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Hong Z, Liu Y, He M, Zhou W, Sui J, Tian X, Guan Q, Yu X, Li K, Bu Q, Li X. A novel functional allele of Ehd3 controls flowering time in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:35. [PMID: 38736650 PMCID: PMC11078898 DOI: 10.1007/s11032-024-01472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024]
Abstract
Rice flowering time determines its geographical distribution and yield traits. As a short-day plant, rice can grow in the northern long-day conditions due to the functional mutations of many photosensitive genes. In this study, to identify novel genes or alleles that regulate flowering time in high latitude region, two cultivar, Dongnong 413 (DN413) and Yukimochi (XN) showing extreme early flowering were used for investigation. DN413 is around 4.0 days earlier than XN, and both cultivars can be grown in II (2500 ℃-2700 ℃) to III (2300 ℃-2500 ℃) accumulated temperature zones. We found that the two cultivars shared the same genotype of heading date genes, including Hd1/2/4/5/6/16/17/18, Ehd2, DTH2, SE5, Hd3a. Importantly, a novel Ehd3 allele characterized by a A1146C substitution was identified, which results in the E382D substitution, hereafter the 382 position E is defined as Hap_E and the 382 position D is defined as Hap_D. Association analysis showed that Hap_E is earlier flowering than Hap_D. Subsequently, we construct DN413 Hap_D line by three times back-crossing DN413 with XN, and found the heading date of DN413 Hap_D was 1.7-3.5 days later than DN413. Moreover, Hap_E and Hap_D of Ehd3 were transformed into ehd3 mutant, respectively, and the Ehd3pro:Ehd3D/ehd3 flowered later than that Ehd3pro:Ehd3E/ehd3 by around 4.3 days. Furthermore, we showed Ehd3 functions as a transcriptional suppressor and the substitution of Asp-382 lost the inhibition activity in protoplasts. Finally, a CAPS marker was developed and used for genotyping and marker assistant breeding. Collectively, we discovered a novel functional allele of Ehd3, which can used as a valuable breeding target. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01472-x.
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Affiliation(s)
- Zhipeng Hong
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yingxiang Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Mingliang He
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenyan Zhou
- College of Life Science, Northeast Forestry University, Harbin, 150040 China
| | - Jingjing Sui
- College of Life Science, Northeast Forestry University, Harbin, 150040 China
| | - Xiaojie Tian
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Qingjie Guan
- College of Life Science, Northeast Forestry University, Harbin, 150040 China
| | - Xinglong Yu
- Beidahuang Group Erdaohe Farm CO., LTD, Harbin, China
| | - Kun Li
- Biotechnology Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150080 China
| | - Qingyun Bu
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
- College of Life Science, Northeast Forestry University, Harbin, 150040 China
| | - Xiufeng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
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Wang X, Zhang J, Liu X, Kong Y, Han L. The Roles of the PSEUDO-RESPONSE REGULATORs in Circadian Clock and Flowering Time in Medicago truncatula. Int J Mol Sci 2023; 24:16834. [PMID: 38069157 PMCID: PMC10706769 DOI: 10.3390/ijms242316834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
PSEUDO-RESPONSE REGULATORs (PRRs) play key roles in the circadian rhythms and flowering in plants. Here, we identified the four members of the PRR family in Medicago truncatula, including MtPRR9a, MtPRR9b, MtPRR7 and MtPRR5, and isolated their Tnt1 retrotransposon-tagged mutants. They were expressed in different organs and were nuclear-localized. The four MtPRRs genes played important roles in normal clock rhythmicity maintenance by negatively regulating the expression of MtGI and MtLHY. Surprisingly, the four MtPRRs functioned redundantly in regulating flowering time under long-day conditions, and the quadruple mutant flowered earlier. Moreover, MtPRR can recruit the MtTPL/MtTPR corepressors and the other MtPRRs to form heterodimers to constitute the core mechanism of the circadian oscillator.
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Affiliation(s)
- Xiao Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Juanjuan Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Xiu Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Yiming Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
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Li Z, Gui R, Yu X, Liang C, Cui J, Zhao X, Zhang X, Yu P, Chen W, Sun J. Genetic basis of the early heading of high-latitude weedy rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1059197. [PMID: 36544870 PMCID: PMC9760980 DOI: 10.3389/fpls.2022.1059197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Japonica rice (Oryza sativa L.) is an important staple food in high-latitude regions and is widely distributed in northern China, Japan, Korea, and Europe. However, the genetic diversity of japonica rice is relatively narrow and poorly adapted. Weedy rice (Oryza sativa f. spontanea) is a semi-domesticated rice. Its headings are earlier than the accompanied japonica rice, making it a potential new genetic resource, which can make up for the defects of wild rice that are difficult to be directly applied to japonica rice improvement caused by reproductive isolation. In this study, we applied a natural population consisting of weedy rice, japonica landrace, and japonica cultivar to conduct a genome-wide association study (GWAS) of the heading date and found four loci that could explain the natural variation of the heading date in this population. At the same time, we developed recombinant inbred lines (RILs) crossed by the early-heading weedy rice WR04-6 and its accompanied japonica cultivar ShenNong 265 (SN265) to carry out a QTL mapping analysis of the heading date and mapped four quantitative trait locus (QTLs) and three epistatic effect gene pairs. The major locus on chromosome 6 overlapped with the GWAS result. Further analysis found that two genes, Hd1 and OsCCT22, on chromosome 6 (Locus 2 and Locus 3) may be the key points of the early-heading character of weedy rice. As minor effect genes, Dth7 and Hd16 also have genetic contributions to the early heading of weedy rice. In the process of developing the RIL population, we introduced fragments of Locus 2 and Locus 3 from the weedy rice into super-high-yielding japonica rice, which successfully promoted its heading date by at least 10 days and expanded the rice suitable cultivation area northward by about 400 km. This study successfully revealed the genetic basis of the early heading of weedy rice and provided a new idea for the genetic improvement of cultivated rice by weedy rice.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wenfu Chen
