1
|
Itoh H, Yamashita H, Wada KC, Yonemaru JI. Real-time emulation of future global warming reveals realistic impacts on the phenological response and quality deterioration in rice. Proc Natl Acad Sci U S A 2024; 121:e2316497121. [PMID: 38739807 PMCID: PMC11126993 DOI: 10.1073/pnas.2316497121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
Decreased production of crops due to climate change has been predicted scientifically. While climate-resilient crops are necessary to ensure food security and support sustainable agriculture, predicting crop growth under future global warming is challenging. Therefore, we aimed to assess the impact of realistic global warming conditions on rice cultivation. We developed a crop evaluation platform, the agro-environment (AE) emulator, which generates diverse environments by implementing the complexity of natural environmental fluctuations in customized, fully artificial lighting growth chambers. We confirmed that the environmental responsiveness of rice obtained in the fluctuation of artificial environments is similar to those exhibited in natural environments by validating our AE emulator using publicly available meteorological data from multiple years at the same location and multiple locations in the same year. Based on the representative concentration pathway, real-time emulation of severe global warming unveiled dramatic advances in the rice life cycle, accompanied by a 35% decrease in grain yield and an 85% increase in quality deterioration, which is higher than the recently reported projections. The transcriptome dynamism showed that increasing temperature and CO2 concentrations synergistically changed the expression of various genes and strengthened the induction of flowering, heat stress adaptation, and CO2 response genes. The predicted severe global warming greatly alters rice environmental adaptability and negatively impacts rice production. Our findings offer innovative applications of artificial environments and insights for enhancing varietal potential and cultivation methods in the future.
Collapse
Affiliation(s)
- Hironori Itoh
- Breeding Big Data Management and Utilization Group, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8518, Japan
| | - Hiroto Yamashita
- Breeding Big Data Management and Utilization Group, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8518, Japan
| | - Kaede C. Wada
- Breeding Big Data Management and Utilization Group, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8518, Japan
- Incubation Laboratory, Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-0856, Japan
| | - Jun-ichi Yonemaru
- Incubation Laboratory, Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-0856, Japan
| |
Collapse
|
2
|
Su Q, Chen L, Cai Y, Wang L, Chen Y, Zhang J, Liu L, Zhang Y, Yuan S, Gao Y, Sun S, Han T, Hou W. The FLOWERING LOCUS T 5b positively regulates photoperiodic flowering and improves the geographical adaptation of soybean. PLANT, CELL & ENVIRONMENT 2024; 47:246-258. [PMID: 37830787 DOI: 10.1111/pce.14739] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Plants can sense the photoperiod to flower at the right time. As a sensitive short-day crop, soybean (Glycine max) flowering varies greatly depending on photoperiods, affecting yields. Adaptive changes in soybeans rely on variable genetic loci such as E1 and FLOWERING LOCUS T orthologs. However, the precise coordination and control of these molecular components remain largely unknown. In this study, we demonstrate that GmFT5b functions as a crucial factor for soybean flowering. Overexpressed or mutated GmFT5b resulted in significantly early or later flowering, altering expression profiles for several downstream flowering-related genes under a long-day photoperiod. GmFT5b interacts with the transcription factor GmFDL15, suggesting transcriptional tuning of flowering time regulatory genes via the GmFT5b/GmFDL15 complex. Notably, GmFT5a partially compensated for GmFT5b function, as ft5a ft5b double mutants exhibited an enhanced late-flowering phenotype. Association mapping revealed that GmFT5b was associated with flowering time, maturity, and geographical distribution of soybean accessions, all associated with the E1 locus. Therefore, GmFT5b is a valuable target for enhancing regional adaptability. Natural variants or multiple mutants in this region can be utilized to generate optimized soybean varieties with precise flowering times.
Collapse
Affiliation(s)
- Qiang Su
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yupeng Cai
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Wang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jialing Zhang
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luping Liu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Zhang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan Yuan
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Gao
- Syngenta Biotechnology (China) Co., Ltd, Beijing, China
| | - Shi Sun
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
3
|
Chen SQ, Luo C, Liu Y, Liang RZ, Huang X, Lu TT, Guo YH, Li RY, Huang CT, Wang Z, He XH. Lack of the CCT domain changes the ability of mango MiCOL14A to resist salt and drought stress in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111826. [PMID: 37574138 DOI: 10.1016/j.plantsci.2023.111826] [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: 02/15/2023] [Revised: 07/30/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
CONSTANS (CO) is the key gene in the photoperiodic pathway that regulates flowering in plants. In this paper, a CONSTANS-like 14A (COL14A) gene was obtained from mango, and its expression patterns and functions were characterized. Sequence analysis shows that MiCOL14A-JH has an additional A base, which leads to code shifting in subsequent coding boxes and loss of the CCT domain. The MiCOL14A-JH and MiCOL14A-GQ genes both belonged to group Ⅲ of the CO/COL gene family. Analysis of tissue expression patterns showed that MiCOL14A was expressed in all tissues, with the highest expression in the leaves of seedling, followed by lower expression levels in the flowers and stems of adult leaves. However, there was no significant difference between different mango varieties. At different development stages of flowering, the expression level of MiCOL14A-GQ was the highest in the leaves before floral induction period, and the lowest at flowering stage, while the highest expression level of MiCOL14A-JH appeared in the leaves at flowering stage. The transgenic functional analysis showed that both MiCOL14A-GQ and MiCOL14A-JH induced delayed flowering of transgenic Arabidopsis. In addition, MiCOL14A-JH enhanced the resistance of transgenic Arabidopsis to drought stress, while MiCOL14A-GQ increased the sensitivity of transgenic Arabidopsis to salt stress. Further proteinprotein interaction analysis showed that MiCOL14A-JH directly interacted with MYB30-INTERACTING E3 LIGASE 1 (MiMIEL1), CBL-interacting protein kinase 9 (MiCIPK9) and zinc-finger protein 4 (MiZFP4), but MiCOL14A-GQ could not interact with these three stress-related proteins. Together, our results demonstrated that MiCOL14A-JH and MiCOL14A-GQ not only regulate flowering but also play a role in the abiotic stress response in mango, and the lack of the CCT domain affects the proteinprotein interaction, thus affecting the gene response to stress. The insertion of an A base can provide a possible detection site for mango resistance breeding.
Collapse
Affiliation(s)
- Shu-Quan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Yuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Rong-Zhen Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Xing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Ting-Ting Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Yi-Hang Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Ruo-Yan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Chu-Ting Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhuo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Xin-Hua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China.
| |
Collapse
|
4
|
Maeda AE, Nakamichi N. Plant clock modifications for adapting flowering time to local environments. PLANT PHYSIOLOGY 2022; 190:952-967. [PMID: 35266545 PMCID: PMC9516756 DOI: 10.1093/plphys/kiac107] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/09/2022] [Indexed: 05/25/2023]
Abstract
During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.
Collapse
Affiliation(s)
- Akari E Maeda
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| |
Collapse
|
5
|
Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
Collapse
Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| |
Collapse
|
6
|
Wang X, Zhou P, Huang R, Zhang J, Ouyang X. A Daylength Recognition Model of Photoperiodic Flowering. FRONTIERS IN PLANT SCIENCE 2021; 12:778515. [PMID: 34868180 PMCID: PMC8638659 DOI: 10.3389/fpls.2021.778515] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 06/01/2023]
Abstract
The photoperiodic flowering pathway is crucial for plant development to synchronize internal signaling events and external seasons. One hundred years after photoperiodic flowering was discovered, the underlying core signaling network has been elucidated in model plants such as Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and soybean (Glycine max). Here, we review the progress made in the photoperiodic flowering area and summarize previously accepted photoperiodic flowering models. We then introduce a new model based on daylength recognition by florigen. By determining the expression levels of the florigen gene, this model can assess the mechanism of daylength sensing and crop latitude adaptation. Future applications of this model under the constraints of global climate change are discussed.
Collapse
Affiliation(s)
- Xiaoying Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Peng Zhou
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Rongyu Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xinhao Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| |
Collapse
|
7
|
Mao F, Wang Z, Zheng Y, Tang S, Luo X, Xiong T, Yan S. Fine mapping of a heading date QTL, Se16(t), under extremely long day conditions in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:70. [PMID: 37309360 PMCID: PMC10236121 DOI: 10.1007/s11032-021-01263-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
Heading date (flowering time) is a key trait that determines the yield and the adaptability of rice varieties. In the past 20 years, a number of genetic studies have been carried out to elucidate the genetic control of rice heading date, and many important genes have been cloned. These genes were identified under natural day (ND) conditions; however, little is known about the heading behavior under extreme day-length conditions. In this study, we identified a japonica variety, Sasanishiki, that showed sensitivity to extremely long days (ELD). Its heading date was significantly delayed for about 20 days under artificial ELD conditions that were achieved by setting a light emitting diode (LED) lamp beside a paddy field. We found that the late heading phenotype of Sasanishiki was induced when the day length was more than 14.75 h, and the LED light intensity was above 2 µmol m-2 s-1. Genetic analysis revealed that the photoperiod sensitivity of Sasanishiki was controlled by a dominant locus, temporarily named Se16(t). It was fine mapped to a 30.4-kb interval on chromosome 3, containing five predicted genes, including PHYC, a phytochrome encoding gene of rice. Our findings provide new information on the heading date under ELD conditions in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01263-8.
