophyll content, and photosynthetic efficiency than wild type. Molecular prediction showed that OsCBE1 (Oryza sativa Cullin4-Based E3 ubiquitin ligase1) encoded a novel substrate receptor of Cullin4-based E3 ubiquitin ligase complex (C4E3). Whereas Oscbe1 mutants had fewer panicles and grains than wild type in the paddy field, the overexpression lines of OsCBE1 had more panicles and grains, suggesting that OsCBE1 is involved in the regulation of both abiotic stress response and development. Oscbe1 mutants also showed ABA hypersensitivity during seed germination, suggesting OsCBE1 function for the stress response via ABA signaling. In silico analysis of OsCBE1 activity predicted a CCCH-type transcription factor, OsC3H32, as a putative substrate. Co-IP (Co-immunoprecipitation) study showed that OsCBE1 interacts with OsDDB1, an expected binding component of OsCBE1 and OsC3H32. Additionally, expression of OsOLE16, OsOLE18, and OsBURP5 were negatively related with expression of OsCBE1. These results suggest that OsCBE1 functions as a regulator of the abiotic stress response via CCCH as a member of the C4E3.
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Affiliation(s)
- Juyoung Choi
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.C.); (W.L.)
| | - Wonkyung Lee
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.C.); (W.L.)
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 17104, Korea;
| | - Seong-Ryong Kim
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.C.); (W.L.)
- Correspondence:
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Fu J, Liu G, Liu B. Foreign Cry1Ab/c Delays Flowering in Insect-Resistant Transgenic Rice via Interaction With Hd3a Florigen. FRONTIERS IN PLANT SCIENCE 2021; 12:608721. [PMID: 33643344 PMCID: PMC7905309 DOI: 10.3389/fpls.2021.608721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Genetic modifications in rice, which resulted in insect resistance, have been highly efficacious. However, they have also induced undesirable secondary phenotypes, such as delayed flowering. The molecular mechanisms associated with these unwanted effects remain unclear. Here, we showed that the flowering time for insect-resistant transgenic cry1Ab/c rice Huahui-1 (HH1) was delayed, compared with that for the parental rice Minghui-63 (MH63), cultivated on farmland and saline-alkaline soils. In contrast, the insect-resistant transgenic cry1C ^* rice cultivars T1C-19 and MH63 had similar flowering times under the same conditions. We quantified the following: the expression of five major flowering genes in HH1, T1C-19, and MH63; florigen Hd3a protein expression levels in HH1 and MH63; interactions between Cry1Ab/c and the five main flowering proteins; and the effects of E3s ubiquitin ligase-mediated Cry1Ab/c expression on florigen Hd3a. Hd3a transcription was significantly lower in HH1 but not in T1C-19, compared with that in MH63. The results of yeast two-hybrid, complementary bimolecular fluorescence, and co-immunoprecipitation assays revealed that florigen Hd3a interacted with the exogenous Cry1Ab/c expressed in HH1 and not the exogenous Cry1C^* expressed in T1C-19. When Cry1Ab/c, Hd3a, and E3s fusion proteins were transiently co-expressed in tobacco cells, the Hd3a expression level was significantly lower than the level of Cry1Ab/c and Hd3a co-expression. Thus, the downregulation of Hd3a expression and the interaction between Cry1Ab/c and Hd3a interfere with Hd3a protein expression and might cooperatively delay HH1 flowering time. To the best of our knowledge, this study is the first to explain the delay in flowering time in insect-resistant transgenic rice, mediated by interactions between exogenous and endogenous proteins. This information might help elucidate the molecular mechanisms associated with these unwanted phenotypes effects and improve the process of biosafety assessment of transgenic rice.