- *Correspondence: Wenfu Chen, ; Jian Sun,
| | - Jian Sun
- *Correspondence: Wenfu Chen, ; Jian Sun,
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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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Niu Y, Huang X, He Z, Zhang Q, Meng H, Shi H, Feng B, Zhou Y, Zhang J, Lu G, Wang Z, Zhang W, Tang D, Wang M. Phosphorylation of OsTGA5 by casein kinase II compromises its suppression of defense-related gene transcription in rice. THE PLANT CELL 2022; 34:3425-3442. [PMID: 35642941 PMCID: PMC9421590 DOI: 10.1093/plcell/koac164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Plants manage the high cost of immunity activation by suppressing the expression of defense genes during normal growth and rapidly switching them on upon pathogen invasion. TGAs are key transcription factors controlling the expression of defense genes. However, how TGAs function, especially in monocot plants like rice with continuously high levels of endogenous salicylic acid (SA) remains elusive. In this study, we characterized the role of OsTGA5 as a negative regulator of rice resistance against blast fungus by transcriptionally repressing the expression of various defense-related genes. Moreover, OsTGA5 repressed PTI responses and the accumulation of endogenous SA. Importantly, we showed that the nucleus-localized casein kinase II (CK2) complex interacts with and phosphorylates OsTGA5 on Ser-32, which reduces the affinity of OsTGA5 for the JIOsPR10 promoter, thereby alleviating the repression of JIOsPR10 transcription and increasing rice resistance. Furthermore, the in vivo phosphorylation of OsTGA5 Ser-32 was enhanced by blast fungus infection. The CK2 α subunit, depending on its kinase activity, positively regulated rice defense against blast fungus. Taken together, our results provide a mechanism for the role of OsTGA5 in negatively regulating the transcription of defense-related genes in rice and the repressive switch imposed by nuclear CK2-mediated phosphorylation during blast fungus invasion.
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Affiliation(s)
- Yuqing Niu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoguang Huang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zexue He
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingqing Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Han Meng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hua Shi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baomin Feng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
| | - Guodong Lu
- Key Laboratory of Biopesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Dingzhong Tang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mo Wang
- Author for correspondence: (Y.Z.), (M.W.)
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Genome-Wide Identification and Characterization of PRR Gene Family and their Diurnal Rhythmic Expression Profile in Maize. Int J Genomics 2022; 2022:6941607. [PMID: 35615408 PMCID: PMC9126661 DOI: 10.1155/2022/6941607] [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: 03/22/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
As essential components of the circadian clock, the pseudo-response regulator (PRR) gene family plays critical roles in plant photoperiod pathway. In this study, we performed a genome-wide identification and a systematic analysis of the PRR gene family in maize. Nine ZmPRRs were identified, and the gene structure, conserved motif, evolution relationship, and expression pattern of ZmPRRs were analyzed comprehensively. Phylogenetic analysis indicated that the nine ZmPRR genes were divided into three groups, except for ZmPRR73, two of which were highly homologous to each of the AtPRR or OsPRR quintet members. Promoter cis-element analysis of ZmPRRs demonstrated that they might be involved in multiple signaling transduction pathways, such as light response, biological or abiotic stress response, and hormone response. qRT-PCR analysis revealed that the levels of ZmPRRs transcripts varied considerably and exhibited a diurnal rhythmic oscillation expression pattern in the given 24-h period under both SD and LD conditions, which indicated that the level of transcription of ZmPRRs expression is subjected to a circadian rhythm and modulated by light and the circadian clock. The present study will provide an insight into further exploring the biological function and regulatory mechanism of ZmPRR genes in circadian rhythm and response to photoperiod in maize.
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Whole-Genome Sequencing Revealed a Late-Maturing Isogenic Rice Koshihikari Integrated with Hd16 Gene Derived from an Ise Shrine Mutant. Int J Genomics 2022; 2022:4565977. [PMID: 35036423 PMCID: PMC8758330 DOI: 10.1155/2022/4565977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 11/18/2022] Open
Abstract
We identified the key genes controlling the late maturation of the Japonica cultivar Isehikari, which was found at Ise Jingu Shrine and matures 6 days later than Koshihikari. We conducted a genetics-based approach through this study. First, the latest mature plants, which flowered later than Isehikari, were segregated in the F2 and F3 generations of Koshihikari×Isehikari. Next, the linkage relationship of a single late-maturing gene with the SSR markers on the long arm of chromosome 3 was inferred by using late-maturing homozygous F2 segregants. Moreover, genetic analyses of late maturity were conducted through the process of six times of continuous backcross with Koshihikari as a recurrent parent by using the late-maturing homozygous F3 line as a nonrecurrent parent, thus developing a late-maturing isogenic Koshihikari (BC6F2). As a result, we elucidated a single late-maturing gene with incomplete dominance that caused the 14-day maturation delay of Koshihikari. The whole-genome sequencing was conducted on both of Koshihikari and the late-maturing isogenic Koshihikari. Then, the SNP call was conducted as the reference genome of Koshihikari. Finally, a single SNP was identified in the key gene Hd16 of the late-maturing isogenic Koshihikari.