Collapse
Affiliation(s)
- Fangming Mao
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Zhiquan Wang
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Yiyun Zheng
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Shusheng Tang
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Xin Luo
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Tao Xiong
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Song Yan
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| |
Collapse
|
8
|
Sun C, Zhang K, Zhou Y, Xiang L, He C, Zhong C, Li K, Wang Q, Yang C, Wang Q, Chen C, Chen D, Wang Y, Liu C, Yang B, Wu H, Chen X, Li W, Wang J, Xu P, Wang P, Fang J, Chu C, Deng X. Dual function of clock component OsLHY sets critical day length for photoperiodic flowering in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1644-1657. [PMID: 33740293 PMCID: PMC8384598 DOI: 10.1111/pbi.13580] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 05/11/2023]
Abstract
Circadian clock, an endogenous time-setting mechanism, allows plants to adapt to unstable photoperiod conditions and induces flowering with proper timing. In Arabidopsis, the central clock oscillator was formed by a series of interlocked transcriptional feedback loops, but little is known in rice so far. By MutMap technique, we identified the candidate gene OsLHY from a later flowering mutant lem1 and further confirmed it through genetic complementation, RNA interference knockdown, and CRISPR/Cas9-knockout. Global transcriptome profiling and expression analyses revealed that OsLHY might be a vital circadian rhythm component. Interestingly, oslhy flowered later under ≥12 h day length but headed earlier under ≤11 h day length. qRT-PCR results exhibited that OsLHY might function through OsGI-Hd1 pathway. Subsequent one-hybrid assays in yeast, DNA affinity purification qPCR, and electrophoretic mobility shift assays confirmed OsLHY could directly bind to the CBS element in OsGI promoter. Moreover, the critical day length (CDL) for function reversal of OsLHY in oslhy (11-12 h) was prolonged in the double mutant oslhy osgi (about 13.5 h), indicating that the CDL set by OsLHY was OsGI dependent. Additionally, the dual function of OsLHY entirely relied on Hd1, as the double mutant oslhy hd1 showed the same heading date with hd1 under about 11.5, 13.5, and 14 h day lengths. Together, OsLHY could fine-tune the CDL by directly regulating OsGI, and Hd1 acts as the final effector of CDL downstream of OsLHY. Our study illustrates a new regulatory mechanism between the circadian clock and photoperiodic flowering.
Collapse
Affiliation(s)
- Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Kuan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yi Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Lin Xiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Changcai He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chao Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Ke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Qiuxia Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chuanpeng Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Qian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Congping Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Dan Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chuanqiang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Bin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Hualin Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xiaoqiong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Jun Fang
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
| | - Chengcai Chu
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| |
Collapse
|
9
|
Qiu L, Wu Q, Wang X, Han J, Zhuang G, Wang H, Shang Z, Tian W, Chen Z, Lin Z, He H, Hu J, Lv Q, Ren J, Xu J, Li C, Wang X, Li Y, Li S, Huang R, Chen X, Zhang C, Lu M, Liang C, Qin P, Huang X, Li S, Ouyang X. Forecasting rice latitude adaptation through a daylength-sensing-based environment adaptation simulator. NATURE FOOD 2021; 2:348-362. [PMID: 37117734 DOI: 10.1038/s43016-021-00280-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/20/2021] [Indexed: 04/30/2023]
Abstract
Global climate change necessitates crop varieties with good environmental adaptability. As a proxy for climate adaptation, crop breeders could select for adaptability to different latitudes, but the lengthy procedures for that slow development. Here, we combined molecular technologies with a streamlined in-house screening method to facilitate rapid selection for latitude adaptation. We established the daylength-sensing-based environment adaptation simulator (DEAS) to assess rice latitude adaptation status via the transcriptional dynamics of florigen genes at different latitudes. The DEAS predicted the florigen expression profiles in rice varieties with high accuracy. Furthermore, the DEAS showed potential for application in different crops. Incorporating the DEAS into conventional breeding programmes would help to develop cultivars for climate adaptation.
Collapse
Affiliation(s)
- Leilei Qiu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qinqin Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaoying Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiupan Han
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Gui Zhuang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiyun Shang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Wei Tian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zechuan Lin
- School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Jie Hu
- School of Mathematical Sciences, Xiamen University, Xiamen, China
| | - Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Juansheng Ren
- Crop Research Institute of Sichuan Academy of Agricultural Science, Chengdu, China
| | - Jun Xu
- Deyang Agricultural Science and Education Management Station, Deyang, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiangfeng Wang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yang Li
- Photobiological Industry Institute, Sanan Sino-Science Photobiotech, Xiamen, China
| | - Shaohua Li
- Photobiological Industry Institute, Sanan Sino-Science Photobiotech, Xiamen, China
| | - Rongyu Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cheng Zhang
- Liaoning Rice Research Institute, Shenyang, China
| | - Ming Lu
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shigui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xinhao Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
| |
Collapse
|
10
|
Zhou L, Lu Y, Huang J, Sha Z, Mo W, Xue J, Ma S, Shi W, Yang Z, Gao J, Bian M. Arabidopsis CIB3 regulates photoperiodic flowering in an FKF1-dependent way. Biosci Biotechnol Biochem 2021; 85:765-774. [PMID: 33686404 DOI: 10.1093/bbb/zbaa120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/22/2020] [Indexed: 01/29/2023]
Abstract
Arabidopsis cryptochrome 2 (CRY2) and FLAVIN-BINDING, KELCH REPEAT, and F-BOX 1 (FKF1) are blue light receptors mediating light regulation of growth and development, such as photoperiodic flowering. CRY2 interacts with a basic helix-loop-helix transcription factor CIB1 in response to blue light to activate the transcription of the flowering integrator gene FLOWERING LOCUS T (FT). CIB1, CIB2, CIB4, and CIB5 function redundantly to promote flowering in a CRY2-dependent way and form various heterodimers to bind to the noncanonical E-box sequence in the FT promoter. However, the function of CIB3 has not been described. We discovered that CIB3 promotes photoperiodic flowering independently of CRY2. Moreover, CIB3 does not interact with CRY2 but interacts with CIB1 and functions synergistically with CIB1 to promote the transcription of the GI gene. FKF1 is required for CIB3 to promote flowering and enhances the CIB1-CIB3 interaction in response to blue light.
Collapse
Affiliation(s)
- Lianxia Zhou
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Yi Lu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Jie Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Zhiwei Sha
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Weiliang Mo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Jiayi Xue
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China.,Humen Foreign Language School, Dongguan, China
| | - Shuodan Ma
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Wuliang Shi
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Zhenming Yang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Jie Gao
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Mingdi Bian
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Singh N, Wang DR, Ali L, Kim H, Akther KM, Harrington SE, Kang JW, Shakiba E, Shi Y, DeClerck G, Meadows B, Govindaraj V, Ahn SN, Eizenga GC, McCouch SR. A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds. FRONTIERS IN PLANT SCIENCE 2020; 11:564824. [PMID: 33281840 PMCID: PMC7688981 DOI: 10.3389/fpls.2020.564824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/12/2020] [Indexed: 05/27/2023]
Abstract
Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed under greenhouse conditions for several simply inherited (Mendelian) traits. These six interspecific populations can be used as individual Chromosome Segment Substitution Line libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.
Collapse
Affiliation(s)
- Namrata Singh
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Diane R. Wang
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Liakat Ali
- Rice Research and Extension Center, University of Arkansas, Stuttgart, AR, United States
| | - HyunJung Kim
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Kazi M. Akther
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sandra E. Harrington
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Ju-Won Kang
- Department of Agronomy, Chungnam National University, Daejeon, South Korea
| | - Ehsan Shakiba
- Rice Research and Extension Center, University of Arkansas, Stuttgart, AR, United States
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Genevieve DeClerck
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Byron Meadows
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Vishnu Govindaraj
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sang-Nag Ahn
- Department of Agronomy, Chungnam National University, Daejeon, South Korea
| | - Georgia C. Eizenga
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, United States
| | - Susan R. McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| |
Collapse
|
13
|
Wu CC, Wei FJ, Chiou WY, Tsai YC, Wu HP, Gotarkar D, Wei ZH, Lai MH, Hsing YIC. Studies of rice Hd1 haplotypes worldwide reveal adaptation of flowering time to different environments. PLoS One 2020; 15:e0239028. [PMID: 32941524 PMCID: PMC7498076 DOI: 10.1371/journal.pone.0239028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/29/2020] [Indexed: 11/30/2022] Open
Abstract
Rice domestication/adaptation is a good model for studies of the development and spread of this important crop. Mutations that caused morphological and physiological change, followed by human selection/expansion, finally led to the improvement of phenotypes suitable for different kinds of environments. We used the sequence information for Heading date 1 (Hd1) gene to reveal the association between sequence changes and flowering phenotypes of rice in different regions. Seven loss-of-function hd1 haplotypes had been reported. By data-mining the genome sequencing information in the public domain, we discovered 3 other types. These loss-of-function allele haplotypes are present in subtropical and tropical regions, which indicates human selection. Some of these haplotypes are present locally. However, types 7 and 13 are present in more than one-third of the world's rice accessions, including landraces and modern varieties. In the present study, phylogenetic, allele network and selection pressure analyses revealed that these two haplotypes might have occurred early in Southeastern Asia and then were introgressed in many local landraces in nearby regions. We also demonstrate that these haplotypes are present in weedy rice populations, which again indicates that these alleles were present in rice cultivation for long time. In comparing the wild rice sequence information, these loss-of-function haplotypes occurred in agro but were not from wild rice.