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Affiliation(s)
- Jianmei Fu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Guoqiang Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Biao Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
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Peng X, Tun W, Dai SF, Li JY, Zhang QJ, Yin GY, Yoon J, Cho LH, An G, Gao LZ. Genome-Wide Analysis of CCT Transcript Factors to Identify Genes Contributing to Photoperiodic Flowering in Oryza rufipogon. FRONTIERS IN PLANT SCIENCE 2021; 12:736419. [PMID: 34819938 PMCID: PMC8606741 DOI: 10.3389/fpls.2021.736419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/08/2021] [Indexed: 05/03/2023]
Abstract
Photoperiod sensitivity is a dominant determinant for the phase transition in cereal crops. CCT (CONSTANS, CO-like, and TOC1) transcription factors (TFs) are involved in many physiological functions including the regulation of the photoperiodic flowering. However, the functional roles of CCT TFs have not been elucidated in the wild progenitors of crops. In this study, we identified 41 CCT TFs, including 19 CMF, 17 COL, and five PRR TFs in Oryza rufipogon, the presumed wild ancestor of Asian cultivated rice. There are thirty-eight orthologous CCT genes in Oryza sativa, of which ten pairs of duplicated CCT TFs are shared with O. rufipogon. We investigated daily expression patterns, showing that 36 OrCCT genes exhibited circadian rhythmic expression. A total of thirteen OrCCT genes were identified as putative flowering suppressors in O. rufipogon based on rhythmic and developmental expression patterns and transgenic phenotypes. We propose that OrCCT08, OrCCT24, and OrCCT26 are the strong functional alleles of rice DTH2, Ghd7, and OsPRR37, respectively. The SD treatment at 80 DAG stimulated flowering of the LD-grown O. rufipogon plants. Our results further showed that the nine OrCCT genes were significantly downregulated under the treatment. Our findings would provide valuable information for the construction of photoperiodic flowering regulatory network and functional characterization of the CCT TFs in both O. rufipogon and O. sativa.
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Affiliation(s)
- Xin Peng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Win Tun
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Shuang-feng Dai
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Jia-yue Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Qun-jie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Guo-ying Yin
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Jinmi Yoon
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Lae-hyeon Cho
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Gynheung An
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
- *Correspondence: Gynheung An,
| | - Li-zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Li-zhi Gao,
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Gawarecka K, Ahn JH. Isoprenoid-Derived Metabolites and Sugars in the Regulation of Flowering Time: Does Day Length Matter? FRONTIERS IN PLANT SCIENCE 2021; 12:765995. [PMID: 35003159 PMCID: PMC8738093 DOI: 10.3389/fpls.2021.765995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/22/2021] [Indexed: 05/06/2023]
Abstract
In plants, a diverse set of pathways regulate the transition to flowering, leading to remarkable developmental flexibility. Although the importance of photoperiod in the regulation of flowering time is well known, increasing evidence suggests the existence of crosstalk among the flowering pathways regulated by photoperiod and metabolic pathways. For example, isoprenoid-derived phytohormones (abscisic acid, gibberellins, brassinosteroids, and cytokinins) play important roles in regulating flowering time. Moreover, emerging evidence reveals that other metabolites, such as chlorophylls and carotenoids, as well as sugar metabolism and sugar accumulation, also affect flowering time. In this review, we summarize recent findings on the roles of isoprenoid-derived metabolites and sugars in the regulation of flowering time and how day length affects these factors.
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Cerise M, Giaume F, Galli M, Khahani B, Lucas J, Podico F, Tavakol E, Parcy F, Gallavotti A, Brambilla V, Fornara F. OsFD4 promotes the rice floral transition via florigen activation complex formation in the shoot apical meristem. THE NEW PHYTOLOGIST 2021; 229:429-443. [PMID: 32737885 DOI: 10.1111/nph.16834] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
In rice, the florigens Heading Date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1), OsFD-like basic leucine zipper (bZIP) transcription factors, and Gf14 proteins assemble into florigen activation/repressor complexes (FACs/FRCs), which regulate transition to flowering in leaves and apical meristem. Only OsFD1 has been described as part of complexes promoting flowering at the meristem, and little is known about the role of other bZIP transcription factors, the combinatorial complexity of FAC formation, and their DNA-binding properties. Here, we used mutant analysis, protein-protein interaction assays and DNA affinity purification (DAP) sequencing coupled to in silico prediction of binding syntaxes to study several bZIP proteins that assemble into FACs or FRCs. We identified OsFD4 as a component of a FAC promoting flowering at the shoot apical meristem, downstream of OsFD1. The osfd4 mutants are late flowering and delay expression of genes promoting inflorescence development. Protein-protein interactions indicate an extensive network of contacts between several bZIPs and Gf14 proteins. Finally, we identified genomic regions bound by bZIPs with promotive and repressive effects on flowering. We conclude that distinct bZIPs orchestrate floral induction at the meristem and that FAC formation is largely combinatorial. While binding to the same consensus motif, their DNA-binding syntax is different, suggesting discriminatory functions.