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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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Kang J, Cui H, Jia S, Liu W, Yu R, Wu Z, Wang Z. Arabidopsis thaliana MLK3, a Plant-specific Casein Kinase 1, Negatively Regulates Flowering and Phosphorylates Histone H3 in Vitro. Genes (Basel) 2020; 11:genes11030345. [PMID: 32214028 PMCID: PMC7141126 DOI: 10.3390/genes11030345] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 12/21/2022] Open
Abstract
Arabidopsis thalianaMUT9-LIKE KINASES (MLKs), a family of the plant-specific casein kinase 1 (CK1), have been implicated collectively in multiple biological processes including flowering. Three of the four MLKs (MLK1/2/4) have been characterized, however, little is known about MLK3, the most divergent member of MLKs. Here, we demonstrated that disruption of MLK3 transcript in mlk3 caused early flowering with retarded leaf growth under long-day conditions. In vitro kinase assay showed the nuclear protein MLK3 phosphorylated histone 3 at threonine 3 (H3T3) and mutation of a conserved residue (K146R) abolished the catalytic activity. Ectopic expression of MLK3 but not MLK3(K146R) rescued the morphological defects of mlk3, indicating that an intact MLK3 is critical for maintaining proper flowering time. Transcriptomic analysis revealed that the floral repressor FLOWERING LOCUS C (FLC) was down-regulated significantly in mlk3, suggesting that MLK3 negatively regulates flowering. Hence, MLK3 plays a role in repressing the transition from vegetative to reproductive phase in A. thaliana. This study sheds light on the delicate control of flowering time by A. thaliana CK1 specific to the plant kingdom.
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Affiliation(s)
- Junmei Kang
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing 10019, China; (J.K.); (W.L.)
| | - Huiting Cui
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (H.C.); (S.J.)
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (H.C.); (S.J.)
| | - Wenwen Liu
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing 10019, China; (J.K.); (W.L.)
| | - Renjie Yu
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China;
| | - Zhihai Wu
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China;
| | - Zhen Wang
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing 10019, China; (J.K.); (W.L.)
- Correspondence: ; Tel.: +10-86-6281-6357
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10
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Kang J, Wang Z. Mut9p-LIKE KINASE Family Members: New Roles of the Plant-Specific Casein Kinase I in Plant Growth and Development. Int J Mol Sci 2020; 21:ijms21051562. [PMID: 32106561 PMCID: PMC7084540 DOI: 10.3390/ijms21051562] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 11/16/2022] Open
Abstract
: Casein kinase I (CK1), a ubiquitous serine/threonine (Ser/Thr) protein kinase in eukaryotes, plays pivotal roles in a wide spectrum of cellular functions including metabolism, cell cycle progression, developmental control and stress responses. Plant CK1 evolves a lineage expansion, resulting in a unique branch of members exclusive to the kingdom. Among them, Arabidopsis Mut9p-LIKE KINASEs (MLKs) target diverse substrates including histones and the key regulatory proteins involving in physiological processes of light signaling, circadian rhythms, phytohormone and plant defense. Deregulation of the kinase activity by mutating the enzyme or the phosphorylation sites of substrates causes developmental disorders and susceptibility to adverse environmental conditions. MLKs have evolved as a general kinase that modifies transcription factors or primary regulatory proteins in a dynamic way. Here, we summarize the current knowledge of the roles of MLKs and MLK orthologs in several commercially important crops.
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Affiliation(s)
| | - Zhen Wang
- Correspondence: ; Tel.: +10-86-62816357
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Saito AN, Matsuo H, Kuwata K, Ono A, Kinoshita T, Yamaguchi J, Nakamichi N. Structure-function study of a novel inhibitor of the casein kinase 1 family in Arabidopsis thaliana. PLANT DIRECT 2019; 3:e00172. [PMID: 31549020 PMCID: PMC6747015 DOI: 10.1002/pld3.172] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/31/2019] [Accepted: 09/03/2019] [Indexed: 05/16/2023]
Abstract
Casein kinase 1 (CK1) is an evolutionarily conserved protein kinase family among eukaryotes. Studies in non-plants have shown CK1-dependent divergent biological processes, but the collective knowledge regarding the biological roles of plant CK1 lags far behind other members of the Eukarya. One reason for this is that plants have many more genes encoding CK1 than do animals. To accelerate our understanding of the plant CK1 family, a strong CK1 inhibitor that efficiently inhibits multiple members of the CK1 protein family in vivo (i.e., in planta) is required. Here, we report a novel, specific, and effective CK1 inhibitor in Arabidopsis. Using circadian period-lengthening activity as an estimation of the CK1 inhibitor effect in vivo, we performed a structure-activity relationship study of analogues of the CK1 inhibitor PHA767491 (1,5,6,7-tetrahydro-2-(4-pyridinyl)-4H-pyrrolo[3,2-c]pyridin-4-one hydrochloride). A propargyl group at the pyrrole nitrogen atom (AMI-212) or a bromine atom at the pyrrole C3 position (AMI-23) had stronger CK1 inhibitory activity than PHA767491. A hybrid molecule of AMI-212 and AMI-23 (AMI-331) was about 100-fold more inhibitory than the parent molecule PHA767491. Affinity proteomics using an AMI-331 probe showed that the targets of AMI-331 inhibition are mostly CK1 kinases. As such, AMI-331 is a potent and selective CK1 inhibitor that shows promise in the research of CK1 in plants.
