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Zhao Z, Tu H, Wang Y, Yang J, Hao G, Wu J. Chemical Driving the Subtype Selectivity of Phytohormone Receptors Is Beneficial for Crop Productivity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39013833 DOI: 10.1021/acs.jafc.4c04446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Chemicals that modulate phytohormones serve as a research tool in plant science and as products to improve crop productivity. Subtype selectivity refers to a ligand to selectively bind to specific subtypes of a receptor rather than binding to all possible subtypes indiscriminately. It allows for precise and specific control of cellular functions and is widely used in medicine. However, subtype selectivity is rarely mentioned in the realm of plant science, and it requires integrated knowledge from chemistry and biology, including structural features of small molecules as ligands, the redundancy of target proteins, and the response of signaling factors. Here, we present a comprehensive review and evaluation of phytohormone receptor subtype selectivity, leveraging the chemical characteristics of phytohormones and their analogues as clues. This work endeavors to provide a valuable research strategy that integrates knowledge from chemistry and biology to advance research efforts geared toward enhancing crop productivity.
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Affiliation(s)
- Zhichao Zhao
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Hong Tu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Ya Wang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jianrong Yang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Gefei Hao
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jian Wu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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Zhang P, Chen Z, Wang F, Wu H, Hao L, Jiang X, Yu Z, Zou L, Jiang H. Response and inversion of skewness parameters to meteorological factors based on RGB model of leaf color digital image. PLoS One 2023; 18:e0288818. [PMID: 37967130 PMCID: PMC10650994 DOI: 10.1371/journal.pone.0288818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/04/2023] [Indexed: 11/17/2023] Open
Abstract
In the natural environment, complex and changeable meteorological factors can influence changes in the internal physiology and phenotype of crops. It is important to learn how to convert complex meteorological factor stimuli into plant perception phenotypes when analyzing the biological data obtained under the natural field condition. We restored the true gradation distribution of leaf color, which is also known as the skewed distribution of color scale, and obtained 20 multi-dimensional color gradation skewness-distribution (CGSD) parameters based on the leaf color skewness parameter system. Furthermore, we analyzed the correlation between the five corresponding meteorological factors and canopy CGSD parameters of peppers growing in a greenhouse and cabbages growing in an open air environment, built response model and inversion mode of leaf color to meteorological factors. Based on the analysis, we find a new method for correlating complex environmental problems with multi-dimensional parameters. This study provides a new idea for building a correlation model that uses leaf color as a bridge between meteorological factors and plants internal physiological state.
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Affiliation(s)
- Pei Zhang
- Jiangsu Meteorological Bureau, Nanjing, China
| | - Zhengmeng Chen
- Longyan Company of Fujian Provincial Tobacco Corporation, Longyan, China
| | - Fuzheng Wang
- QinGengRen Modern Agricultural Science and Technology Development (Huai’an) Co., Ltd., Huai’an, China
| | - Hongyan Wu
- Jiangsu Meteorological Bureau, Nanjing, China
| | - Ling Hao
- Lianyungang Meteorological Bureau, Lianyungang, China
| | - Xu Jiang
- Tufts University, Boston, MA, United States of America
| | - Zhiming Yu
- Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Prodution, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Lina Zou
- Longyan Company of Fujian Provincial Tobacco Corporation, Longyan, China
| | - Haidong Jiang
- Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Prodution, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
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Mahto A, Yadav A, P V A, Parida SK, Tyagi AK, Agarwal P. Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size. BMC Biol 2023; 21:91. [PMID: 37076907 PMCID: PMC10116700 DOI: 10.1186/s12915-023-01577-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/27/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Rice grain size (GS) is an essential agronomic trait. Though several genes and miRNA modules influencing GS are known and seed development transcriptomes analyzed, a comprehensive compendium connecting all possible players is lacking. This study utilizes two contrasting GS indica rice genotypes (small-grained SN and large-grained LGR). Rice seed development involves five stages (S1-S5). Comparative transcriptome and miRNome atlases, substantiated with morphological and cytological studies, from S1-S5 stages and flag leaf have been analyzed to identify GS proponents. RESULTS Histology shows prolonged endosperm development and cell enlargement in LGR. Stand-alone and comparative RNAseq analyses manifest S3 (5-10 days after pollination) stage as crucial for GS enhancement, coherently with cell cycle, endoreduplication, and programmed cell death participating genes. Seed storage protein and carbohydrate accumulation, cytologically and by RNAseq, is shown to be delayed in LGR. Fourteen transcription factor families influence GS. Pathway genes for four phytohormones display opposite patterns of higher expression. A total of 186 genes generated from the transcriptome analyses are located within GS trait-related QTLs deciphered by a cross between SN and LGR. Fourteen miRNA families express specifically in SN or LGR seeds. Eight miRNA-target modules display contrasting expressions amongst SN and LGR, while 26 (SN) and 43 (LGR) modules are differentially expressed in all stages. CONCLUSIONS Integration of all analyses concludes in a "Domino effect" model for GS regulation highlighting chronology and fruition of each event. This study delineates the essence of GS regulation, providing scope for future exploits. The rice grain development database (RGDD) ( www.nipgr.ac.in/RGDD/index.php ; https://doi.org/10.5281/zenodo.7762870 ) has been developed for easy access of data generated in this paper.
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Affiliation(s)
- Arunima Mahto
- National Institute of Plant Genome Research, New Delhi, India
| | - Antima Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Aswathi P V
- National Institute of Plant Genome Research, New Delhi, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, New Delhi, India
| | - Akhilesh K Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, India.