Collapse
Affiliation(s)
- Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Institute of Plant Science, National Taiwan University, Taipei, Taiwan
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Yi Chiou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yuan-Ching Tsai
- Department of Agronomy, National Chia-yi University, Chiayi, Taiwan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Dhananjay Gotarkar
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Zhi-Han Wei
- Department of Agronomy, National Chia-yi University, Chiayi, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Yue-Ie Caroline Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
14
|
The Response of COL and FT Homologues to Photoperiodic Regulation in Carrot (Daucus carota L.). Sci Rep 2020; 10:9984. [PMID: 32561786 PMCID: PMC7305175 DOI: 10.1038/s41598-020-66807-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/22/2020] [Indexed: 11/13/2022] Open
Abstract
Carrot (Daucus carota L.) is a biennial plant requiring vernalization to induce flowering, but long days can promote its premature bolting and flowering. The basic genetic network controlling the flowering time has been constructed for carrot, but there is limited information on the molecular mechanisms underlying the photoperiodic flowering response. The published carrot genome could provide an effective tool for systematically retrieving the key integrator genes of GIGANTEA (GI), CONSTANS-LIKE (COL), FLOWERING LOCUS T (FT), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) homologues in the photoperiod pathway. In this study, the bolting time of wild species “Songzi” (Ws) could be regulated by different photoperiods, but the orange cultivar “Amsterdam forcing” (Af) displayed no bolting phenomenon. According to the carrot genome and previous de novo transcriptome, 1 DcGI, 15 DcCOLs, 2 DcFTs, and 3 DcSOC1s were identified in the photoperiod pathway. The circadian rhythm peaks of DcGI, DcCOL2, DcCOL5a, and DcCOL13b could be delayed under long days (LDs). The peak value of DcCOL2 in Af (12.9) was significantly higher than that in Ws (6.8) under short day (SD) conditions, and was reduced under LD conditions (5.0). The peak values of DcCOL5a in Ws were constantly higher than those in Af under the photoperiod treatments. The expression levels of DcFT1 in Ws (463.0) were significantly upregulated under LD conditions compared with those in Af (1.4). These responses of DcCOL2, DcCOL5a, and DcFT1 might be related to the different bolting responses of Ws and Af. This study could provide valuable insights into understanding the key integrator genes in the carrot photoperiod pathway.
Collapse
|
15
|
Evolution and functional diversification of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in plants. Semin Cell Dev Biol 2020; 109:20-30. [PMID: 32507412 DOI: 10.1016/j.semcdb.2020.05.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 01/01/2023]
Abstract
Plant growth and development, particularly the induction of flowering, are tightly controlled by key regulators in response to endogenous and environmental cues. The FLOWERING LOCUS T (FT)/TERMINAL FLOWER 1 (TFL1) family of phosphatidylethanolamine-binding protein (PEBP) genes is central to plant development, especially the regulation of flowering time and plant architecture. FT, the long-sought florigen, promotes flowering and TFL1 represses flowering. The balance between FT and TFL1 modulates plant architecture by switching the meristem from indeterminate to determinate growth, or vice versa. Recent studies in a broad range of plant species demonstrated that, in addition to their roles in flowering time and plant architecture, FT/TFL1 family genes participate in diverse aspects of plant development, such as bamboo seed germination and potato tuber formation. In this review, we briefly summarize the evolution of the FT/TFL1 family and highlight recent findings on their conserved and divergent functions in different species.
Collapse
|
16
|
Ke M, Li Y, Qu Q, Ye Y, Peijnenburg WJGM, Zhang Z, Xu N, Lu T, Sun L, Qian H. Offspring toxicity of silver nanoparticles to Arabidopsis thaliana flowering and floral development. JOURNAL OF HAZARDOUS MATERIALS 2020; 386:121975. [PMID: 31884364 DOI: 10.1016/j.jhazmat.2019.121975] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Accepted: 12/23/2019] [Indexed: 05/16/2023]
Abstract
Many studies have considered silver nanoparticles (AgNPs) cytotoxicity to mammalian and human cell lines and plant growth. However, only few studies considered toxic effects of AgNPs on plant offspring, especially on flowering. Arabidopsis thaliana was treated with 12.5 mg/kg AgNPs employing parental-(P-AgNPs) and offspring-generation (O-AgNPs) exposure to study the effects of AgNPs on flowering and floral development. Exposure to P-AgNPs was found to significantly decrease petal and pollen viability and subsequently reduced pod production. The inhibition of A. thaliana vegetative growth caused by P-AgNPs exposure was transferred to offspring and even became more severe in the O-AgNPs group. Further, the transcription of genes related to flowering and floral organ development in P-AgNPs and O-Con plants was downregulated by approximately 10-40% compared to the transcription in P-Con plants and showed a stronger decrease in the O-AgNPs group to 30-50% of that in the P-AgNPs group. This resulted in a delay in flowering of 4, 3 and 8 days in P-AgNPs, O-Con and O-AgNPs plants, respectively. Our research shows that the negative effects on floral development can be transferred to the offspring in A. thaliana, which may have significant implications with regard to the risks posed by NPs to food safety and security.
Collapse
Affiliation(s)
- Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Yizhi Ye
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, RA Leiden 2300, the Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, the Netherlands
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China.
| |
Collapse
|
17
|
Saito H, Okumoto Y, Tsukiyama T, Xu C, Teraishi M, Tanisaka T. Allelic Differentiation at the E1/Ghd7 Locus Has Allowed Expansion of Rice Cultivation Area. PLANTS 2019; 8:plants8120550. [PMID: 31795099 PMCID: PMC6963527 DOI: 10.3390/plants8120550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/22/2022]
Abstract
The photoperiod-insensitivity allele e1 is known to be essential for the extremely low photoperiod sensitivity of rice, and thereby enabled rice cultivation in high latitudes (42–53° north (N)). The E1 locus regulating photoperiod-sensitivity was identified on chromosome 7 using a cross between T65 and its near-isogenic line T65w. Sequence analyses confirmed that the E1 and the Ghd7 are the same locus, and haplotype analysis showed that the e1/ghd7-0a is a pioneer allele that enabled rice production in Hokkaido (42–45° N). Further, we detected two novel alleles, e1-ret/ghd7-0ret and E1-r/Ghd7-r, each harboring mutations in the promoter region. These mutant alleles alter the respective expression profiles, leading to marked alteration of flowering time. Moreover, e1-ret/ghd7-0ret, as well as e1/ghd7-0a, was found to have contributed to the establishment of Hokkaido varieties through the marked reduction effect on photoperiod sensitivity, whereas E1-r/Ghd7-r showed a higher expression than the E1/Ghd7 due to the nucleotide substitutions in the cis elements. The haplotype analysis showed that two photoperiod-insensitivity alleles e1/ghd7-0a and e1-ret/ghd7-0ret, originated independently from two sources. These results indicate that naturally occurring allelic variation at the E1/Ghd7 locus allowed expansion of the rice cultivation area through diversification and fine-tuning of flowering time.