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Affiliation(s)
- Ami N. Saito
- Department of Applied ChemistryWaseda UniversityShinjuku, TokyoJapan
| | - Hiromi Matsuo
- Institute of Transformative Bio‐molecules (WPI‐ITbM)Nagoya UniversityChikusa, NagoyaJapan
| | - Keiko Kuwata
- Institute of Transformative Bio‐molecules (WPI‐ITbM)Nagoya UniversityChikusa, NagoyaJapan
| | - Azusa Ono
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityChikusa, NagoyaJapan
| | - Toshinori Kinoshita
- Institute of Transformative Bio‐molecules (WPI‐ITbM)Nagoya UniversityChikusa, NagoyaJapan
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityChikusa, NagoyaJapan
| | | | - Norihito Nakamichi
- Institute of Transformative Bio‐molecules (WPI‐ITbM)Nagoya UniversityChikusa, NagoyaJapan
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityChikusa, NagoyaJapan
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12
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Harper J, De Vega J, Swain S, Heavens D, Gasior D, Thomas A, Evans C, Lovatt A, Lister S, Thorogood D, Skøt L, Hegarty M, Blackmore T, Kudrna D, Byrne S, Asp T, Powell W, Fernandez-Fuentes N, Armstead I. Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits. ANNALS OF BOTANY 2019; 123:977-992. [PMID: 30715119 PMCID: PMC6589518 DOI: 10.1093/aob/mcy230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/28/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND AND AIMS Lolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic architectures of key agricultural traits and crop characteristics that deliver wider environmental services. Our aim was to identify genomic regions associated with agriculturally important traits by integrating a bacterial artificial chromosome (BAC)-based physical map with a genome-wide association study (GWAS). METHODS BAC-based physical maps for L. perenne were constructed from ~212 000 high-information-content fingerprints using Fingerprint Contig and Linear Topology Contig software. BAC clones were associated with both BAC-end sequences and a partial minimum tiling path sequence. A panel of 716 L. perenne diploid genotypes from 90 European accessions was assessed in the field over 2 years, and genotyped using a Lolium Infinium SNP array. The GWAS was carried out using a linear mixed model implemented in TASSEL, and extended genomic regions associated with significant markers were identified through integration with the physical map. KEY RESULTS Between ~3600 and 7500 physical map contigs were derived, depending on the software and probability thresholds used, and integrated with ~35 k sequenced BAC clones to develop a resource predicted to span the majority of the L. perenne genome. From the GWAS, eight different loci were significantly associated with heading date, plant width, plant biomass and water-soluble carbohydrate accumulation, seven of which could be associated with physical map contigs. This allowed the identification of a number of candidate genes. CONCLUSIONS Combining the physical mapping resource with the GWAS has allowed us to extend the search for candidate genes across larger regions of the L. perenne genome and identified a number of interesting gene model annotations. These physical maps will aid in validating future sequence-based assemblies of the L. perenne genome.
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Affiliation(s)
- J Harper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - J De Vega
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - S Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - D Heavens
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - D Gasior
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - A Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - C Evans
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - A Lovatt
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - S Lister
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - D Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - L Skøt
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - M Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - T Blackmore
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - D Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - S Byrne
- Teagasc, Department of Crop Science, Carlow, Ireland
| | - T Asp
- Department of Molecular Biology and Genetics, Crop Genetics and Biotechnology, Aarhus University, Slagelse, Denmark
| | - W Powell
- Scotland’s Rural College, Edinburgh, UK
| | - N Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - I Armstead
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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13
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Ogiso-Tanaka E, Shimizu T, Hajika M, Kaga A, Ishimoto M. Highly multiplexed AmpliSeq technology identifies novel variation of flowering time-related genes in soybean (Glycine max). DNA Res 2019; 26:243-260. [PMID: 31231761 PMCID: PMC6589554 DOI: 10.1093/dnares/dsz005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/11/2019] [Indexed: 02/02/2023] Open
Abstract
Whole-genome re-sequencing is a powerful approach to detect gene variants, but it is expensive to analyse only the target genes. To circumvent this problem, we attempted to detect novel variants of flowering time-related genes and their homologues in soybean mini-core collection by target re-sequencing using AmpliSeq technology. The average depth of 382 amplicons targeting 29 genes was 1,237 with 99.85% of the sequence data mapped to the reference genome. Totally, 461 variants were detected, of which 150 sites were novel and not registered in dbSNP. Known and novel variants were detected in the classical maturity loci-E1, E2, E3, and E4. Additionally, large indel alleles, E1-nl and E3-tr, were successfully identified. Novel loss-of-function and missense variants were found in FT2a, MADS-box, WDR61, phytochromes, and two-component response regulators. The multiple regression analysis showed that four genes-E2, E3, Dt1, and two-component response regulator-can explain 51.1-52.3% of the variation in flowering time of the mini-core collection. Among them, the two-component response regulator with a premature stop codon is a novel gene that has not been reported as a soybean flowering time-related gene. These data suggest that the AmpliSeq technology is a powerful tool to identify novel alleles.
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Affiliation(s)
- Eri Ogiso-Tanaka
- Institute of Crop Science (NICS), NARO (National Agriculture and Food Research Organization), 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Takehiko Shimizu
- Institute of Crop Science (NICS), NARO (National Agriculture and Food Research Organization), 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Makita Hajika
- Institute of Crop Science (NICS), NARO (National Agriculture and Food Research Organization), 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Akito Kaga
- Institute of Crop Science (NICS), NARO (National Agriculture and Food Research Organization), 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Masao Ishimoto
- Institute of Crop Science (NICS), NARO (National Agriculture and Food Research Organization), 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
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14
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Liu H, Li Q, Xing Y. Genes Contributing to Domestication of Rice Seed Traits and Its Global Expansion. Genes (Basel) 2018; 9:genes9100489. [PMID: 30308970 PMCID: PMC6211083 DOI: 10.3390/genes9100489] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022] Open
Abstract
Asian rice (Oryza sativa) and African rice (Oryza glaberrima) are separately domesticated from their wild ancestors Oryza rufipogon and Oryza barthii, which are very sensitive to daylength. In the process of domestication, some traits that are favorable for the natural survival of wild rice such as seed dormancy and shattering have become favorable ones for human consumption due to the loss-of-function mutations in the genes that are underlying these traits. As a consequence, many genes that are related to these kinds of traits have been fixed with favorable alleles in modern cultivars by artificial selection. After domestication, Oryza sativa cultivars gradually spread to temperate and cool regions from the tropics and subtropics due to the loss of their photoperiod sensitivity. In this paper, we review the characteristics of domestication-related seed traits and heading dates in rice, including the key genes controlling these traits, the differences in allelic diversity between wild rice and cultivars, the geographic distribution of alleles, and the regulatory pathways of these traits. A comprehensive comparison shows that these genes contributed to rice domestication and its global expansion. In addition, these traits have also experienced parallel evolution by artificial selection on the homologues of key genes in other cereals.