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Matsunami M, Murai-Hatano M, Kuwagata T, Matsushima U, Hashida Y, Tominaga Y, Masuya Y, Nagano AJ. Transcriptome dynamics of rice in natura: Response of above and below ground organs to microclimate. PLANT, CELL & ENVIRONMENT 2023; 46:1176-1194. [PMID: 36111882 DOI: 10.1111/pce.14439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/12/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
The long-term dynamics of the transcriptome under natural field conditions remain unclear. We conducted comprehensive gene expression analyses of rice leaves and roots grown under natural field conditions for a long period, from the tillering stage to the ripening stage. In this experiment, changes in the transcriptome were captured in relation to microclimatic parameters, particularly potential evaporation (Ep), which is a multiple meteorological factor and acts as an indicator of transpirational demand. The results indicated that many genes were regulated by changes in temperature and Ep in both leaves and roots. Furthermore, the correlation between gene expression and meteorological factors differed significantly between the vegetative and reproductive stages. Since Ep triggers transpiration, we analyzed aquaporin gene expression, which is responsible for water transport, and found that many aquaporin genes in leaves were positively correlated with Ep throughout the growth period, whereas in roots, two plasma membrane intrinsic aquaporins, PIP2;4 and PIP2;5 were strongly correlated with Ep during reproductive growth. Other genes closely related to productivity, such as those involved in nutrient absorption and photosynthesis, exhibited different responses to meteorological factors at different growth stages. The stage-dependent shift in the microclimate response provides an important perspective on crop physiology in light of climate change.
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Affiliation(s)
- Maya Matsunami
- Department of Plant Biosciences, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Mari Murai-Hatano
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Japan
| | - Tsuneo Kuwagata
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Uzuki Matsushima
- Department of Food Production and Environmental Management, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Yoichi Hashida
- Faculty of Agriculture, Takasaki University of Health and Welfare, Gunma, Japan
| | - Yoko Tominaga
- Section of Liberal Arts and Sciences, National Institute of Technology, Ichinoseki College, Ichinoseki, Japan
| | - Yusuke Masuya
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
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Chen D, Zou W, Zhang M, Liu J, Chen L, Peng T, Ye G. Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice. Int J Mol Sci 2023; 24:ijms24076117. [PMID: 37047087 PMCID: PMC10094323 DOI: 10.3390/ijms24076117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Seed dormancy is a key factor used to determine seed germination in rice production. So far, only a few genes controlling seed dormancy have been reported, and the genetic mechanism of rice seed dormancy is still elusive. In this study, a population of 195 diverse re-sequenced accessions from 40 countries was evaluated for the seed germination rate (GR) without dormancy breaking (WDB) as a control and under dry heating (DH) and gibberellic acid (GA) treatments, as dormancy breaking agents to identify QTLs for seed dormancy. Phenotypic assessment revealed that these accessions had abundant variations in seed dormancy. GWAS using 1,120,223 high-quality single nucleotide polymorphisms (SNPs) and a mixed linear model (MLM) incorporating both principal components (PCs) and kinship (K) identified 30 QTLs on 10 chromosomes, accounting for 7.3-20.4% of the phenotypic variance in GR. Ten of the QTLs were located in the regions of previously reported QTLs, while the rest were novel ones. Thirteen high-confidence candidate genes were predicted for the four QTLs detected in two or three conditions (qGR4-4, qGR4-5, qGR8 and qGR11-4) and one QTL with a large effect (qGR3). These genes were highly expressed during seed development and were significantly regulated by various hormone treatments. This study provides new insights into the genetic and molecular basis of rice seed dormancy/germination. The accessions with moderate and strong dormancy and markers for the QTLs and candidate genes are useful for attaining a proper level of seed dormancy.
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Affiliation(s)
- Dandan Chen
- Key Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenli Zou
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mingpei Zhang
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Jindong Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Liang Chen
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ting Peng
- Key Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Rice Breeding Innovations Platform, International Rice Research Institute (IRRI), Metro Manila 1301, Philippines
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Huang C, Qin A, Gao Y, Ma S, Liu Z, Zhao B, Ning D, Zhang K, Gong W, Sun M, Liu Z. Effects of water deficit at different stages on growth and ear quality of waxy maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1069551. [PMID: 36818831 PMCID: PMC9930991 DOI: 10.3389/fpls.2023.1069551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Extreme weather has occurred more frequently in recent decades, which results in more frequent drought disasters in the maize growing season. Severe drought often decreases remarkably plant growth and yield of maize, and even reduces significantly the quality of maize production, especially for waxy maize. RESULTS To study the changes in plant growth, fresh ear yield, and fresh grain quality of waxy maize under water deficits occurring at different growth stages, and further strengthen the field water management of waxy maize, water deficit experiments were carried out under a rain shelter in 2019 and 2020. Water deficit treatments were imposed respectively at the V6-VT (DV6-VT), VT-R2 (DVT-R2), and R2-R3 (DR2-R3) stages of waxy maize, and treatment with non-water deficit in the whole growing season was taken as the control (CK). The lower limit of soil water content was 50% of field capacity for a water deficit period and 65% of field capacity for a non-water deficit period. RESULTS In this study, water deficits imposed at V6-VT and VT-R2 stages decreased plant growth rate and leaf gas exchange parameters, accelerated leaf senescence, and limited ear growth of waxy maize, which resulted in 11.6% and 23.1% decreases in grains per ear, 19.4% and 7.3% declines in 100-grain weight, 20.3% and 14.2% losses in fresh ear yield in 2019 and 2020 growing seasons, respectively, while water deficit at R2-R3 stage had no significant effect on ear traits and fresh ear yield, but the fresh ear yield with husk of DR2-R3 decreased by 9.1% (P<0.05). The obvious water deficit imposed at the V6-VT and VT-R2 stages also lowered grain quality. Water deficits at the V6-VT and VT-R2 stages led to accelerated maturity, resulting in increased total protein, starch, and lysine content in grains at the R3 stage and decreased soluble sugar content. Principal component analysis revealed that when water deficits occurred in the waxy maize growing season, they firstly altered maize physiological processes, then affected ear characteristics and yield, and finally resulted in significant grain quality changes. In conclusion, a water deficit during V6-VT and VT-R2 not only reduced fresh ear yield but also adversely affected grain quality. However, water deficit during R2-R3 had little effect on total protein, starch, and soluble sugar content,but increased obviously lysine content. DISCUSSION The above results suggested that avoiding serious water deficits at the V6-VT and VT-R2 stages of waxy maize while imposing a slight water deficit at the R2-R3 stage has not only little effects on fresh ear yield but also a remarkable improvement in grain quality.