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Affiliation(s)
- Martina Cerise
- Department of Biosciences, University of Milan, Milan, 20123, Italy
- Department of Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Francesca Giaume
- Department of Biosciences, University of Milan, Milan, 20123, Italy
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Bahman Khahani
- Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Jérémy Lucas
- CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, University Grenoble Alpes, 17 avenue des martyrs, Grenoble, F-38054, France
| | - Federico Podico
- Department of Biosciences, University of Milan, Milan, 20123, Italy
| | - Elahe Tavakol
- Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - François Parcy
- CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, University Grenoble Alpes, 17 avenue des martyrs, Grenoble, F-38054, France
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Vittoria Brambilla
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, 20123, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Milan, 20123, Italy
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Izawa T. What is going on with the hormonal control of flowering in plants? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:431-445. [PMID: 33111430 DOI: 10.1111/tpj.15036] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/17/2020] [Accepted: 09/01/2020] [Indexed: 05/12/2023]
Abstract
Molecular genetic studies using Arabidopsis thaliana as a model system have overwhelmingly revealed many important molecular mechanisms underlying the control of various biological events, including floral induction in plants. The major genetic pathways of flowering have been characterized in-depth, and include the photoperiod, vernalization, autonomous and gibberellin pathways. In recent years, novel flowering pathways are increasingly being identified. These include age, thermosensory, sugar, stress and hormonal signals to control floral transition. Among them, hormonal control of flowering except the gibberellin pathway is not formally considered a major flowering pathway per se, due to relatively weak and often pleiotropic genetic effects, complex phenotypic variations, including some controversial ones. However, a number of recent studies have suggested that various stress signals may be mediated by hormonal regulation of flowering. In view of molecular diversity in plant kingdoms, this review begins with an assessment of photoperiodic flowering, not in A. thaliana, but in rice (Oryza sativa); rice is a staple crop for human consumption worldwide, and is a model system of short-day plants, cereals and breeding crops. The rice flowering pathway is then compared with that of A. thaliana. This review then aims to update our knowledge on hormonal control of flowering, and integrate it into the entire flowering gene network.
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Affiliation(s)
- Takeshi Izawa
- Laboratory of Plant Breeding & Genetics, Department of Agricultural and Environmental Biology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
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41
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Lebedeva MA, Dodueva IE, Gancheva MS, Tvorogova VE, Kuznetsova KA, Lutova LA. The Evolutionary Aspects of Flowering Control: Florigens and Anti-Florigens. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542011006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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Wei H, Wang X, Xu H, Wang L. Molecular basis of heading date control in rice. ABIOTECH 2020; 1:219-232. [PMID: 36304129 PMCID: PMC9590479 DOI: 10.1007/s42994-020-00019-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/06/2020] [Indexed: 01/25/2023]
Abstract
Flowering time is of great significance for crop reproduction, yield, and regional adaptability, which is intricately regulated by various environmental cues and endogenous signals. Genetic approaches in Arabidopsis have revealed the elaborate underlying mechanisms of sensing the dynamic change of photoperiod via a coincidence between light signaling and circadian clock, the cellular time keeping system, to precisely control photoperiodic flowering time, and many other signaling pathways including internal hormones and external temperature cues. Extensive studies in rice (Oryza sativa.), one of the short-day plants (SDP), have uncovered the multiple major genetic components in regulating heading date, and revealed the underlying mechanisms for regulating heading date. Here we summarize the current progresses on the molecular basis for rice heading date control, especially focusing on the integration mechanism between photoperiod and circadian clock, and epigenetic regulation and heading procedures in response to abiotic stresses.