Collapse
Affiliation(s)
- Hiroki Saito
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
- Tropical Agriculture Research Front, Japan International Research Center of Agricultural Science, Ishigaki, Okinawa 907-0002, Japan
- Correspondence: ; Tel.: +81-980-82-2396
| | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
| | - Takuji Tsukiyama
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
- Faculty of Agriculture, Kindai University, Nara, Nara 631-8505, Japan
| | - Chong Xu
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
- School of Agriculture, Kibi International University, Minami-Awaji 656-0484, Japan
| | - Masayoshi Teraishi
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
| | - Takatoshi Tanisaka
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
- School of Agriculture, Kibi International University, Minami-Awaji 656-0484, Japan
| |
Collapse
|
18
|
Liu J, Cheng Z, Li X, Xie L, Bai Y, Peng L, Li J, Gao J. Expression Analysis and Regulation Network Identification of the CONSTANS-Like Gene Family in Moso Bamboo ( Phyllostachys edulis) Under Photoperiod Treatments. DNA Cell Biol 2019; 38:607-626. [PMID: 31210530 DOI: 10.1089/dna.2018.4611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CONSTANS (CO)/CONSTANS-like (COL) genes that have been studied in annual model plants such as Arabidopsis thaliana and Oryza sativa play key roles in the photoperiodic flowering pathway. Moso bamboo is a perennial plant characterized by a long vegetative stage and flowers synchronously followed by widespread death. However, the characteristics of COL in moso bamboo remain unclear. In view of this, we performed a genome-wide identification and expression analysis of the COL gene family in moso bamboo. Fourteen nonredundant PheCOL genes were identified, and we analyzed gene structures, phylogeny, and subcellular location predictions. Phylogenetic analyses indicated that 14 PheCOLs could be clustered into three groups, and each clade was well supported by conserved intron/exon structures and motifs. A number of light-related and tissue-specific cis-elements were randomly distributed within the promoter sequences of the PheCOLs. The expression profiling of PheCOL genes in various tissues and developmental stages revealed that most of PheCOL genes were most highly expressed in the leaves and took part in moso bamboo flower development and rapid shoot growth. In addition, the transcription of PheCOLs exhibited a clear diurnal oscillation in both long-day and short-day conditions. Most of the PheCOL genes were inhibited under light treatment and upregulated in dark conditions. PheCOLs can interact with each other. Subcellular localization result showed that PheCOL14 encoded a cell membrane protein, and it bound to the promoter of PheCOL3. Taken together, the results of this study will be useful not only as they contribute to comprehensive information for further analyses of the molecular functions of the PheCOL gene family, but also will provide a theoretical foundation for the further construction of moso bamboo photoperiod regulation networks.
Collapse
Affiliation(s)
- Jun Liu
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Zhanchao Cheng
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Xiangyu Li
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Lihua Xie
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Yucong Bai
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Lixin Peng
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Juan Li
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| |
Collapse
|
19
|
Moghadam NN, Kurbalija Novicic Z, Pertoldi C, Kristensen TN, Bahrndorff S. Effects of photoperiod on life-history and thermal stress resistance traits across populations of Drosophila subobscura. Ecol Evol 2019; 9:2743-2754. [PMID: 30891213 PMCID: PMC6405525 DOI: 10.1002/ece3.4945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/29/2018] [Accepted: 01/08/2019] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION Organisms use environmental cues to match their phenotype with the future availability of resources and environmental conditions. Changes in the magnitude and frequency of environmental cues such as photoperiod and temperature along latitudes can be used by organisms to predict seasonal changes. While the role of temperature variation on the induction of plastic and seasonal responses is well established, the importance of photoperiod for predicting seasonal changes is less explored. MATERIALS AND METHODS Here we studied changes in life-history and thermal stress resistance traits in Drosophila subobscura in response to variation in photoperiod (6:18, 12:12 and 18:6 light:dark cycles) mimicking seasonal variations in day length. The populations of D. subobscura were collected from five locations along a latitudinal gradient (from North Africa and Europe). These populations were exposed to different photoperiods for two generations, whereafter egg-to-adult viability, productivity, dry body weight, thermal tolerance, and starvation resistance were assessed. RESULTS We found strong effects of photoperiod, origin of populations, and their interactions on life-history and stress resistance traits. Thermal resistance varied between the populations and the effect of photoperiod depended on the trait and the method applied for the assessment of thermal resistance. PERSPECTIVES Our results show a strong effect of the origin of population and photoperiod on a range of fitness-related traits and provide evidence for local adaptation to environmental cues (photoperiod by population interaction). The findings emphasize an important and often neglected role of photoperiod in studies on thermal resistance and suggest that cues induced by photoperiod may provide some buffer enabling populations to cope with a more variable and unpredictable future climate.
Collapse
Affiliation(s)
- Neda N. Moghadam
- Department of Chemistry and BioscienceAalborg UniversityAalborg EDenmark
- Department of Biological and Environmental Science, Centre of Excellence in Biological InteractionsUniversity of JyvaskylaJyväskyläFinland
| | - Zorana Kurbalija Novicic
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology CenterUppsala UniversityUppsalaSweden
| | - Cino Pertoldi
- Department of Chemistry and BioscienceAalborg UniversityAalborg EDenmark
- Aalborg ZooAalborgDenmark
| | - Torsten N. Kristensen
- Department of Chemistry and BioscienceAalborg UniversityAalborg EDenmark
- Department of BioscienceAarhus UniversityAarhus CDenmark
| | - Simon Bahrndorff
- Department of Chemistry and BioscienceAalborg UniversityAalborg EDenmark
| |
Collapse
|
20
|
Stephenson E, Estrada S, Meng X, Ourada J, Muszynski MG, Habben JE, Danilevskaya ON. Over-expression of the photoperiod response regulator ZmCCT10 modifies plant architecture, flowering time and inflorescence morphology in maize. PLoS One 2019; 14:e0203728. [PMID: 30726207 PMCID: PMC6364868 DOI: 10.1371/journal.pone.0203728] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/11/2019] [Indexed: 11/19/2022] Open
Abstract
Maize originated as a tropical plant that required short days to transition from vegetative to reproductive development. ZmCCT10 [CO, CONSTANS, CO-LIKE and TIMING OF CAB1 (CCT) transcription factor family] is a regulator of photoperiod response and was identified as a major QTL controlling photoperiod sensitivity in maize. We modulated expression of ZmCCT10 in transgenic maize using two constitutive promoters with different expression levels. Transgenic plants over expressing ZmCCT10 with either promoter were delayed in their transition from vegetative to reproductive development but were not affected in their switch from juvenile-to-adult vegetative growth. Strikingly, transgenic plants containing the stronger expressing construct had a prolonged period of vegetative growth accompanied with dramatic modifications to plant architecture that impacted both vegetative and reproductive traits. These plants did not produce ears, but tassels were heavily branched. In more than half of the transgenic plants, tassels were converted into a branched leafy structure resembling phyllody, often composed of vegetative plantlets. Analysis of expression modules controlling the floral transition and meristem identity linked these networks to photoperiod dependent regulation, whereas phase change modules appeared to be photoperiod independent. Results from this study clarified the influence of the photoperiod pathway on vegetative and reproductive development and allowed for the fine-tuning of the maize flowering time model.
Collapse
Affiliation(s)
- Elizabeth Stephenson
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Stacey Estrada
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Xin Meng
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Jesse Ourada
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Michael G. Muszynski
- University of Hawaii at Manoa, Tropical Plant and Soil Sciences, Honolulu, Hawaii; United States of America
| | - Jeffrey E. Habben
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Olga N. Danilevskaya
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
- * E-mail:
| |
Collapse
|
21
|
Ke M, Qu Q, Peijnenburg WJGM, Li X, Zhang M, Zhang Z, Lu T, Pan X, Qian H. Phytotoxic effects of silver nanoparticles and silver ions to Arabidopsis thaliana as revealed by analysis of molecular responses and of metabolic pathways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:1070-1079. [PMID: 30743820 DOI: 10.1016/j.scitotenv.2018.07.061] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 06/09/2023]
Abstract
The acute (3 days) and chronic (whole life history) responses of Arabidopsis thaliana following exposure to silver nanoparticles (AgNPs) and Ag+ ions (AgNO3) in respectively a hydroponic medium and in soil were studied. After 3 days of hydroponic exposure, AgNPs (1.0 and 2.5 mg/L) exerted more severe inhibitory effects on plant (shoot and root) growth and photosynthesis than the same concentrations of Ag+ ions. In soil cultivation, the photoperiod, the autonomous, and the vernalization pathways were down-regulated to 0.15- to 0.5-fold of the control after 12.5 mg/kg AgNPs treatment. This exposure caused a decrease of approximately 25%-40% as compared to the control of the transcription of flowering key genes including AP1, LFY, FT and SOC1, and finally resulted in a delayed flowering time of 5 days. Only autonomous and vernalization pathways were inhibited by Ag+ ion treatment and ultimately the time of flowering in treated plants was delayed by 3 days. The energy production related metabolic pathways in the tricarboxylic acid cycle and in sugar metabolism were stimulated stronger by AgNPs than by Ag+ ion treatment, thus releasing more energy and accelerating the physiological metabolic responses against stress in the AgNPs treatment while subsequently reducing the plant growth and yield at the maturation stage. Importantly, shikimate-phenylpropanoid biosynthesis, and tryptophan and galactose metabolisms were regulated only by the AgNPs treatment, which was a specific effect of nanoparticles. This work provides a systematic understanding at the molecular, physiological as well as metabolic level of the effects of AgNPs and Ag+ ions in A. thaliana.