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Affiliation(s)
- Chao Huang
- Institute of Farmland Irrigation, Chinese Academy of Agriculture Sciences, Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Anzhen Qin
- Institute of Farmland Irrigation, Chinese Academy of Agriculture Sciences, Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Yang Gao
- Institute of Farmland Irrigation, Chinese Academy of Agriculture Sciences, Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Shoutian Ma
- Institute of Farmland Irrigation, Chinese Academy of Agriculture Sciences, Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Zugui Liu
- Institute of Farmland Irrigation, Chinese Academy of Agriculture Sciences, Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Ben Zhao
- Institute of Farmland Irrigation, Chinese Academy of Agriculture Sciences, Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Dongfeng Ning
- Institute of Farmland Irrigation, Chinese Academy of Agriculture Sciences, Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Kai Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, China
| | - Wenjun Gong
- Guangli Irrigation Authority, Jiaozuo, China
| | | | - Zhandong Liu
- Institute of Farmland Irrigation, Chinese Academy of Agriculture Sciences, Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture and Rural Affairs, Xinxiang, China
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Michael TP. Time of Day Analysis over a Field Grown Developmental Time Course in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 12:166. [PMID: 36616295 PMCID: PMC9823482 DOI: 10.3390/plants12010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Plants integrate time of day (TOD) information over an entire season to ensure optimal growth, flowering time, and grain fill. However, most TOD expression studies have focused on a limited number of combinations of daylength and temperature under laboratory conditions. Here, an Oryza sativa (rice) expression study that followed TOD expression in the field over an entire growing season was re-analyzed. Similar to Arabidopsis thaliana, almost all rice genes have a TOD-specific expression over the developmental time course. As has been suggested in other grasses, thermocycles were a stronger cue for TOD expression than the photocycles over the growing season. All the core circadian clock genes display consistent TOD expression over the season with the interesting exception that the two grass paralogs of EARLY FLOWERING 3 (ELF3) display a distinct phasing based on the interaction between thermo- and photo-cycles. The dataset also revealed how specific pathways are modulated to distinct TOD over the season consistent with the changing biology. The data presented here provide a resource for researchers to study how TOD expression changes under natural conditions over a developmental time course, which will guide approaches to engineer more resilient and prolific crops.
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Affiliation(s)
- Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4696-4715. [PMID: 35429161 DOI: 10.1093/jxb/erac155] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyun Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaonan Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binfan Lai
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dandan Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakun Xie
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Badoni S, Parween S, Henry RJ, Sreenivasulu N. Systems seed biology to understand and manipulate rice grain quality and nutrition. Crit Rev Biotechnol 2022:1-18. [PMID: 35723584 DOI: 10.1080/07388551.2022.2058460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
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Affiliation(s)
- Saurabh Badoni
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Sabiha Parween
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Robert J Henry
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Nese Sreenivasulu
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
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10
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Teramoto S, Yamasaki M, Uga Y. Identification of a unique allele in the quantitative trait locus for crown root number in japonica rice from Japan using genome-wide association studies. BREEDING SCIENCE 2022; 72:222-231. [PMID: 36408322 PMCID: PMC9653191 DOI: 10.1270/jsbbs.22010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/10/2022] [Indexed: 06/16/2023]
Abstract
To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2.
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Affiliation(s)
- Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo 675-2103, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
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11
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Over-Expression of Dehydroascorbate Reductase Improves Salt Tolerance, Environmental Adaptability and Productivity in Oryza sativa. Antioxidants (Basel) 2022; 11:antiox11061077. [PMID: 35739975 PMCID: PMC9220092 DOI: 10.3390/antiox11061077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/21/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022] Open
Abstract
Abiotic stress induces reactive oxygen species (ROS) generation in plants, and high ROS levels can cause partial or severe oxidative damage to cellular components that regulate the redox status. Here, we developed salt-tolerant transgenic rice plants that overexpressed the dehydroascorbate reductase gene (OsDHAR1) under the control of a stress-inducible sweet potato promoter (SWPA2). OsDHAR1-expressing transgenic plants exhibited improved environmental adaptability compared to wild-type plants, owing to enhanced ascorbate levels, redox homeostasis, photosynthetic ability, and membrane stability through cross-activation of ascorbate-glutathione cycle enzymes under paddy-field conditions, which enhanced various agronomic traits, including root development, panicle number, spikelet number per panicle, and total grain yield. dhar2-knockdown plants were susceptible to salt stress, and owing to poor seed maturation, exhibited reduced biomass (root growth) and grain yield under paddy field conditions. Microarray revealed that transgenic plants highly expressed genes associated with cell growth, plant growth, leaf senescence, root development, ROS and heavy metal detoxification systems, lipid metabolism, isoflavone and ascorbate recycling, and photosynthesis. We identified the genetic source of functional genomics‒based molecular breeding in crop plants and provided new insights into the physiological processes underlying environmental adaptability, which will enable improvement of stress tolerance and crop species productivity in response to climate change.