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Affiliation(s)
- Hua Wei
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiling Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Hang Xu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
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Comparative transcriptome analysis of Tilletia horrida infection in resistant and susceptible rice (Oryza sativa L.) male sterile lines reveals potential candidate genes and resistance mechanisms. Genomics 2020; 112:5214-5226. [PMID: 32966859 DOI: 10.1016/j.ygeno.2020.09.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 07/21/2020] [Accepted: 09/16/2020] [Indexed: 11/20/2022]
Abstract
Rice kernel smut (RKS), caused by the basidiomycete fungus Tilletia horrida, is one of the most devastating diseases affecting the production of male sterile lines of rice (Oryza sativa) worldwide. However, the molecular mechanisms of resistance to T. horrida have not yet been explored. In the present study, RNA sequencing analysis of rice male sterile lines, that are resistant and susceptible to RKS (Jiangcheng 3A and 9311A, respectively) was conducted after T. horrida infection. Transcriptomic analysis showed that a greater number of differentially expressed gene (DEGs) was observed in Jiangcheng 3A compared with 9311A after T. horrida inoculation. Furthermore, 4, 425 DEGs were uniquely detected in Jiangcheng 3A, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these DEGs revealed that oxidoreductase activity, peroxidase activity, cutin, suberine and wax biosynthesis, and flavonoid biosynthesis were key pathways for T. horrida resistance. In summary and based on transcriptome analysis, we suggest a preliminary regulatory mechanism for Jiangcheng 3A cultivar resistance response to T. horrida inoculation.
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Yoon J, Cho LH, Yang W, Pasriga R, Wu Y, Hong WJ, Bureau C, Wi SJ, Zhang T, Wang R, Zhang D, Jung KH, Park KY, Périn C, Zhao Y, An G. Homeobox transcription factor OsZHD2 promotes root meristem activity in rice by inducing ethylene biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5348-5364. [PMID: 32449922 PMCID: PMC7501826 DOI: 10.1093/jxb/eraa209] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 04/27/2020] [Indexed: 05/11/2023]
Abstract
Root meristem activity is the most critical process influencing root development. Although several factors that regulate meristem activity have been identified in rice, studies on the enhancement of meristem activity in roots are limited. We identified a T-DNA activation tagging line of a zinc-finger homeobox gene, OsZHD2, which has longer seminal and lateral roots due to increased meristem activity. The phenotypes were confirmed in transgenic plants overexpressing OsZHD2. In addition, the overexpressing plants showed enhanced grain yield under low nutrient and paddy field conditions. OsZHD2 was preferentially expressed in the shoot apical meristem and root tips. Transcriptome analyses and quantitative real-time PCR experiments on roots from the activation tagging line and the wild type showed that genes for ethylene biosynthesis were up-regulated in the activation line. Ethylene levels were higher in the activation lines compared with the wild type. ChIP assay results suggested that OsZHD2 induces ethylene biosynthesis by controlling ACS5 directly. Treatment with ACC (1-aminocyclopropane-1-carboxylic acid), an ethylene precursor, induced the expression of the DR5 reporter at the root tip and stele, whereas treatment with an ethylene biosynthesis inhibitor, AVG (aminoethoxyvinylglycine), decreased that expression in both the wild type and the OsZHD2 overexpression line. These observations suggest that OsZHD2 enhances root meristem activity by influencing ethylene biosynthesis and, in turn, auxin.