Collapse
Affiliation(s)
- Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA Leiden, The Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, The Netherlands
| | - Xingxing Li
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Meng Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, PR China; Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Chinese Academy of Sciences, Urumqi, PR China.
| |
Collapse
|
22
|
Yan J, Mao D, Liu X, Wang L, Xu F, Wang G, Zhang W, Liao Y. Isolation and functional characterization of a circadian-regulated CONSTANS homolog (GbCO) from Ginkgo biloba. PLANT CELL REPORTS 2017; 36:1387-1399. [PMID: 28616659 DOI: 10.1007/s00299-017-2162-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
This is the first report to clone and functionally characterize a flowering time gene GbCO in perennial gymnosperm Ginkgo biloba. GbCO complements the co mutant of Arabidopsis, restoring normal early flowering. CONSTANS (CO) is a central regulator of photoperiod pathway, which channels inputs from light, day length, and circadian clock to promote the floral transition. In order to understand the role of CO in gymnosperm Ginkgo biloba, which has a long juvenile phase (15-20 years), a CO homolog (GbCO) was isolated and characterized from G. biloba. GbCO encodes a 1741-bp gene with a predicted protein of 400 amino acids with two zinc finger domains (B-box I and B-box II) and a CCT domain. Phylogenic analysis classified GbCO into the group 1a clade of CO families in accordance with the grouping scheme for Arabidopsis CO (AtCO). Southern blot analysis indicated that GbCO belongs to a multigene family in G. biloba. Real-time PCR analysis showed that GbCO was expressed in aerial parts of Ginkgo, with the highest transcript level of GbCO being observed in shoot apexes. GbCO transcript level exhibited a strong diurnal rhythm under flowering-inductive long days and peaked during early morning, suggesting that GbCO is tightly coupled to the floral inductive long-day signal. In addition, an increasing trend of GbCO transcript level was observed both in shoot tips and leaves as the shoot growth under long-day condition, whereas GbCO transcript level decreased in both tissues under short-day condition prior to growth cessation of shoot in G. biloba. GbCO complemented the Arabidopsis co-2 mutant, restoring normal early flowering. All the evidence being taken together, our findings suggested that GbCO served as a potential inducer of flowering in G. biloba.
Collapse
Affiliation(s)
- Jiaping Yan
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Dun Mao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xiaomeng Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Lanlan Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Guiyuan Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| |
Collapse
|
23
|
Okada R, Nemoto Y, Endo-Higashi N, Izawa T. Synthetic control of flowering in rice independent of the cultivation environment. NATURE PLANTS 2017; 3:17039. [PMID: 28346447 DOI: 10.1038/nplants.2017.39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 02/26/2017] [Indexed: 05/03/2023]
Abstract
For genetically homogeneous crops, the timing of flowering is determined largely by the cultivation environment and is strongly associated with the yield and quality of the harvest1. Flowering time and other agronomical traits are often tightly correlated, which can lead to difficulty excluding the effects of flowering time when evaluating the characteristics of different genetic varieties2. Here, we describe the development of transgenic rice plants whose flowering time can be controlled by specific agrochemicals. We first developed non-flowering rice plants by overexpressing a floral repressor gene, Grain number, plant height and heading date 7 (Ghd7)3,4, to inhibit any environmentally induced spontaneous flowering. We then co-transformed plants with a rice florigen gene, Heading date 3a (Hd3a)5, which is induced by the application of specific agrochemicals. This permitted the flowering time to be experimentally controlled regardless of the cultivation environment: some transgenic plants flowered only after agrochemical treatment. Furthermore, plant size and yield-related traits could, in some cases, be increased owing to both a longer duration of vegetative growth and an increased panicle size. This ability to control flowering time experimentally, independently of environmental variables, may lead to production of crops suitable for growth in different climates and facilitate breeding for various agronomical traits.
Collapse
Affiliation(s)
- Ryo Okada
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Yasue Nemoto
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Naokuni Endo-Higashi
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Takeshi Izawa
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Laoratory of Plant Breeding &Genetics, Department of Agriculture, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
24
|
Ku L, Tian L, Su H, Wang C, Wang X, Wu L, Shi Y, Li G, Wang Z, Wang H, Song X, Dou D, Ren Z, Chen Y. Dual functions of the ZmCCT-associated quantitative trait locus in flowering and stress responses under long-day conditions. BMC PLANT BIOLOGY 2016; 16:239. [PMID: 27809780 PMCID: PMC5094027 DOI: 10.1186/s12870-016-0930-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/24/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Photoperiodism refers to the ability of plants to measure day length to determine the season. This ability enables plants to coordinate internal biological activities with external changes to ensure normal growth. However, the influence of the photoperiod on maize flowering and stress responses under long-day (LD) conditions has not been analyzed by comparative transcriptome sequencing. The ZmCCT gene was previously identified as a homolog of the rice photoperiod response regulator Ghd7, and associated with the major quantitative trait locus (QTL) responsible for Gibberella stalk rot resistance in maize. However, its regulatory mechanism has not been characterized. RESULTS We mapped the ZmCCT-associated QTL (ZmCCT-AQ), which is approximately 130 kb long and regulates photoperiod responses and resistance to Gibberella stalk rot and drought in maize. To investigate the effects of ZmCCT-AQ under LD conditions, the transcriptomes of the photoperiod-insensitive inbred line Huangzao4 (HZ4) and its near-isogenic line (HZ4-NIL) containing ZmCCT-AQ were sequenced. A set of genes identified by RNA-seq exhibited higher basal expression levels in HZ4-NIL than in HZ4. These genes were associated with responses to circadian rhythm changes and biotic and abiotic stresses. The differentially expressed genes in the introgressed regions of HZ4-NIL conferred higher drought and heat tolerance, and stronger disease resistance relative to HZ4. Co-expression analysis and the diurnal expression rhythms of genes related to stress responses suggested that ZmCCT and one of the circadian clock core genes, ZmCCA1, are important nodes linking the photoperiod to stress tolerance responses under LD conditions. CONCLUSION Our study revealed that the photoperiod influences flowering and stress responses under LD conditions. Additionally, ZmCCT and ZmCCA1 are important functional links between the circadian clock and stress tolerance. The establishment of this particular molecular link has uncovered a new relationship between plant photoperiodism and stress responses.
Collapse
Affiliation(s)
- Lixia Ku
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Lei Tian
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Huihui Su
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Cuiling Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471003 China
| | - Xiaobo Wang
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Liuji Wu
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Yong Shi
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Guohui Li
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Zhiyong Wang
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Huitao Wang
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Xiaoheng Song
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Dandan Dou
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Zhaobin Ren
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Yanhui Chen
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| |
Collapse
|
25
|
Wei J, Choi H, Jin P, Wu Y, Yoon J, Lee YS, Quan T, An G. GL2-type homeobox gene Roc4 in rice promotes flowering time preferentially under long days by repressing Ghd7. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:133-143. [PMID: 27717449 DOI: 10.1016/j.plantsci.2016.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
Under long day (LD) lengths, flowering can be delayed in rice by modulating several regulatory genes. We found activation tagging lines that showed an early flowering phenotype preferentially under LD conditions. Expression of Rice outermost cell-specific gene 4 (Roc4), encoding a homeodomain Leu-zipper class IV family protein, was significantly increased. Transcript levels of Grain number, plant height, and heading date7 (Ghd7) were significantly reduced while those of Ghd7 downstream genes were increased. However, other flowering regulators were unaffected. Whereas constitutive overexpression of Roc4 in 'Dongjin' japonica rice, which carries active Ghd7, also caused LD-preferential early flowering, its overexpression in 'Longjing27' rice, which is defective in functional Ghd7, did not produce the same result. This confirmed that Roc4 regulates flowering time mainly through Ghd7. Phytochromes and O. sativa GIGANTEA (OsGI) function upstream of Roc4. Transgenic plants showed ubiquitous expression of the β-glucuronidase reporter gene under the Roc4 promoter. Furthermore, Roc4 had transcriptional activation activity in the N-terminal region of the StAR-related lipid-transfer domain. All of these findings are evidence that Roc4 is an LD-preferential flowering enhancer that functions downstream of phytochromes and OsGI, but upstream of Ghd7.
Collapse
Affiliation(s)
- Jinhuan Wei
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Heebak Choi
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea; Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Ping Jin
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Yunfei Wu
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Jinmi Yoon
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Yang-Seok Lee
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Taiyong Quan
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, College of Life Science, Shandong University, Jinan 250100, People's Republic of China
| | - Gynheung An
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea.
| |
Collapse
|
26
|
Cho LH, Yoon J, Pasriga R, An G. Homodimerization of Ehd1 Is Required to Induce Flowering in Rice. PLANT PHYSIOLOGY 2016; 170:2159-71. [PMID: 26864016 PMCID: PMC4825144 DOI: 10.1104/pp.15.01723] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/02/2016] [Indexed: 05/20/2023]
Abstract
In plants, flowering time is elaborately controlled by various environment factors. Ultimately, florigens such as FLOWERING LOCUS T (FT) or FT-like molecules induce flowering. In rice (Oryza sativa), Early heading date 1 (Ehd1) is a major inducer of florigen gene expression. Although Ehd1 is highly homologous to the type-B response regulator (RR) family in the cytokinin signaling pathway, its precise molecular mechanism is not well understood. In this study, we showed that the C-terminal portion of the protein containing the GARP DNA-binding (G) domain can promote flowering when overexpressed. We also observed that the N-terminal portion of Ehd1, carrying the receiver (R) domain, delays flowering by inhibiting endogenous Ehd1 activity. Ehd1 protein forms a homomer via a 16-amino acid region in the inter domain between R and G. From the site-directed mutagenesis analyses, we demonstrated that phosphorylation of the Asp-63 residue within the R domain induces the homomerization of Ehd1, which is crucial for Ehd1 activity. A type-A RR, OsRR1, physically interacts with Ehd1 to form a heterodimer. In addition, OsRR1-overexpressing plants show a late-flowering phenotype. Based on these observations, we conclude that OsRR1 inhibits Ehd1 activity by binding to form an inactive complex.