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Takehisa H, Ando F, Takara Y, Ikehata A, Sato Y. Transcriptome and hyperspectral profiling allows assessment of phosphorus nutrient status in rice under field conditions. PLANT, CELL & ENVIRONMENT 2022; 45:1507-1519. [PMID: 35128701 DOI: 10.1111/pce.14280] [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: 07/28/2021] [Revised: 11/11/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Phosphorus (P) is one of the macronutrients indispensable for crop production, and therefore it is important to understand the potential of plants to adapt to low P conditions. We compared growth and leaf genome-wide transcriptome of four rice cultivars during growth between two fields with different amount of available phosphate and further analysed the acceptable range of P levels for normal growth from the view of both appearance traits and internal P nutrient status, which was measured by profiling the expression of the P indicator gene. This demonstrated that rice plants have a robustness to moderate P-deficient conditions expressing a system for P acquisition and usage without any effects on yield potential and that P indicator gene expression could be a useful index for early diagnosis of P status in plants. To develop a simple method for assessment of P status, we tried to predict the expression level using reflectance spectroscopy and hyperspectral imaging, thereby providing models with good performance. Our findings suggest that rice plants have the potential to adapt to moderate low P conditions in the field and showed that the hyperspectral technique is one of the useful tools for simple measurement of molecular-level dynamics reflecting internal nutrient conditions.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | | | | | - Akifumi Ikehata
- Institute of Food Research, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Wang X, Liang J, Liu Z, Kuang Y, Han L, Chen H, Xie X, Hu W, Tang M. Transcriptional regulation of metal metabolism- and nutrient absorption-related genes in Eucalyptus grandis by arbuscular mycorrhizal fungi at different zinc concentrations. BMC PLANT BIOLOGY 2022; 22:76. [PMID: 35193499 PMCID: PMC8862258 DOI: 10.1186/s12870-022-03456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/04/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Eucalyptus spp. are candidates for phytoremediation in heavy metal (HM)-polluted soils as they can adapt to harsh environments, grow rapidly, and have good economic value. Arbuscular mycorrhizal fungi (AMF) are the most widely distributed plant symbiotic fungi in nature, and they play an important role in promoting the phytoremediation of HM-polluted soils. However, few studies have evaluated the HM detoxification mechanism of E. spp. in symbiosis with AMF, and thus, the molecular mechanism remains unclear. RESULTS The gene transcription and metabolic pathways of E. grandis were studied with and without inoculation with AMF and at different zinc (Zn) concentrations. Here, we focused on the transcript level of six HM-related gene families (ZNT, COPT/Ctr, YSL, ZIFL and CE). Under high-Zn conditions, thirteen genes (ZNT:2, COPT/Ctr:5, YSL:3, ZIFL:1, CE:2) were upregulated, whereas ten genes (ZNT:3, COPT/Ctr:2, YSL:3, ZIFL:1, CE:1) were downregulated. With AMF symbiosis under high-Zn conditions, ten genes (ZNT:4, COPT/Ctr:2, YSL:3, CE:1) were upregulated, whereas nineteen genes (ZNT:9, COPT/Ctr:2, YSL:3, ZIFL:4, CE:1) were downregulated. Under high-Zn conditions, genes of three potassium-related transporters, six phosphate transporters (PHTs), and two nitrate transporters (NRTs) were upregulated, whereas genes of four potassium-related transporters,four PHTs, and four nitrogen-related transporters were downregulated. With AMF symbiosis under high-Zn conditions, genes of two potassium-related transporters, six ammonium transporters (AMTs) and five PHTs were upregulated, whereas genes of six potassium-related transporters, two AMTs and five PHTs were downregulated. CONCLUSIONS Our results indicates that AMF increases the resistance of E. grandis to high-Zn stress by improving nutrients uptake and regulating Zn uptake at the gene transcription level. Meanwhile, our findings provide a genome-level resource for the functional assignments of key genes regulated by Zn treatment and AM symbiosis in six HM-associated gene families and macromineral nutrient-related gene families of E. grandis. This may contribute to the elucidation of the molecular mechanisms of the response to Zn stress in E. grandis with AM symbiosis at the aspect of the interaction between HM tolerance and nutrient acquisition.
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Affiliation(s)
- Xinyang Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Jingwei Liang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ziyi Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yuxuan Kuang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Lina Han
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Wentao Hu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
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Conservation and Divergence of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE ( SPL) Gene Family between Wheat and Rice. Int J Mol Sci 2022; 23:ijms23042099. [PMID: 35216210 PMCID: PMC8874652 DOI: 10.3390/ijms23042099] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022] Open
Abstract
The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family affects plant architecture, panicle structure, and grain development, representing key genes for crop improvements. The objective of the present study is to utilize the well characterized SPLs’ functions in rice to facilitate the functional genomics of TaSPL genes. To achieve these goals, we combined several approaches, including genome-wide analysis of TaSPLs, comparative genomic analysis, expression profiling, and functional study of TaSPL3 in rice. We established the orthologous relationships of 56 TaSPL genes with the corresponding OsSPLs, laying a foundation for the comparison of known SPL functions between wheat and rice. Some TaSPLs exhibited different spatial–temporal expression patterns when compared to their rice orthologs, thus implicating functional divergence. TaSPL2/6/8/10 were identified to respond to different abiotic stresses through the combination of RNA-seq and qPCR expression analysis. Additionally, ectopic expression of TaSPL3 in rice promotes heading dates, affects leaf and stem development, and leads to smaller panicles and decreased yields per panicle. In conclusion, our work provides useful information toward cataloging of the functions of TaSPLs, emphasized the conservation and divergence between TaSPLs and OsSPLs, and identified the important SPL genes for wheat improvement.
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The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses. PLANTS 2021; 10:plants10102169. [PMID: 34685978 PMCID: PMC8538510 DOI: 10.3390/plants10102169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/01/2023]
Abstract
Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. β-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes.
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16
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Utilization of urea and chicken litter biochar to improve rice production. Sci Rep 2021; 11:9955. [PMID: 33976307 PMCID: PMC8113579 DOI: 10.1038/s41598-021-89332-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 04/20/2021] [Indexed: 11/28/2022] Open
Abstract
The use of N fertilizers on tropical acid soils is increasing because of their low native fertility. Chicken litter biochar was used to improve N use efficiency and rice yield. The objective of this study was to determine the effects of chicken litter biochar on selected chemical properties of a tropical acid soil under rice (MR219) cultivation. Treatments evaluated were in this study were as follows: (1) T1, soil only, (2) T2, existing recommended fertilization, (3) T3, chicken litter biochar alone, and (4) T4, chicken litter biochar + existing recommended fertilization. Plant and soil analyses were conducted using standard procedures. The use of chicken litter biochar increased soil pH, total carbon, total P, available P, total N, and exchangeable N. Also, this practice decreased soil total acidity and exchangeable Al3+. Compared with T2, T4 significantly increased Crop Recovery Efficiency and Agronomic Recovery Efficiency of N. This resulted in a significant increase in the grain yield (11 t ha−1) of MR219 (Malaysia hybrid rice) for T4 compared with the existing rice grain yield of 5.9 t ha−1 (T2). Moreover, application of chicken litter biochar (5 t ha−1) to tropical acid soil suggested that N application can be reduced to 26.67%, 30.03%, 30.15%, and 14.15% of the recommended rates by MADA on days 10, 30, 50, and 70 after transplanting, respectively. Chicken litter biochar can improve the chemical properties of tropical acid soils and rice (MR219) grain yield.