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Affiliation(s)
- Jinmi Yoon
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Lae-Hyeon Cho
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
| | - Wenzhu Yang
- Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Richa Pasriga
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Yunfei Wu
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Woo-Jong Hong
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Charlotte Bureau
- Agricultural Research Centre For International Development, Paris, France
| | - Soo Jin Wi
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Korea
| | - Tao Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Rongchen Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide Urrbrae, SA, Australia
| | - Ki-Hong Jung
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Ky Young Park
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Korea
| | - Christophe Périn
- Agricultural Research Centre For International Development, Paris, France
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
- Correspondence:
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OsbHLH073 Negatively Regulates Internode Elongation and Plant Height by Modulating GA Homeostasis in Rice. PLANTS 2020; 9:plants9040547. [PMID: 32340222 PMCID: PMC7238965 DOI: 10.3390/plants9040547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 11/16/2022]
Abstract
Internode elongation is one of the key agronomic traits determining a plant’s height and biomass. However, our understanding of the molecular mechanisms controlling internode elongation is still limited in crop plant species. Here, we report the functional identification of an atypical basic helix-loop-helix transcription factor (OsbHLH073) through gain-of-function studies using overexpression (OsbHLH073-OX) and activation tagging (osbhlh073-D) lines of rice. The expression of OsbHLH073 was significantly increased in the osbhlh073-D line. The phenotype of osbhlh073-D showed semi-dwarfism due to deficient elongation of the first internode and poor panicle exsertion. Transgenic lines overexpressing OsbHLH073 confirmed the phenotype of the osbhlh073-D line. Exogenous gibberellic acid (GA3) treatment recovered the semi-dwarf phenotype of osbhlh073-D plants at the seedling stage. In addition, quantitative expression analysis of genes involving in GA biosynthetic and signaling pathway revealed that the transcripts of rice ent-kaurene oxidases 1 and 2 (OsKO1 and OsKO2) encoding the GA biosynthetic enzyme were significantly downregulated in osbhlh073-D and OsbHLH073-OX lines. Yeast two-hybrid and localization assays showed that the OsbHLH073 protein is a nuclear localized-transcriptional activator. We report that OsbHLH073 participates in regulating plant height, internode elongation, and panicle exsertion by regulating GA biosynthesis associated with the OsKO1 and OsKO2 genes.
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Wu M, Liu H, Lin Y, Chen J, Fu Y, Luo J, Zhang Z, Liang K, Chen S, Wang F. In-Frame and Frame-Shift Editing of the Ehd1 Gene to Develop Japonica Rice With Prolonged Basic Vegetative Growth Periods. FRONTIERS IN PLANT SCIENCE 2020; 11:307. [PMID: 32265960 PMCID: PMC7096585 DOI: 10.3389/fpls.2020.00307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/03/2020] [Indexed: 05/05/2023]
Abstract
Japonica rice has become increasingly popular in China owing to its superior grain quality. Over the past decades, "indica to japonica" projects have been proposed to promote cultivation of japonica rice in low latitudes in China. Traditionally, japonica varieties were planted mainly in mid latitudes in the northeast plain and Yangtze River region. The key obstacle for introducing elite mid-latitude japonica varieties to low latitudes is the severe shortening of growth period of the japonica varieties due to their sensitivity to low-latitude short photoperiod and high temperature. Here we report development of new japonica rice with prolonged basic vegetative growth (BVG) periods for low latitudes by targeted editing the Early heading date 1 (Ehd1) gene. Using CRISPR/Cas9 system, we generated both frame-shift and/or in-frame deletion mutants in four japonica varieties, Nipponbare, Longdao16, Longdao24, and Xiushui134. When planting at low-latitude stations, the frame-shift homozygous lines exhibited significantly longer BVG periods compared with wild-types. Interestingly, we observed that minor deletion of the first few residues within the receiver domain could quantitatively impair the function of Ehd1 on activation of Hd3a and RFT1, resulting in an intermediate-long BVG period phenotype in the homozygous in-frame deletion ehd1 lines. Field investigation further showed that, both the in-frame and frame-shift lines exhibited significantly improved yield potential compared with wild-types. Our study demonstrates an effective approach to rapid breeding of elite japonica varieties with intermediate-long and long BVG periods for flexible cropping systems in diverse areas or under different seasons in southern China, and other low-latitude regions.