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Affiliation(s)
- Haiyang Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
- Wuhan Life Origin Biotech Joint Stock Co., Ltd., Wuhan 430206, China.
| | - Qiuping Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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15
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Minh-Thu PT, Kim JS, Chae S, Jun KM, Lee GS, Kim DE, Cheong JJ, Song SI, Nahm BH, Kim YK. A WUSCHEL Homeobox Transcription Factor, OsWOX13, Enhances Drought Tolerance and Triggers Early Flowering in Rice. Mol Cells 2018; 41:781-798. [PMID: 30078233 PMCID: PMC6125423 DOI: 10.14348/molcells.2018.0203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 12/14/2022] Open
Abstract
Plants have evolved strategies to cope with drought stress by maximizing physiological capacity and adjusting developmental processes such as flowering time. The WOX13 orthologous group is the most conserved among the clade of WOX homeodomain-containing proteins and is found to function in both drought stress and flower development. In this study, we isolated and characterized OsWOX13 from rice. OsWOX13 was regulated spatially in vegetative organs but temporally in flowers and seeds. Overexpression of OsWOX13 (OsWOX13-ov) in rice under the rab21 promoter resulted in drought resistance and early flowering by 7-10 days. Screening of gene expression profiles in mature leaf and panicles of OsWOX13-ov showed a broad spectrum of effects on biological processes, such as abiotic and biotic stresses, exerting a cross-talk between responses. Protein binding microarray and electrophoretic mobility shift assay analyses supported ATTGATTG as the putative cis-element binding of OsWOX13. OsDREB1A and OsDREB1F, drought stress response transcription factors, contain ATTGATTG motif(s) in their promoters and are preferentially expressed in OsWOX13-ov. In addition, Heading date 3a and OsMADS14, regulators in the flowering pathway and development, were enhanced in OsWOX13-ov. These results suggest that OsWOX13 mediates the stress response and early flowering and, thus, may be a regulator of genes involved in drought escape.
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Affiliation(s)
- Pham-Thi Minh-Thu
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Joung Sug Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Songhwa Chae
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Kyong Mi Jun
- Genomics Genetics Institute, GreenGene Biotech Inc., Yongin 17058,
Korea
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54875,
Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029,
Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826,
Korea
| | - Sang Ik Song
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Baek Hie Nahm
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
- Genomics Genetics Institute, GreenGene Biotech Inc., Yongin 17058,
Korea
| | - Yeon-Ki Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
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16
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Nemoto Y, Hori K, Izawa T. Fine-tuning of the setting of critical day length by two casein kinases in rice photoperiodic flowering. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:553-565. [PMID: 29237079 PMCID: PMC5853454 DOI: 10.1093/jxb/erx412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/03/2017] [Indexed: 05/03/2023]
Abstract
Many short-day plants have a critical day length that fixes the schedule for flowering time, limiting the range of natural growth habitats (or growth and cultivation areas). Thus, fine-tuning of the critical day-length setting in photoperiodic flowering determines ecological niches within latitudinal clines; however, little is known about the molecular mechanisms controlling the fine-tuning of the critical day-length setting in plants. Previously, we determined that florigen genes are regulated by day length, and identified several key genes involved in setting the critical day length in rice. Using a set of chromosomal segment substitution lines with the genetic background of an elite temperate japonica cultivar, we performed a series of expression analyses of flowering-time genes to identify those responsible for setting the critical day-length in rice. Here, we identified two casein kinase genes, Hd16 and Hd6, which modulate the expression of florigen genes within certain restricted ranges of photoperiod, thereby fine-tuning the critical day length. In addition, we determined that Hd16 functions as an enhancer of the bifunctional action of Hd1 (the Arabidopsis CONSTANS ortholog) in rice. Utilization of the natural variation in Hd16 and Hd6 was only found among temperate japonica cultivars adapted to northern areas. Therefore, this fine-tuning of the setting of the critical day length may contribute to the potential northward expansion of rice cultivation areas.
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Affiliation(s)
- Yasue Nemoto
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kiyosumi Hori
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Takeshi Izawa
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
- University of Tokyo, Faculty of Agriculture, Laboratory of Plant Genetics and Breeding, Bunkyo-ku, Tokyo, Japan
- Correspondence:
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17
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Kim SH, Kwon CT, Song G, Koh HJ, An G, Paek NC. The rice zebra3 (z3) mutation disrupts citrate distribution and produces transverse dark-green/green variegation in mature leaves. RICE (NEW YORK, N.Y.) 2018; 11:1. [PMID: 29305728 PMCID: PMC5756232 DOI: 10.1186/s12284-017-0196-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/27/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND Rice zebra mutants are leaf variegation mutants that exhibit transverse sectors of green/yellow or green/white in developing or mature leaves. In most cases, leaf variegation is caused by defects in chloroplast biogenesis pathways, leading to an accumulation of reactive oxygen species in a transverse pattern in the leaves. Here, we examine a new type of leaf variegation mutant in rice, zebra3 (z3), which exhibits transverse dark-green/green sectors in mature leaves and lacks the typical yellow or white sectors. RESULTS Map-based cloning revealed that the Z3 locus encodes a putative citrate transporter that belongs to the citrate-metal hydrogen symport (CitMHS) family. CitMHS family members have been extensively studied in bacteria and function as secondary transporters that can transport metal-citrate complexes, but whether CitMHS family transporters exist in eukaryotes remains unknown. To investigate whether Z3 acts as a citrate transporter in rice, we measured citrate levels in wild-type leaves and in the dark-green and green sectors of the leaves of z3 mutants. The results showed that citrates accumulated to high levels in the dark-green sectors of z3 mutant leaves, but not in the green sectors as compared with the wild-type leaves. CONCLUSIONS These results suggest that leaf variegation in the z3 mutant is caused by an unbalanced accumulation of citrate in a transverse pattern in the leaves. Taking these results together, we propose that Z3 plays an important role in citrate transport and distribution during leaf development and is a possible candidate for a CitMHS family member in plants.