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17
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Current Understanding of Leaf Senescence in Rice. Int J Mol Sci 2021; 22:ijms22094515. [PMID: 33925978 PMCID: PMC8123611 DOI: 10.3390/ijms22094515] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022] Open
Abstract
Leaf senescence, which is the last developmental phase of plant growth, is controlled by multiple genetic and environmental factors. Leaf yellowing is a visual indicator of senescence due to the loss of the green pigment chlorophyll. During senescence, the methodical disassembly of macromolecules occurs, facilitating nutrient recycling and translocation from the sink to the source organs, which is critical for plant fitness and productivity. Leaf senescence is a complex and tightly regulated process, with coordinated actions of multiple pathways, responding to a sophisticated integration of leaf age and various environmental signals. Many studies have been carried out to understand the leaf senescence-associated molecular mechanisms including the chlorophyll breakdown, phytohormonal and transcriptional regulation, interaction with environmental signals, and associated metabolic changes. The metabolic reprogramming and nutrient recycling occurring during leaf senescence highlight the fundamental role of this developmental stage for the nutrient economy at the whole plant level. The strong impact of the senescence-associated nutrient remobilization on cereal productivity and grain quality is of interest in many breeding programs. This review summarizes our current knowledge in rice on (i) the actors of chlorophyll degradation, (ii) the identification of stay-green genotypes, (iii) the identification of transcription factors involved in the regulation of leaf senescence, (iv) the roles of leaf-senescence-associated nitrogen enzymes on plant performance, and (v) stress-induced senescence. Compiling the different advances obtained on rice leaf senescence will provide a framework for future rice breeding strategies to improve grain yield.
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Paajanen P, Lane de Barros Dantas L, Dodd AN. Layers of crosstalk between circadian regulation and environmental signalling in plants. Curr Biol 2021; 31:R399-R413. [PMID: 33905701 DOI: 10.1016/j.cub.2021.03.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Circadian regulation has a pervasive influence upon plant development, physiology and metabolism, impacting upon components of fitness and traits of agricultural importance. Circadian regulation is inextricably connected to the responses of plants to their abiotic environments, from the cellular to whole plant scales. Here, we review the crosstalk that occurs between circadian regulation and responses to the abiotic environment from the intracellular scale through to naturally fluctuating environments. We examine the spatial crosstalk that forms part of plant circadian regulation, at the subcellular, tissue, organ and whole-plant scales. This includes a focus on chloroplast and mitochondrial signalling, alternative splicing, long-distance circadian signalling and circadian regulation within natural environments. We also consider mathematical models for plant circadian regulation, to suggest future areas for advancing understanding of roles for circadian regulation in plant responses to environmental cues.
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Affiliation(s)
- Pirita Paajanen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Antony N Dodd
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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19
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Ram H, Singh A, Katoch M, Kaur R, Sardar S, Palia S, Satyam R, Sonah H, Deshmukh R, Pandey AK, Gupta I, Sharma TR. Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2212-2230. [PMID: 33197257 DOI: 10.1093/jxb/eraa536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
Rice, a staple food worldwide, contains varying amounts of nutrients in different grain tissues. The underlying molecular mechanism of such distinct nutrient partitioning remains poorly investigated. Here, an optimized rapid laser capture microdissection (LCM) approach was used to individually collect pericarp, aleurone, embryo and endosperm from grains 10 days after fertilization. Subsequent RNA-Seq analysis in these tissues identified 7760 differentially expressed genes. Analysis of promoter sequences of tissue-specific genes identified many known and novel cis-elements important for grain filling and seed development. Using the identified differentially expressed genes, comprehensive spatial gene expression pathways were built for accumulation of starch, proteins, lipids, and iron. The extensive transcriptomic analysis provided novel insights about nutrient partitioning mechanisms; for example, it revealed a gradient in seed storage protein accumulation across the four tissue types analysed. The analysis also revealed that the partitioning of various minerals, such as iron, is most likely regulated through transcriptional control of their transporters. We present the extensive analysis from this study as an interactive online tool that provides a much-needed resource for future functional genomics studies aimed to improve grain quality and seed development.