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Affiliation(s)
- Mingji Wu
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Huaqing Liu
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yan Lin
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianmin Chen
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yanping Fu
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jiami Luo
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Zhujian Zhang
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Kangjing Liang
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Songbiao Chen
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Feng Wang
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
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47
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Yoon J, Cho LH, Lee S, Pasriga R, Tun W, Yang J, Yoon H, Jeong HJ, Jeon JS, An G. Chromatin Interacting Factor OsVIL2 Is Required for Outgrowth of Axillary Buds in Rice. Mol Cells 2019; 42:858-868. [PMID: 31771322 PMCID: PMC6939655 DOI: 10.14348/molcells.2019.0141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/17/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022] Open
Abstract
Shoot branching is an essential agronomic trait that impacts on plant architecture and yield. Shoot branching is determined by two independent steps: axillary meristem formation and axillary bud outgrowth. Although several genes and regulatory mechanism have been studied with respect to shoot branching, the roles of chromatin-remodeling factors in the developmental process have not been reported in rice. We previously identified a chromatin-remodeling factor OsVIL2 that controls the trimethylation of histone H3 lysine 27 (H3K27me3) at target genes. In this study, we report that loss-of-function mutants in OsVIL2 showed a phenotype of reduced tiller number in rice. The reduction was due to a defect in axillary bud (tiller) outgrowth rather than axillary meristem initiation. Analysis of the expression patterns of the tiller-related genes revealed that expression of OsTB1, which is a negative regulator of bud outgrowth, was increased in osvil2 mutants. Chromatin immunoprecipitation assays showed that OsVIL2 binds to the promoter region of OsTB1 chromatin in wild-type rice, but the binding was not observed in osvil2 mutants. Tiller number of double mutant osvil2 ostb1 was similar to that of ostb1, suggesting that osvil2 is epistatic to ostb1. These observations indicate that OsVIL2 suppresses OsTB1 expression by chromatin modification, thereby inducing bud outgrowth.
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Affiliation(s)
- Jinmi Yoon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Lae-Hyeon Cho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
- Department of Plant Bioscience, Pusan National University, Miryang 50463,
Korea
| | - Sichul Lee
- Center for Plant Aging Research, Institute for Basic Science, Daegu 42988,
Korea
| | - Richa Pasriga
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Win Tun
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Jungil Yang
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Hyeryung Yoon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Hee Joong Jeong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
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48
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Weng X, Lovell JT, Schwartz SL, Cheng C, Haque T, Zhang L, Razzaque S, Juenger TE. Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C 4 grass. PLANT, CELL & ENVIRONMENT 2019; 42:2165-2182. [PMID: 30847928 DOI: 10.1111/pce.13546] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day length. Using a cost-effective 3'-Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C4 perennial grass, Panicum hallii. We show that the vast majority of photoperiod responses are driven by complex interactions between day length and sampling periods. A fine-scale contrast analysis at each sampling time revealed a detailed picture of the temporal reprogramming of cis-regulatory elements and biological processes under short- and long-day conditions. Phase shift analysis reveals quantitative variation among genes with photoperiod-dependent diurnal patterns. In addition, we identify three photoperiod enriched transcription factor families with key genes involved in photoperiod flowering regulatory networks. Finally, coexpression networks analysis of GIGANTEA homolog predicted 1,668 potential coincidence partners, including five well-known GI-interacting proteins. Our results not only provide a resource for understanding the mechanisms of photoperiod regulation in perennial grasses but also lay a foundation to increase biomass yield in biofuel crops.