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Affiliation(s)
- Suk-Hwan Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Choon-Tak Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Present address: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Giha Song
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Crop Biotechnology Institute, Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea.
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18
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Kim JA, Kim HS, Choi SH, Jang JY, Jeong MJ, Lee SI. The Importance of the Circadian Clock in Regulating Plant Metabolism. Int J Mol Sci 2017; 18:E2680. [PMID: 29232921 PMCID: PMC5751282 DOI: 10.3390/ijms18122680] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 11/16/2022] Open
Abstract
Carbohydrates are the primary energy source for plant development. Plants synthesize sucrose in source organs and transport them to sink organs during plant growth. This metabolism is sensitive to environmental changes in light quantity, quality, and photoperiod. In the daytime, the synthesis of sucrose and starch accumulates, and starch is degraded at nighttime. The circadian clock genes provide plants with information on the daily environmental changes and directly control many developmental processes, which are related to the path of primary metabolites throughout the life cycle. The circadian clock mechanism and processes of metabolism controlled by the circadian rhythm were studied in the model plant Arabidopsis and in the crops potato and rice. However, the translation of molecular mechanisms obtained from studies of model plants to crop plants is still difficult. Crop plants have specific organs such as edible seed and tuber that increase the size or accumulate valuable metabolites by harvestable metabolic components. Human consumers are interested in the regulation and promotion of these agriculturally significant crops. Circadian clock manipulation may suggest various strategies for the increased productivity of food crops through using environmental signal or overcoming environmental stress.
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Affiliation(s)
- Jin A Kim
- National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500, Korea.
| | - Hyun-Soon Kim
- Plant System Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea.
| | - Seo-Hwa Choi
- National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500, Korea.
| | - Ji-Young Jang
- Plant System Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea.
| | - Mi-Jeong Jeong
- National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500, Korea.
| | - Soo In Lee
- National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500, Korea.
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19
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Yoshitsu Y, Takakusagi M, Abe A, Takagi H, Uemura A, Yaegashi H, Terauchi R, Takahata Y, Hatakeyama K, Yokoi S. QTL-seq analysis identifies two genomic regions determining the heading date of foxtail millet, Setaria italica (L.) P.Beauv. BREEDING SCIENCE 2017; 67:518-527. [PMID: 29398946 PMCID: PMC5790050 DOI: 10.1270/jsbbs.17061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/30/2017] [Indexed: 05/29/2023]
Abstract
Heading date is an important event to ensure successful seed production. Although foxtail millet (Setaria italica (L.) P.Beauv.) is an important foodstuff in semiarid regions around the world, the genetic basis determining heading date is unclear. To identify genomic regions regulating days to heading (DTH), we conducted a QTL-seq analysis based on combining whole-genome re-sequencing and bulked-segregant analysis of an F2 population derived from crosses between the middle-heading cultivar Shinanotsubuhime and the early-heading cultivar Yuikogane. Under field conditions, transgressive segregation of DTH toward late heading was observed in the F2 population. We made three types of bulk samples: Y-bulk (early-heading), S-bulk (late-heading) and L-bulk (extremely late-heading). By genome-wide comparison of SNPs in the Y-bulk vs. the S-bulk and the Y-bulk vs. the L-bulk, we identified two QTLs associated with DTH. The first QTL, qDTH2, was detected on chromosome 2 from the Y-bulk and S-bulk comparison. The second QTL, qDTH7, was detected on chromosome 7 from the Y-bulk and L-bulk comparison. The Shinanotsubuhime allele for qDTH2 caused late heading in the F2 population, whereas the Yuikogane allele for qDTH7 led to extremely late heading. These results suggest that allelic differences in both qDTH2 and qDTH7 determine regional adaptability in S. italica.
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Affiliation(s)
- Yuki Yoshitsu
- Faculty of Agriculture, Iwate University,
Morioka, Iwate 020-8550,
Japan
| | - Masato Takakusagi
- Kenpoku Agricultural Research Institute, Iwate Agricultural Research Center,
Karumai, Iwate 028-6222,
Japan
| | - Akira Abe
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
| | - Hiroki Takagi
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
- Ishikawa Prefectural University,
Nonoichi, Ishikawa 921-8836,
Japan
| | - Aiko Uemura
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
| | - Hiroki Yaegashi
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
| | - Yoshihito Takahata
- Faculty of Agriculture, Iwate University,
Morioka, Iwate 020-8550,
Japan
| | | | - Shuji Yokoi
- Faculty of Agriculture, Iwate University,
Morioka, Iwate 020-8550,
Japan
- Graduate School of Life and Environmental Science, Osaka Prefecture University,
Sakai, Osaka 599-8531,
Japan
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20
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Kwon CT, Kim SH, Song G, Kim D, Paek NC. Two NADPH: Protochlorophyllide Oxidoreductase (POR) Isoforms Play Distinct Roles in Environmental Adaptation in Rice. RICE (NEW YORK, N.Y.) 2017; 10:1. [PMID: 28078486 PMCID: PMC5226909 DOI: 10.1186/s12284-016-0141-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/29/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND NADPH: protochlorophyllide oxidoreductase (POR) is an essential enzyme that catalyzes the photoreduction of protochlorophyllide to chlorophyllide, which is ultimately converted to chlorophyll in developing leaves. Rice has two POR isoforms, OsPORA and OsPORB. OsPORA is expressed in the dark during early leaf development; OsPORB is expressed throughout leaf development regardless of light conditions. The faded green leaf (fgl) is a loss-of-function osporB mutant that displays necrotic lesions and variegation in the leaves due to destabilized grana thylakoids, and has increased numbers of plastoglobules in the chloroplasts. To investigate whether the function of OsPORA can complement that of OsPORB, we constitutively overexpressed OsPORA in fgl mutant. RESULTS In the 35S:OsPORA/fgl (termed OPAO) transgenic plants, the necrotic lesions of the mutant disappeared and the levels of photosynthetic pigments and proteins, as well as plastid structure, were recovered in developing leaves under natural long days in the paddy field and under short days in an artificially controlled growth room. Under constant light conditions, however, total chlorophyll and carotenoid levels in the developing leaves of OPAO plants were lower than those of wild type. Moreover, the OPAO plants exhibited mild defects in mature leaves beginning at the early reproductive stage in the paddy field. CONCLUSIONS The physiological function of OsPORB in response to constant light or during reproductive growth cannot be completely replaced by constitutive activity of OsPORA, although the biochemical functions of OsPORA and OsPORB are redundant. Therefore, we suggest that the two OsPORs have differentiated over the course of evolution, playing distinct roles in the adaptation of rice to the environment.