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Affiliation(s)
- Hasthi Ram
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Anmol Singh
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Megha Katoch
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Ravneet Kaur
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Shaswati Sardar
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Shubham Palia
- Department of Biochemical Engineering and Biotechnology, Block I, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Rohit Satyam
- Department of Biochemical Engineering and Biotechnology, Block I, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Block I, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
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20
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Takehisa H, Sato Y. Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production. BREEDING SCIENCE 2021; 71:76-88. [PMID: 33762878 PMCID: PMC7973498 DOI: 10.1270/jsbbs.20098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Genome-wide transcriptome profiling is a powerful tool for identifying key genes and pathways involved in plant development and physiological processes. This review summarizes studies that have used transcriptome profiling mainly in rice to focus on responses to macronutrients such as nitrogen, phosphorus and potassium, and spatio-temporal root profiling in relation to the regulation of root system architecture as well as nutrient uptake and transport. We also discuss strategies based on meta- and co-expression analyses with different attributed transcriptome data, which can be used for investigating the regulatory mechanisms and dynamics of nutritional responses and adaptation, and speculate on further advances in transcriptome profiling that could have potential application to crop breeding and cultivation.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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21
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Guo Y, Wang T, Fu FF, El-Kassaby YA, Wang G. Temporospatial Flavonoids Metabolism Variation in Ginkgo biloba Leaves. Front Genet 2020; 11:589326. [PMID: 33329734 PMCID: PMC7728922 DOI: 10.3389/fgene.2020.589326] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/05/2020] [Indexed: 11/18/2022] Open
Abstract
Ginkgo (Ginkgo biloba L.) is a high-value medicinal tree species characterized by its flavonoids beneficial effects that are abundant in leaves. We performed a temporospatial comprehensive transcriptome and metabolome dynamics analyses of clonally propagated Ginkgo plants at four developmental stages (time: May to August) across three different environments (space) to unravel leaves flavonoids biosynthesis variation. Principal component analysis revealed clear gene expression separation across samples from different environments and leaf-developmental stages. We found that flavonoid-related metabolism was more active in the early stage of leaf development, and the content of total flavonoid glycosides and the expression of some genes in flavonoid biosynthesis pathway peaked in May. We also constructed a co-expression regulation network and identified eight GbMYBs and combining with other TF genes (3 GbERFs, 1 GbbHLH, and 1 GbTrihelix) positively regulated the expression of multiple structural genes in the flavonoid biosynthesis pathway. We found that part of these GbTFs (Gb_11316, Gb_32143, and Gb_00128) expressions was negatively correlated with mean minimum temperature and mean relative humidity, while positively correlated with sunshine duration. This study increased our understanding of the molecular mechanisms of flavonoids biosynthesis in Ginkgo leaves and provided insight into the proper production and management of Ginkgo commercial plantations.
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Affiliation(s)
- Ying Guo
- Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.,College of Forestry, Nanjing Forestry University, Nanjing, China.,Department of Forest & Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Tongli Wang
- Department of Forest & Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Fang-Fang Fu
- Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.,College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yousry A El-Kassaby
- Department of Forest & Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Guibin Wang
- Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.,College of Forestry, Nanjing Forestry University, Nanjing, China
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Raza Q, Riaz A, Bashir K, Sabar M. Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars. PLANT MOLECULAR BIOLOGY 2020; 104:97-112. [PMID: 32643113 DOI: 10.1007/s11103-020-01027-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
By integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars. Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α-Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences from Arabidopsis heat-shock genes also suggest that OsBIP2 may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars.
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Affiliation(s)
- Qasim Raza
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Lahore, Punjab, Pakistan.
| | - Awais Riaz
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Lahore, Punjab, Pakistan
| | - Khurram Bashir
- Plant Genomic Network Research Team, Center for Sustainable Resource Science, RIKEN, Yokohama Campus, Yokohama, Japan
| | - Muhammad Sabar
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Lahore, Punjab, Pakistan
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Mathew IE, Priyadarshini R, Mahto A, Jaiswal P, Parida SK, Agarwal P. SUPER STARCHY1/ONAC025 participates in rice grain filling. PLANT DIRECT 2020; 4:e00249. [PMID: 32995698 PMCID: PMC7507516 DOI: 10.1002/pld3.249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/10/2020] [Accepted: 07/10/2020] [Indexed: 05/04/2023]
Abstract
NAC transcription factors (TFs) are known for their role in development and stress. This article attempts to functionally validate the role of rice SS1/ ONAC025 (LOC_Os11g31330) during seed development. The gene is seed-specific and its promoter directs reporter expression in the developing endosperm and embryo in rice transgenic plants. Furthermore, rice transgenic plants ectopically expressing SS1/ ONAC025 have a plantlet lethal phenotype with hampered vegetative growth, but increased tillers and an altered shoot apical meristem structure. The vegetative cells of these plantlets are filled with distinct starch granules. RNAseq analysis of two independent plantlets reveals the differential expression of reproductive and photosynthetic genes. A comparison with seed development transcriptome indicates differential regulation of many seed-related genes by SS1/ ONAC025. Genes involved in starch biosynthesis, especially amylopectin and those encoding seed storage proteins, and regulating seed size are also differentially expressed. In conjunction, SS1/ ONAC025 shows highest expression in japonica rice. As a TF, SS1/ ONAC025 is a transcriptional repressor localized to endoplasmic reticulum and nucleus. The article shows that SS1/ ONAC025 is a seed-specific gene promoting grain filling in rice, and negatively affecting vegetative growth.
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Affiliation(s)
| | | | - Arunima Mahto
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Priya Jaiswal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
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Osnato M, Matias-Hernandez L, Aguilar-Jaramillo AE, Kater MM, Pelaz S. Genes of the RAV Family Control Heading Date and Carpel Development in Rice. PLANT PHYSIOLOGY 2020; 183:1663-1680. [PMID: 32554473 PMCID: PMC7401134 DOI: 10.1104/pp.20.00562] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/03/2020] [Indexed: 05/11/2023]
Abstract
In plants, correct formation of reproductive organs is critical for successful seedset and perpetuation of the species. Plants have evolved different molecular mechanisms to coordinate flower and seed development at the proper time of the year. Among the plant-specific RELATED TO ABI3 AND VP1 (RAV) family of transcription factors, only TEMPRANILLO1 (TEM1) and TEM2 have been shown to affect reproductive development in Arabidopsis (Arabidopsis thaliana). They negatively regulate the floral transition through direct repression of FLOWERING LOCUS T and GIBBERELLIN 3-OXIDASE1/2, encoding major components of the florigen. Here we identify RAV genes from rice (Oryza sativa), and unravel their regulatory roles in key steps of reproductive development. Our data strongly suggest that, like TEMs, OsRAV9/OsTEM1 has a conserved function as a repressor of photoperiodic flowering upstream of the floral activators OsMADS14 and Hd3a, through a mechanism reminiscent of that one underlying floral transition in temperate cereals. Furthermore, OsRAV11 and OsRAV12 may have acquired a new function in the differentiation of the carpel and the control of seed size, acting downstream of floral homeotic factors. Alternatively, this function may have been lost in Arabidopsis. Our data reveal conservation of RAV gene function in the regulation of flowering time in monocotyledonous and dicotyledonous plants, but also unveil roles in the development of rice gynoecium.