Collapse
Affiliation(s)
- Lae-Hyeon Cho
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea (L.-H.C., J.Y., R.P., G.A.);Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea (L.-H.C., J.Y.); andGraduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea (R.P., G.A.)
| | - Jinmi Yoon
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea (L.-H.C., J.Y., R.P., G.A.);Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea (L.-H.C., J.Y.); andGraduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea (R.P., G.A.)
| | - Richa Pasriga
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea (L.-H.C., J.Y., R.P., G.A.);Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea (L.-H.C., J.Y.); andGraduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea (R.P., G.A.)
| | - Gynheung An
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea (L.-H.C., J.Y., R.P., G.A.);Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea (L.-H.C., J.Y.); andGraduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea (R.P., G.A.)
| |
Collapse
|
27
|
Zhao C, Takeshima R, Zhu J, Xu M, Sato M, Watanabe S, Kanazawa A, Liu B, Kong F, Yamada T, Abe J. A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog. BMC PLANT BIOLOGY 2016; 16:20. [PMID: 26786479 PMCID: PMC4719747 DOI: 10.1186/s12870-016-0704-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/06/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Understanding the molecular mechanisms of flowering and maturity is important for improving the adaptability and yield of seed crops in different environments. In soybean, a facultative short-day plant, genetic variation at four maturity genes, E1 to E4, plays an important role in adaptation to environments with different photoperiods. However, the molecular basis of natural variation in time to flowering and maturity is poorly understood. Using a cross between early-maturing soybean cultivars, we performed a genetic and molecular study of flowering genes. The progeny of this cross segregated for two maturity loci, E1 and E9. The latter locus was subjected to detailed molecular analysis to identify the responsible gene. RESULTS Fine mapping, sequencing, and expression analysis revealed that E9 is FT2a, an ortholog of Arabidopsis FLOWERING LOCUS T. Regardless of daylength conditions, the e9 allele was transcribed at a very low level in comparison with the E9 allele and delayed flowering. Despite identical coding sequences, a number of single nucleotide polymorphisms and insertions/deletions were detected in the promoter, untranslated regions, and introns between the two cultivars. Furthermore, the e9 allele had a Ty1/copia-like retrotransposon, SORE-1, inserted in the first intron. Comparison of the expression levels of different alleles among near-isogenic lines and photoperiod-insensitive cultivars indicated that the SORE-1 insertion attenuated FT2a expression by its allele-specific transcriptional repression. SORE-1 was highly methylated, and did not appear to disrupt FT2a RNA processing. CONCLUSIONS The soybean maturity gene E9 is FT2a, and its recessive allele delays flowering because of lower transcript abundance that is caused by allele-specific transcriptional repression due to the insertion of SORE-1. The FT2a transcript abundance is thus directly associated with the variation in flowering time in soybean. The e9 allele may maintain vegetative growth in early-flowering genetic backgrounds, and also be useful as a long-juvenile allele, which causes late flowering under short-daylength conditions, in low-latitude regions.
Collapse
Affiliation(s)
- Chen Zhao
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
| | - Ryoma Takeshima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
| | - Jianghui Zhu
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
| | - Meilan Xu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Masako Sato
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
| | | | - Akira Kanazawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
| |
Collapse
|
28
|
Wei FJ, Tsai YC, Wu HP, Huang LT, Chen YC, Chen YF, Wu CC, Tseng YT, Hsing YIC. Both Hd1 and Ehd1 are important for artificial selection of flowering time in cultivated rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:187-194. [PMID: 26566836 DOI: 10.1016/j.plantsci.2015.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/31/2015] [Accepted: 09/04/2015] [Indexed: 05/04/2023]
Abstract
Rice is a facultative short-day plant, and it requires a photoperiod shorter than the critical day length to get flowering. Sensitivity to photoperiod has been suggested as a major selection target in cultivated or weedy rice. The modern rice varieties in Taiwan may be cultivated twice a year. These varieties contain loss-of-function of two important flowering-time related genes, Heading date 1 (Hd1) and Early heading date 1 (Ehd1), and are mainly from a mega variety, Taichung 65. However, the parental lines of this variety were sensitive to photoperiod, thus, how Taichung 65 loss its sensitivity is a mystery. In this study, we used accession-specific single nucleotide polymorphism analysis to reveal the gene flow that occurred between different rice accessions decades ago and demonstrate that two landraces introgressed during the breeding process, which led to the loss of photoperiod sensitivity. Both Hd1 and Ehd1 may be important during artificial selection for flowering time, especially in a subtropical region such as Taiwan. This is a good example of introgression playing important roles during rice domestication.
Collapse
Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; Department of Agronomy, National Taiwan University, Taipei 106, Taiwan.
| | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.
| | - Yu-Chi Chen
- Taiwan International Cooperation and Development Fund, Taipei 111, Taiwan.
| | - Yi-Fang Chen
- Soil and Water Conservation Bureau, Council of Agriculture, Nantou 540, Taiwan.
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; Institute of Botany, National Taiwan University, Taipei 106, Taiwan.
| | - Yi-Tzu Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; Institute of Botany, National Taiwan University, Taipei 106, Taiwan.
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.
| |
Collapse
|
29
|
Evans J, Crisovan E, Barry K, Daum C, Jenkins J, Kunde-Ramamoorthy G, Nandety A, Ngan CY, Vaillancourt B, Wei CL, Schmutz J, Kaeppler SM, Casler MD, Buell CR. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:800-15. [PMID: 26426343 DOI: 10.1111/tpj.13041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 05/11/2023]
Abstract
Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
Collapse
Affiliation(s)
- Joseph Evans
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily Crisovan
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Chris Daum
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Aruna Nandety
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Chew Yee Ngan
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Brieanne Vaillancourt
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chia-Lin Wei
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shawn M Kaeppler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - Carol Robin Buell
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
30
|
Xu M, Yamagishi N, Zhao C, Takeshima R, Kasai M, Watanabe S, Kanazawa A, Yoshikawa N, Liu B, Yamada T, Abe J. The Soybean-Specific Maturity Gene E1 Family of Floral Repressors Controls Night-Break Responses through Down-Regulation of FLOWERING LOCUS T Orthologs. PLANT PHYSIOLOGY 2015; 168:1735-46. [PMID: 26134161 PMCID: PMC4528769 DOI: 10.1104/pp.15.00763] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/29/2015] [Indexed: 05/19/2023]
Abstract
Photoperiodism is a rhythmic change of sensitivity to light, which helps plants to adjust flowering time according to seasonal changes in daylength and to adapt to growing conditions at various latitudes. To reveal the molecular basis of photoperiodism in soybean (Glycine max), a facultative short-day plant, we analyzed the transcriptional profiles of the maturity gene E1 family and two FLOWERING LOCUS T (FT) orthologs (FT2a and FT5a). E1, a repressor for FT2a and FT5a, and its two homologs, E1-like-a (E1La) and E1Lb, exhibited two peaks of expression in long days. Using two different approaches (experiments with transition between light and dark phases and night-break experiments), we revealed that the E1 family genes were expressed only during light periods and that their induction after dawn in long days required a period of light before dusk the previous day. In the cultivar Toyomusume, which lacks the E1 gene, virus-induced silencing of E1La and E1Lb up-regulated the expression of FT2a and FT5a and led to early flowering. Therefore, E1, E1La, and E1Lb function similarly in flowering. Regulation of E1 and E1L expression by light was under the control of E3 and E4, which encode phytochrome A proteins. Our data suggest that phytochrome A-mediated transcriptional induction of E1 and its homologs by light plays a critical role in photoperiodic induction of flowering in soybean.