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Affiliation(s)
- Choon-Tak Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea
| | - Suk-Hwan Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea
| | - Giha Song
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea
| | - Dami Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea
- Crop Biotechnology Institute, Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354 Republic of Korea
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Alternative functions of Hd1 in repressing or promoting heading are determined by Ghd7 status under long-day conditions. Sci Rep 2017; 7:5388. [PMID: 28710485 PMCID: PMC5511259 DOI: 10.1038/s41598-017-05873-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/05/2017] [Indexed: 11/12/2022] Open
Abstract
Previous studies suggested that Hd1 promoted heading under short-day conditions (SD) and delayed heading under long-day conditions (LD). However in this study, Hd1 was demonstrated to consistently promote heading date in Zhenshan 97 (ZS97) background by upregulating Ehd1, Hd3a and RFT1 expression under both SD and LD. While the high photoperiod sensitivity of Hd1 was observed in Minghui 63 (MH63) background, with heading being suppressed in LD but promoted in SD. Comparative analysis of two sets of near isogenic lines of Hd1 in MH63 and ZS97 backgrounds indicated that the alternative functions of Hd1 in promoting or suppressing heading under LD are dependent on the previously cloned flowering repressor gene Ghd7. The interaction between proteins Ghd7 and Hd1 occurred through binding of the CCT domain of Ghd7 to the transcription-activating domain of Hd1, resulting in suppression of Ehd1 and florigen gene expression. The involvement of the transcription-activating domain of Hd1 in this protein-protein interaction probably blocked or weakened its transcriptional activity. These findings suggest that Hd1 alone essentially acts as a promoter of heading date, and the protein interaction between Ghd7 and Hd1 determines photoperiod sensitivity and integrated Hd1-mediated and Ehd1-mediated flowering pathways in rice.
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Zhu S, Wang J, Cai M, Zhang H, Wu F, Xu Y, Li C, Cheng Z, Zhang X, Guo X, Sheng P, Wu M, Wang J, Lei C, Wang J, Zhao Z, Wu C, Wang H, Wan J. The OsHAPL1-DTH8-Hd1 complex functions as the transcription regulator to repress heading date in rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:553-568. [PMID: 28043949 PMCID: PMC6055584 DOI: 10.1093/jxb/erw468] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Heading date is an important agronomic trait related to crop yield. Many genes related to heading date have already been identified in rice (Oryza sativa), and a complicated, preliminary regulatory genetic network has also already been established, but the protein regulatory network is poorly understood. We have identified a novel heading date regulator, Heme Activator Protein like 1 (OsHAPL1), which inhibits flowering under long-day conditions. OsHAPL1 is a nuclear-localized protein that is highly expressed in leaves in a rhythmic manner. OsHAPL1 can physically interact with Days To Heading on chromosome 8 (DTH8), which physically interacts with Heading date 1 (Hd1) both in vitro and in vivo. OsHAPL1 forms a complex with DTH8 and Hd1 in Escherichia coli. OsHAPL1, DTH8, and Hd1 physically interact with the HAP complex, and also with general transcription factors in yeast (Saccharomyces cerevisiae). Further studies showed that OsHAPL1 represses the expression of the florigen genes and FLOWERING LOCUS T 1 (RFT1) and Hd3a through Early heading date 1 (Ehd1). We propose that OsHAPL1 functions as a transcriptional regulator and, together with DTH8, Hd1, the HAP complex, and general transcription factors, regulates the expression of target genes and then affects heading date by influencing the expression of Hd3a and RFT1 through Ehd1.
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Affiliation(s)
- Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Jiachang Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, PR China
| | - Maohong Cai
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, PR China
| | - Huan Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, PR China
| | - Fuqing Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Yang Xu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, PR China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Peike Sheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Mingming Wu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, PR China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Zhichao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Chuanyin Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, PR China
- Correspondence:
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23
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Zhang C, Liu J, Zhao T, Gomez A, Li C, Yu C, Li H, Lin J, Yang Y, Liu B, Lin C. A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice. PLANT PHYSIOLOGY 2016; 171:334-43. [PMID: 26945049 PMCID: PMC4854678 DOI: 10.1104/pp.16.01691] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/02/2016] [Indexed: 05/04/2023]
Abstract
The molecular mechanisms underlying photoperiod or temperature control of flowering time have been recently elucidated, but how plants regulate flowering time in response to other external factors, such as water availability, remains poorly understood. Using a large-scale Hybrid Transcription Factor approach, we identified a bZIP transcriptional factor, O. sativa ABA responsive element binding factor 1 (OsABF1), which acts as a suppressor of floral transition in a photoperiod-independent manner. Simultaneous knockdown of both OsABF1 and its closest homologous gene, OsbZIP40, in rice (Oryza sativa) by RNA interference results in a significantly earlier flowering phenotype. Molecular and genetic analyses demonstrate that a drought regime enhances expression of the OsABF1 gene, which indirectly suppresses expression of the Early heading date 1 (Ehd1) gene that encodes a key activator of rice flowering. Furthermore, we identified a drought-inducible gene named OsWRKY104 that is under the direct regulation of OsABF1 Overexpression of OsWRKY104 can suppress Ehd1 expression and confers a later flowering phenotype in rice. Together, these findings reveal a novel pathway by which rice modulates heading date in response to the change of ambient water availability.