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Affiliation(s)
- Michela Osnato
- Centre for Research in Agricultural Genomics, Centro de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universidad Autónoma de Barcelona-Universidad de Barcelona, Campus Universidad Autónoma de Barcelona, 08193 Barcelona, Spain
- Department BioSciences, University of Milan, 20133 Milan, Italy
| | - Luis Matias-Hernandez
- Centre for Research in Agricultural Genomics, Centro de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universidad Autónoma de Barcelona-Universidad de Barcelona, Campus Universidad Autónoma de Barcelona, 08193 Barcelona, Spain
| | - Andrea Elizabeth Aguilar-Jaramillo
- Centre for Research in Agricultural Genomics, Centro de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universidad Autónoma de Barcelona-Universidad de Barcelona, Campus Universidad Autónoma de Barcelona, 08193 Barcelona, Spain
| | - Martin M Kater
- Department BioSciences, University of Milan, 20133 Milan, Italy
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, Centro de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universidad Autónoma de Barcelona-Universidad de Barcelona, Campus Universidad Autónoma de Barcelona, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
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25
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Dantas LLB, Calixto CPG, Dourado MM, Carneiro MS, Brown JWS, Hotta CT. Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane. FRONTIERS IN PLANT SCIENCE 2019; 10:1614. [PMID: 31921258 PMCID: PMC6936171 DOI: 10.3389/fpls.2019.01614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/15/2019] [Indexed: 05/05/2023]
Abstract
Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 46% in rice, and 38% in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to test if the daily dynamics of AS forms of circadian clock genes are regulated by environmental factors, such as temperature, in the field. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95, and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature- and organ-dependent expression of at least one alternatively spliced isoform in all genes. Expression of AS isoforms varied according to the season. Our results suggest that AS events in circadian clock genes are correlated with temperature.
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Affiliation(s)
- Luíza L. B. Dantas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Cristiane P. G. Calixto
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Maira M. Dourado
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Monalisa S. Carneiro
- Departmento de Biotecnologia, Produção Vegetal e Animal, Centro de Ciências Agrícolas, Universidade Federal de São Carlos, Araras, Brazil
| | - John W. S. Brown
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Carlos T. Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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Dhatt BK, Abshire N, Paul P, Hasanthika K, Sandhu J, Zhang Q, Obata T, Walia H. Metabolic Dynamics of Developing Rice Seeds Under High Night-Time Temperature Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:1443. [PMID: 31781147 PMCID: PMC6857699 DOI: 10.3389/fpls.2019.01443] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/17/2019] [Indexed: 05/03/2023]
Abstract
High temperature stress during rice reproductive development results in yield losses. Reduced grain yield and grain quality has been associated with high temperature stress, and specifically with high night-time temperatures (HNT). Characterizing the impact of HNT on the phenotypic and metabolic status of developing rice seeds can provide insights into the mechanisms involved in yield and quality decline. Here, we examined the impact of warmer nights on the morphology and metabolome during early seed development in six diverse rice accessions. Seed size was sensitive to HNT in four of the six genotypes, while seed fertility and seed weight were unaffected. We observed genotypic differences for negative impact of HNT on grain quality. This was evident from the chalky grain appearance due to impaired packaging of starch granules. Metabolite profiles during early seed development (3 and 4 days after fertilization; DAF) were distinct from the early grain filling stages (7 and 10 DAF) under optimal conditions. We observed that accumulation of sugars (sucrose, fructose, and glucose) peaked at 7 DAF suggesting a major flux of carbon into glycolysis, tricarboxylic acid cycle, and starch biosynthesis during grain filling. Next, we determined hyper (HNT > control) and hypo (HNT < control) abundant metabolites and found 19 of the 57 metabolites to differ significantly between HNT and control treatments. The most prominent changes were exhibited by differential abundance of sugar and sugar alcohols under HNT, which could be linked to a protective mechanism against the HNT damage. Overall, our results indicate that combining metabolic profiles of developing grains with yield and quality parameters under high night temperature stress could provide insight for exploration of natural variation for HNT tolerance in the rice germplasm.
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Affiliation(s)
- Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nathan Abshire
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kalani Hasanthika
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Qi Zhang
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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Beier MP, Fujita T, Sasaki K, Kanno K, Ohashi M, Tamura W, Konishi N, Saito M, Imagawa F, Ishiyama K, Miyao A, Yamaya T, Kojima S. The urea transporter DUR3 contributes to rice production under nitrogen-deficient and field conditions. PHYSIOLOGIA PLANTARUM 2019; 167:75-89. [PMID: 30426495 DOI: 10.1111/ppl.12872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/29/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Nitrogen is one of the most important elements for plant growth, and urea is one of the most frequently used nitrogen fertilizers worldwide. Besides the exogenously-supplied urea to the soil, urea is endogenously synthesized during secondary nitrogen metabolism. Here, we investigated the contribution of a urea transporter, DUR3, to rice production using a reverse genetic approach combined with localization studies. Tos17 insertion lines for DUR3 showed a 50% yield reduction in hydroponic culture, and a 26.2% yield reduction in a paddy field, because of decreased grain filling. Because shoot biomass production and shoot total N was not reduced, insertion lines were disordered not only in nitrogen acquisition but also in nitrogen allocation. During seed development, DUR3 insertion lines accumulated nitrogen in leaves and could not sufficiently develop their panicles, although shoot and root dry weights were not significantly different from the wild-type. The urea concentration in old leaf harvested from DUR3 insertion lines was lower than that in wild-type. DUR3 promoter-dependent β-glucuronidase (GUS) activity was localized in vascular tissue and the midribs of old leaves. These results indicate that DUR3 contributes to nitrogen translocation and rice yield under nitrogen-deficient and field conditions.