Collapse
Affiliation(s)
- Meilan Xu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Noriko Yamagishi
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Chen Zhao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Ryoma Takeshima
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Megumi Kasai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Satoshi Watanabe
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Akira Kanazawa
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Nobuyuki Yoshikawa
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Baohui Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Tetsuya Yamada
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| | - Jun Abe
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.)
| |
Collapse
|
31
|
Nagano H, Clark LV, Zhao H, Peng J, Yoo JH, Heo K, Yu CY, Anzoua KG, Matsuo T, Sacks EJ, Yamada T. Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4227-4237. [PMID: 26089536 PMCID: PMC4493791 DOI: 10.1093/jxb/erv292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The genus Miscanthus is a perennial C4 grass native to eastern Asia and is a promising candidate bioenergy crop for cool temperate areas. Flowering time is a crucial factor governing regional and seasonal adaptation; in addition, it is also a key target trait for extending the vegetative phase to improve biomass potential. Homologues of CONSTANS (CO)/Heading date 1(Hd1) were cloned from Miscanthus sinensis and named MsiHd1. Sequences of MsiHd1 homologues were compared among 24 wild M. sinensis accessions from Japan, 14 from China, and three from South Korea. Two to five MsiHd1 alleles in each accession were identified, suggesting that MsiHd1 consists of at least three loci in the Miscanthus genome. Verifying the open reading frame in MsiHd1, they were classified as putative functional alleles without mutations or non-functional alleles caused by indels. The Neighbor-Joining tree indicated that one of the multiple MsiHd1 loci is a pseudogene locus without any functional alleles. The pseudogene locus was named MsiHd1b, and the other loci were considered to be part of the MsiHd1a multi-locus family. Interestingly, in most Japanese accessions 50% or more of the MsiHd1a alleles were non-functional, whereas accessions from the East Asian mainland harboured only functional alleles. Five novel miniature inverted transposable elements (MITEs) (MsiMITE1-MsiMITE5) were observed in MsiHd1a/b. MsiMITE1, detected in exon 1 of MsiHd1a, was only observed in Japanese accessions and its revertant alleles derived from retransposition were predominantly in Chinese accessions. These differences in MsiHd1a show that the dependency on functional MsiHd1a alleles is different between accessions from the East Asian mainland and Japan.
Collapse
Affiliation(s)
- Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Lindsay V Clark
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Hua Zhao
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Junhua Peng
- Science and Technology Center, China Seed Group Co. Ltd, Wuhan, Hubei 430206, China
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | | | - Tomoaki Matsuo
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| |
Collapse
|
32
|
Hori K, Nonoue Y, Ono N, Shibaya T, Ebana K, Matsubara K, Ogiso-Tanaka E, Tanabata T, Sugimoto K, Taguchi-Shiobara F, Yonemaru JI, Mizobuchi R, Uga Y, Fukuda A, Ueda T, Yamamoto SI, Yamanouchi U, Takai T, Ikka T, Kondo K, Hoshino T, Yamamoto E, Adachi S, Nagasaki H, Shomura A, Shimizu T, Kono I, Ito S, Mizubayashi T, Kitazawa N, Nagata K, Ando T, Fukuoka S, Yamamoto T, Yano M. Genetic architecture of variation in heading date among Asian rice accessions. BMC PLANT BIOLOGY 2015; 15:115. [PMID: 25953146 PMCID: PMC4424449 DOI: 10.1186/s12870-015-0501-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/22/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Heading date, a crucial factor determining regional and seasonal adaptation in rice (Oryza sativa L.), has been a major selection target in breeding programs. Although considerable progress has been made in our understanding of the molecular regulation of heading date in rice during last two decades, the previously isolated genes and identified quantitative trait loci (QTLs) cannot fully explain the natural variation for heading date in diverse rice accessions. RESULTS To genetically dissect naturally occurring variation in rice heading date, we collected QTLs in advanced-backcross populations derived from multiple crosses of the japonica rice accession Koshihikari (as a common parental line) with 11 diverse rice accessions (5 indica, 3 aus, and 3 japonica) that originate from various regions of Asia. QTL analyses of over 14,000 backcrossed individuals revealed 255 QTLs distributed widely across the rice genome. Among the detected QTLs, 128 QTLs corresponded to genomic positions of heading date genes identified by previous studies, such as Hd1, Hd6, Hd3a, Ghd7, DTH8, and RFT1. The other 127 QTLs were detected in different chromosomal regions than heading date genes. CONCLUSIONS Our results indicate that advanced-backcross progeny allowed us to detect and confirm QTLs with relatively small additive effects, and the natural variation in rice heading date could result from combinations of large- and small-effect QTLs. We also found differences in the genetic architecture of heading date (flowering time) among maize, Arabidopsis, and rice.
Collapse
Affiliation(s)
- Kiyosumi Hori
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Yasunori Nonoue
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Taeko Shibaya
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kaworu Ebana
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kazuki Matsubara
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Eri Ogiso-Tanaka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Takanari Tanabata
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kazuhiko Sugimoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Fumio Taguchi-Shiobara
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Ritsuko Mizobuchi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Yusaku Uga
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Atsunori Fukuda
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Tadamasa Ueda
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Shin-ichi Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Utako Yamanouchi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Toshiyuki Takai
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Takashi Ikka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Katsuhiko Kondo
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Tomoki Hoshino
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Eiji Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Shunsuke Adachi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Hideki Nagasaki
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Ayahiko Shomura
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Takehiko Shimizu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Izumi Kono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Sachie Ito
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Tatsumi Mizubayashi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Noriyuki Kitazawa
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kazufumi Nagata
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Tsuyu Ando
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Shuichi Fukuoka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Toshio Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Masahiro Yano
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| |
Collapse
|
33
|
Nakamichi N. Adaptation to the local environment by modifications of the photoperiod response in crops. PLANT & CELL PHYSIOLOGY 2015; 56:594-604. [PMID: 25432974 PMCID: PMC4387313 DOI: 10.1093/pcp/pcu181] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/12/2014] [Indexed: 05/02/2023]
Abstract
Flowering plants produce a meristem at the shoot tip where specialized tissue generates shoot apical meristems at the appropriate time to differentiate into reproductive structures, pollinate and efficiently generate seeds. The complex set of molecular and phenological events culminating in development of a flowering meristem is referred to as 'flowering time'. Flowering time affects plant productivity because plants dedicate energy to produce flowers and seeds rather than vegetative tissue once the molecular decision to initiate flowering has been taken. Thus, initiation of flowering time is an important decision in plants, especially in annual plants including crops. Humans have introduced crops into latitudes and climate areas far from their origin or natural ecosystem, requiring in many cases modification of native flowering times. Recent molecular-genetic studies shed light on the genetic basis related to such introductions. In this review, recent progress regarding crop introductions and their genetic bases are summarized, as well as the potential of other agricultural plants to be introduced into different climatic zones.
Collapse
Affiliation(s)
- Norihito Nakamichi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602 Japan Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602 Japan Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0022 Japan
| |
Collapse
|
34
|
Yoshitake Y, Yokoo T, Saito H, Tsukiyama T, Quan X, Zikihara K, Katsura H, Tokutomi S, Aboshi T, Mori N, Inoue H, Nishida H, Kohchi T, Teraishi M, Okumoto Y, Tanisaka T. The effects of phytochrome-mediated light signals on the developmental acquisition of photoperiod sensitivity in rice. Sci Rep 2015; 5:7709. [PMID: 25573482 PMCID: PMC4287723 DOI: 10.1038/srep07709] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 12/08/2014] [Indexed: 11/30/2022] Open
Abstract
Plants commonly rely on photoperiodism to control flowering time. Rice development before floral initiation is divided into two successive phases: the basic vegetative growth phase (BVP, photoperiod-insensitive phase) and the photoperiod-sensitive phase (PSP). The mechanism responsible for the transition of rice plants into their photoperiod-sensitive state remains elusive. Here, we show that se13, a mutation detected in the extremely early flowering mutant X61 is a nonsense mutant gene of OsHY2, which encodes phytochromobilin (PΦB) synthase, as evidenced by spectrometric and photomorphogenic analyses. We demonstrated that some flowering time and circadian clock genes harbor different expression profiles in BVP as opposed to PSP, and that this phenomenon is chiefly caused by different phytochrome-mediated light signal requirements: in BVP, phytochrome-mediated light signals directly suppress Ehd2, while in PSP, phytochrome-mediated light signals activate Hd1 and Ghd7 expression through the circadian clock genes' expression. These findings indicate that light receptivity through the phytochromes is different between two distinct developmental phases corresponding to the BVP and PSP in the rice flowering process. Our results suggest that these differences might be involved in the acquisition of photoperiod sensitivity in rice.
Collapse
Affiliation(s)
- Yoshihiro Yoshitake
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Takayuki Yokoo
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroki Saito
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Takuji Tsukiyama
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Xu Quan
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kazunori Zikihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Hitomi Katsura
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Satoru Tokutomi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Takako Aboshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Naoki Mori
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiromo Inoue
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hidetaka Nishida
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Masayoshi Teraishi
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yutaka Okumoto
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Takatoshi Tanisaka
- 1] Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan [2] Department of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Hyogo, 656-0484, Japan
| |
Collapse
|
35
|
Thurber CS, Reagon M, Olsen KM, Jia Y, Caicedo AL. The evolution of flowering strategies in US weedy rice. AMERICAN JOURNAL OF BOTANY 2014; 101:1737-1747. [PMID: 25326616 DOI: 10.3732/ajb.1400154] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Local adaptation in plants often involves changes in flowering time in response to day length and temperature. Many crops have been selected for uniformity in flowering time. In contrast, variable flowering may be important for increased competitiveness in weed species invading the agricultural environment. Given the shared species designation of cultivated rice (Oryza sativa) and its the invasive conspecific weed, weedy rice, we assessed the extent to which flowering time differed between these groups. We further assessed whether genes affecting flowering time variation in rice could play a role in the evolution of weedy rice in the United States.• METHODS We quantified flowering time under day-neutral conditions in weedy, cultivated, and wild Oryza groups. We also sequenced two candidate gene regions: Hd1, a locus involved in promotion of flowering under short days, and the promoter of Hd3a, a locus encoding the mobile signal that induces flowering.• KEY RESULTS We found that flowering time has diverged between two distinct weedy rice groups, such that straw-hull weeds tend to flower earlier and black-hull awned weeds tend to flower later than cultivated rice. These differences are consistent with weed Hd1 alleles. At both loci, weeds share haplotypes with their cultivated progenitors, despite significantly different flowering times.• CONCLUSIONS Our phenotypic data indicate the existence of multiple flowering strategies in weedy rice. Flowering differences between weeds and ancestors suggest this trait has evolved rapidly. From a weed management standpoint, there is the potential for overlap in flowering of black-hull awned weeds and crops in the United States, permitting hybridization and the potential escape of genes from crops.