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Affiliation(s)
- Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806
| | - Scott L Schwartz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Changde Cheng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Taslima Haque
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Li Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Samsad Razzaque
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
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49
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Pasriga R, Yoon J, Cho LH, An G. Overexpression of RICE FLOWERING LOCUS T 1 ( RFT1) Induces Extremely Early Flowering in Rice. Mol Cells 2019; 42:406-417. [PMID: 31085810 PMCID: PMC6537653 DOI: 10.14348/molcells.2019.0009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/24/2019] [Accepted: 03/05/2019] [Indexed: 11/27/2022] Open
Abstract
RICE FLOWERING LOCUS T 1 (RFT1) is a major florigen that functions to induce reproductive development in the shoot apical meristem (SAM). To further our study of RFT1, we overexpressed the gene and examined the expression patterns of major regulatory genes during floral transition and inflorescence development. Overexpression induced extremely early flowering in the transgenics, and a majority of those calli directly formed spikelets with a few spikelets, thus bypassing normal vegetative development. FRUITFULL (FUL)-clade genes OsMADS14, OsMADS15, and OsMADS18 were highly induced in the RFT1-expressing meristems. Os-MADS34 was also induced in the meristems. This indicated that RFT1 promotes the expression of major regulatory genes that are important for inflorescence development. RFT1 overexpression also induced SEPALLATA (SEP)-clade genes OsMADS1, OsMADS5, and OsMADS7 in the greening calli before floral transition occurred. This suggested their possible roles at the early reproductive stages. We found it interesting that expression of OsFD1 as well as OsFD2 and OsFD3 was strongly increased in the RFT1-expressing calli and spikelets. At a low frequency, those calli produced plants with a few leaves that generated a panicle with a small number of spikelets. In the transgenic leaves, the FULclade genes and OsMADS34 were induced, but SEP-clade gene expression was not increased. This indicated that OsMADS14, OsMADS15, OsMADS18, and OsMADS34 act immediately downstream of RFT1.
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Affiliation(s)
- Richa Pasriga
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Jinmi Yoon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Lae-Hyeon Cho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
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50
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Duan E, Wang Y, Li X, Lin Q, Zhang T, Wang Y, Zhou C, Zhang H, Jiang L, Wang J, Lei C, Zhang X, Guo X, Wang H, Wan J. OsSHI1 Regulates Plant Architecture Through Modulating the Transcriptional Activity of IPA1 in Rice. THE PLANT CELL 2019; 31:1026-1042. [PMID: 30914468 PMCID: PMC6533028 DOI: 10.1105/tpc.19.00023] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/27/2019] [Accepted: 03/24/2019] [Indexed: 05/20/2023]
Abstract
Tillering and panicle branching are important determinants of plant architecture and yield potential in rice (Oryza sativa). IDEAL PLANT ARCHITECTURE1 (IPA1) encodesSQUAMOSA PROMOTER BINDING PROTEIN-LIKE14, which acts as a key transcription factor regulating tiller outgrowth and panicle branching by directly activating the expression of O. sativa TEOSINTE BRANCHED1 (OsTB1) and O. sativa DENSE AND ERECT PANICLE1 (OsDEP1), thereby influencing grain yield in rice. Here, we report the identification of a rice mutant named shi1 that is characterized by dramatically reduced tiller number, enhanced culm strength, and increased panicle branch number. Map-based cloning revealed that O. sativa SHORT INTERNODES1 (OsSHI1) encodes a plant-specific transcription factor of the SHI family with a characteristic family-specific IGGH domain and a conserved zinc-finger DNA binding domain. Consistent with the mutant phenotype, OsSHI1 is predominantly expressed in axillary buds and young panicle, and its encoded protein is exclusively targeted to the nucleus. We show that OsSHI1 physically interacts with IPA1 both in vitro and in vivo. Moreover, OsSHI1 could bind directly to the promoter regions of both OsTB1 and OsDEP1 through a previously unrecognized cis-element (T/GCTCTAC motif). OsSHI1 repressed the transcriptional activation activity of IPA1 by affecting its DNA binding activity toward the promoters of both OsTB1 and OsDEP1, resulting in increased tiller number and diminished panicle size. Taken together, our results demonstrate that OsSHI1 regulates plant architecture through modulating the transcriptional activity of IPA1 and provide insight into the establishment of plant architecture in rice.
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Affiliation(s)
- Erchao Duan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohui Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ting Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yupeng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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