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Affiliation(s)
- Chunyu Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Tao Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Adam Gomez
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Cong Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Chunsheng Yu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Hongyu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Jianzhong Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Yuanzhu Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Bin Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Chentao Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
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Kim SK, Park HY, Jang YH, Lee KC, Chung YS, Lee JH, Kim JK. OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice. PLANTA 2016; 243:563-76. [PMID: 26542958 DOI: 10.1007/s00425-015-2426-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 10/23/2015] [Indexed: 05/21/2023]
Abstract
OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response through the modulation of three flowering-time genes ( Ehd1, Hd3a , and RFT1 ) in rice. Plant NUCLEAR FACTOR Y (NF-Y) transcription factors control numerous developmental processes by forming heterotrimeric complexes, but little is known about their roles in flowering in rice. In this study, it is shown that some subunits of OsNF-YB and OsNF-YC interact with each other, and among them, OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response of rice. Protein interaction studies showed that the physical interactions occurred between the three OsNF-YC proteins (OsNF-YC2, OsNF-YC4 and OsNF-YC6) and three OsNF-YB proteins (OsNF-YB8, OsNF-YB10 and OsNF-YB11). Repression and overexpression of the OsNF-YC2 and OsNF-YC4 genes revealed that they act as inhibitors of flowering only under long-day (LD) conditions. Overexpression of OsNF-YC6, however, promoted flowering only under LD conditions, suggesting it could function as a flowering promoter. These phenotypes correlated with the changes in the expression of three rice flowering-time genes [Early heading date 1 (Ehd1), Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1)]. The diurnal and tissue-specific expression patterns of the subsets of OsNF-YB and OsNF-YC genes were similar to those of CCT domain encoding genes such as OsCO3, Heading date 1 (Hd1) and Ghd7. We propose that OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response by interacting directly with OsNF-YB8, OsNF-YB10 or OsNF-YB11 proteins in rice.
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Affiliation(s)
- Soon-Kap Kim
- Division of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-Gu, Seoul, 136-701, Republic of Korea
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Hyo-Young Park
- Division of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-Gu, Seoul, 136-701, Republic of Korea
| | - Yun Hee Jang
- Division of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-Gu, Seoul, 136-701, Republic of Korea
| | - Keh Chien Lee
- Division of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-Gu, Seoul, 136-701, Republic of Korea
| | - Young Soo Chung
- Department of Genetic Engineering, Dong-A University, Busan, 604-714, Republic of Korea
| | - Jeong Hwan Lee
- Department of Bioresource Engineering and Plant Engineering Research Institute, Sejong University, 98 Gunja-dong, Gwangjin-Gu, Seoul, 143-747, Republic of Korea.
| | - Jeong-Kook Kim
- Division of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-Gu, Seoul, 136-701, Republic of Korea.
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25
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Kwon CT, Kim SH, Kim D, Paek NC. The Rice Floral Repressor Early flowering1 Affects Spikelet Fertility By Modulating Gibberellin Signaling. RICE (NEW YORK, N.Y.) 2015; 8:58. [PMID: 26202549 PMCID: PMC4584262 DOI: 10.1186/s12284-015-0058-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/13/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Gibberellic acid (GA; or gibberellin) affects the development of floral organs, especially anthers and pollen, and perturbation of development of male floral organs can cause sterility. Many studies of GA signaling have concentrated on anther development, but the effect of GA on grain production remains to be examined. RESULTS Using a cross of 'Milyang23 (M23)', which has a functional allele of Early flowering1 (EL1), and 'H143', which has a nonfunctional el1 allele, we generated heterogeneous inbred family-near isogenic lines (HNILs) that are homozygous for EL1 [HNIL(M23)] or el1 [HNIL(H143)]. Here, we found that HNIL(H143) exhibited anther deformities and low pollen viability. The expression of GAMYB, a major activator of GA signaling, and its downstream genes CYP703A3 and KAR, mainly involved in pollen formation, increased abnormally during spikelet development; this activation of GA signaling may cause the sterility. To confirm the negative effect of the el1 mutation on spikelet fertility, we examined a line carrying a T-DNA insertion el1 mutant [hereafter ZH11(el1)] and its parental cultivar 'Zhonghua11 (ZH11)'. ZH11(el1) showed nearly identical defects in anther development and pollen viability as HNIL(H143), leading to decreased seed setting rate. However, the elite japonica cultivar Koshihikari, which has a nonfunctional el1 allele for early flowering in long days, produces fertile spikelets and normal grain yields, like other elite japonica cultivars. This indicates that as-yet-unknown regulator(s) that can overcome the male sterile phenotype of the el1 mutation must have been introduced into Koshihikari. CONCLUSIONS The el1 mutation contributes to early flowering in japonica rice under long days but fails to limit GA signaling, thus negatively affecting spikelet fertility, which results in a loss of grain yield. Thus, EL1 is essential for photoperiod sensitivity in flowering as well as spikelet fertility in grain production.
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Affiliation(s)
- Choon-Tak Kwon
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Republic of Korea
| | - Suk-Hwan Kim
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Republic of Korea
| | - Dami Kim
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Republic of Korea
| | - Nam-Chon Paek
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Republic of Korea
- />Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916 Republic of Korea
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