Collapse
Affiliation(s)
- Carrie S Thurber
- Biology Department, University of Massachusetts, Amherst, Massachusetts 01003 USA
| | - Michael Reagon
- Department of Biology, The Ohio State University-Lima, Lima, Ohio 45804 USA
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, Missouri 63130 USA
| | - Yulin Jia
- USDA-ARS Dale Bumpers Rice Research Center, Stuttgart, Arkansas 72160 USA
| | - Ana L Caicedo
- Biology Department, University of Massachusetts, Amherst, Massachusetts 01003 USA
| |
Collapse
|
36
|
Understanding the genetic and epigenetic architecture in complex network of rice flowering pathways. Protein Cell 2014; 5:889-98. [PMID: 25103896 PMCID: PMC4259885 DOI: 10.1007/s13238-014-0068-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 04/21/2014] [Indexed: 12/03/2022] Open
Abstract
Although the molecular basis of flowering time control is well dissected in the long day (LD) plant Arabidopsis, it is still largely unknown in the short day (SD) plant rice. Rice flowering time (heading date) is an important agronomic trait for season adaption and grain yield, which is affected by both genetic and environmental factors. During the last decade, as the nature of florigen was identified, notable progress has been made on exploration how florigen gene expression is genetically controlled. In Arabidopsis expression of certain key flowering integrators such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT) are also epigenetically regulated by various chromatin modifications, however, very little is known in rice on this aspect until very recently. This review summarized the advances of both genetic networks and chromatin modifications in rice flowering time control, attempting to give a complete view of the genetic and epigenetic architecture in complex network of rice flowering pathways.
Collapse
|
37
|
Li W, Cui X. Focus on rice: towards better understanding of the life cycle of crop plants. MOLECULAR PLANT 2014; 7:931-933. [PMID: 24891313 DOI: 10.1093/mp/ssu057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Wei Li
- Scientific Editor, Molecular Plant
| | | |
Collapse
|
38
|
Yang S, Weers BD, Morishige DT, Mullet JE. CONSTANS is a photoperiod regulated activator of flowering in sorghum. BMC PLANT BIOLOGY 2014; 14:148. [PMID: 24884377 PMCID: PMC4046011 DOI: 10.1186/1471-2229-14-148] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/13/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sorghum genotypes used for grain production in temperate regions are photoperiod insensitive and flower early avoiding adverse environments during the reproductive phase. In contrast, energy sorghum hybrids are highly photoperiod sensitive with extended vegetative phases in long days, resulting in enhanced biomass accumulation. SbPRR37 and SbGHD7 contribute to photoperiod sensitivity in sorghum by repressing expression of SbEHD1 and FT-like genes, thereby delaying flowering in long days with minimal influence in short days (PNAS_108:16469-16474, 2011; Plant Genome_in press, 2014). The GIGANTEA (GI)-CONSTANS (CO)-FLOWERING LOCUS T (FT) pathway regulates flowering time in Arabidopsis and the grasses (J Exp Bot_62:2453-2463, 2011). In long day flowering plants, such as Arabidopsis and barley, CONSTANS activates FT expression and flowering in long days. In rice, a short day flowering plant, Hd1, the ortholog of CONSTANS, activates flowering in short days and represses flowering in long days. RESULTS Quantitative trait loci (QTL) that modify flowering time in sorghum were identified by screening Recombinant Inbred Lines (RILs) derived from BTx642 and Tx7000 in long days, short days, and under field conditions. Analysis of the flowering time QTL on SBI-10 revealed that BTx642 encodes a recessive CONSTANS allele containing a His106Tyr substitution in B-box 2 known to inactivate CONSTANS in Arabidopsis thaliana. Genetic analysis characterized sorghum CONSTANS as a floral activator that promotes flowering by inducing the expression of EARLY HEADING DATE 1 (SbEHD1) and sorghum orthologs of the maize FT genes ZCN8 (SbCN8) and ZCN12 (SbCN12). The floral repressor PSEUDORESPONSE REGULATOR PROTEIN 37 (PRR37) inhibits sorghum CONSTANS activity and flowering in long days. CONCLUSION Sorghum CONSTANS is an activator of flowering that is repressed post-transcriptionally in long days by the floral inhibitor PRR37, contributing to photoperiod sensitive flowering in Sorghum bicolor, a short day plant.
Collapse
Affiliation(s)
- Shanshan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Brock D Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Daryl T Morishige
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - John E Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| |
Collapse
|
39
|
Yokoo T, Saito H, Yoshitake Y, Xu Q, Asami T, Tsukiyama T, Teraishi M, Okumoto Y, Tanisaka T. Se14, encoding a JmjC domain-containing protein, plays key roles in long-day suppression of rice flowering through the demethylation of H3K4me3 of RFT1. PLoS One 2014; 9:e96064. [PMID: 24759811 PMCID: PMC3997562 DOI: 10.1371/journal.pone.0096064] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/02/2014] [Indexed: 12/17/2022] Open
Abstract
Floral transition from the vegetative to the reproductive growth phase is a major change in the plant life cycle and a key factor in reproductive success. In rice (Oryza sativa L.), a facultative short-day plant, numerous flowering time and flower formation genes that control floral transition have been identified and their physiological effects and biochemical functions have been clarified. In the present study, we used a Se14-deficient mutant line (HS112) and other flowering mutant lines to investigate the photoperiodic response, chromosomal location and function in the photoperiod sensitivity of the Se14 gene. We also studied the interactive effects of this locus with other crucial flowering time genes. We found that Se14 is independent of the known photoperiod-sensitive genes, such as Hd1 and Ghd7, and is identical to Os03g0151300, which encodes a Jumonji C (JmjC) domain-containing protein. Expression analysis revealed that the expressions of RFT1, a floral initiator known as a "florigen-like gene", and Ehd1 were up-regulated in HS112, whereas this up-regulation was not observed in the original variety of 'Gimbozu'. ChIP assays of the methylation states of histone H3 at lysine 4 (H3K4) revealed that the trimethylated H3K4 in the promoter region of the RFT1 chromatin was significantly increased in HS112. We conclude that Se14 is a novel photoperiod-sensitivity gene that has a suppressive effect on floral transition (flowering time) under long day-length conditions through the modification of chromatin structure by H3K4me3 demethylation in the promoter region of RFT1.
Collapse
Affiliation(s)
- Takayuki Yokoo
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroki Saito
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Quan Xu
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takehito Asami
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | | | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | |
Collapse
|
40
|
Co-option of a photoperiodic growth-phase transition system during land plant evolution. Nat Commun 2014; 5:3668. [DOI: 10.1038/ncomms4668] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 03/17/2014] [Indexed: 12/21/2022] Open
|
41
|
|
42
|
Matsubara K, Hori K, Ogiso-Tanaka E, Yano M. Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering pathways in Arabidopsis and rice. FRONTIERS IN PLANT SCIENCE 2014; 5:193. [PMID: 24860584 PMCID: PMC4026727 DOI: 10.3389/fpls.2014.00193] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 04/23/2014] [Indexed: 05/20/2023]
Abstract
Flowering time in rice (Oryza sativa L.) is determined primarily by daylength (photoperiod), and natural variation in flowering time is due to quantitative trait loci involved in photoperiodic flowering. To date, genetic analysis of natural variants in rice flowering time has resulted in the positional cloning of at least 12 quantitative trait genes (QTGs), including our recently cloned QTGs, Hd17, and Hd16. The QTGs have been assigned to specific photoperiodic flowering pathways. Among them, 9 have homologs in the Arabidopsis genome, whereas it was evident that there are differences in the pathways between rice and Arabidopsis, such that the rice Ghd7-Ehd1-Hd3a/RFT1 pathway modulated by Hd16 is not present in Arabidopsis. In this review, we describe QTGs underlying natural variation in rice flowering time. Additionally, we discuss the implications of the variation in adaptive divergence and its importance in rice breeding.
Collapse
Affiliation(s)
| | - Kiyosumi Hori
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Eri Ogiso-Tanaka
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Masahiro Yano
- NARO Institute of Crop ScienceTsukuba, Japan
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
- *Correspondence: Masahiro Yano, Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan e-mail:
| |
Collapse
|