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Affiliation(s)
- Marcel P Beier
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
- Graduate School of Life and Environmental Science, Osaka Prefecture University, Sakai 599-8531, Japan
| | - Takayuki Fujita
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Kazuhiro Sasaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 188-0002, Japan
| | - Keiichi Kanno
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Miwa Ohashi
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Wataru Tamura
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Noriyuki Konishi
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Masahide Saito
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Fumi Imagawa
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Keiki Ishiyama
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Akio Miyao
- National Institute of Agrobiological Science, Tsukuba, Ibaraki 3058602, Japan
| | - Tomoyuki Yamaya
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Soichi Kojima
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
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Field transcriptome revealed a novel relationship between nitrate transport and flowering in Japanese beech. Sci Rep 2019; 9:4325. [PMID: 30867453 PMCID: PMC6416253 DOI: 10.1038/s41598-019-39608-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/29/2019] [Indexed: 11/09/2022] Open
Abstract
Recent advances in molecular and genetic studies about flowering time control have been increasingly available to elucidate the physiological mechanism underlying masting, the intermittent and synchronized production of a large amount of flowers and seeds in plant populations. To identify unexplored developmental and physiological processes associated with masting, genome-wide transcriptome analysis is a promising tool, but such analyses have yet to be performed. We established a field transcriptome using a typical masting species, Japanese beech (Fagus crenata Blume), over two years, and analyzed the data using a nonlinear time-series analysis called convergent cross mapping. Our field transcriptome was found to undergo numerous changes depending on the status of floral induction and season. An integrated approach of high-throughput transcriptomics and causal inference was successful at detecting novel causal regulatory relationships between nitrate transport and florigen synthesis/transport in a forest tree species. The synergistic activation of nitrate transport and floral transition could be adaptive to simultaneously satisfy floral transition at the appropriate timing and the nitrogen demand needed for flower formation.
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29
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Takehisa H, Sato Y. Transcriptome monitoring visualizes growth stage-dependent nutrient status dynamics in rice under field conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1048-1060. [PMID: 30481387 DOI: 10.1111/tpj.14176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 11/09/2018] [Accepted: 11/16/2018] [Indexed: 05/24/2023]
Abstract
Crop plants undergo morpho-physiological changes throughout the growth process in response to both the internal and the external environment, and that eventually determine the yield. The system-level adjustment of the morpho-physiological changes has remained largely unclear, however, especially in field conditions. Here, we reveal changes in nutrient status associated with tiller development and soil conditions based on the leaf transcriptome profile of rice (Oryza sativa) throughout the entire period of growth. We performed gene co-expression network analysis and identified three gene sets as indicators for monitoring the internal nitrogen and phosphorus status. Expression profiling reveals that the phosphorus starvation response is expressed during the tillering stage and is then switched off with the transition to nitrogen deficiency. Coincident with phosphorus status dynamics, the level of phosphate in the leaf is demonstrated to be low during the tillering stage and subsequently increases drastically. The phosphorus dynamics are genetically validated by analysing mutants with a defect in phosphorus homeostasis. Notably, we show that nitrogen limitation directly suppresses the phosphorus starvation response. Finally, the phosphorus starvation response is demonstrated to be activated in soil with a high phosphate retention capacity, without the visible phenotypes associated with phosphorus starvation. Our results reveal a growth stage- and soil condition-dependent reaction that requires phosphorus, which is expressed to promote the phosphorus uptake required for developing tillers and is directly adjusted by nitrogen status. A molecular framework for elucidating nutrient status dynamics under field conditions would provide insights into improving crop productivity.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
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30
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Zhang F, Liu X, Zhang A, Jiang Z, Chen L, Zhang X. Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis. BMC PLANT BIOLOGY 2019; 19:11. [PMID: 30616516 PMCID: PMC6323737 DOI: 10.1186/s12870-018-1589-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/04/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND The flowering transition which is controlled by a complex and intricate gene regulatory network plays an important role in the reproduction for offspring of plants. It is a challenge to identify the critical transition state as well as the genes that control the transition of flower development. With the emergence of massively parallel sequencing, a great number of time-course transcriptome data greatly facilitate the exploration of the developmental phase transition in plants. Although some network-based bioinformatics analyses attempted to identify the genes that control the phase transition, they generally overlooked the dynamics of regulation and resulted in unreliable results. In addition, the results of these methods cannot be self-explained. RESULTS In this work, to reveal a critical transition state and identify the transition-specific genes of flower development, we implemented a genome-wide dynamic network analysis on temporal gene expression data in Arabidopsis by dynamic network biomarker (DNB) method. In the analysis, DNB model which can exploit collective fluctuations and correlations of different metabolites at a network level was used to detect the imminent critical transition state or the tipping point. The genes that control the phase transition can be identified by the difference of weighted correlations between the genes interested and the other genes in the global network. To construct the gene regulatory network controlling the flowering transition, we applied NARROMI algorithm which can reduce the noisy, redundant and indirect regulations on the expression data of the transition-specific genes. In the results, the critical transition state detected during the formation of flowers corresponded to the development of flowering on the 7th to 9th day in Arabidopsis. Among of 233 genes identified to be highly fluctuated at the transition state, a high percentage of genes with maximum expression in pollen was detected, and 24 genes were validated to participate in stress reaction process, as well as other floral-related pathways. Composed of three major subnetworks, a gene regulatory network with 150 nodes and 225 edges was found to be highly correlated with flowering transition. The gene ontology (GO) annotation of pathway enrichment analysis revealed that the identified genes are enriched in the catalytic activity, metabolic process and cellular process. CONCLUSIONS This study provides a novel insight to identify the real causality of the phase transition with genome-wide dynamic network analysis.
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Affiliation(s)
- Fuping Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 10049 China
| | - Xiaoping Liu
- Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Aidi Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Zhonglin Jiang
- Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Xiujun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
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Moon S, Chandran AKN, An G, Lee C, Jung KH. Genome-wide analysis of root hair-preferential genes in rice. RICE (NEW YORK, N.Y.) 2018; 11:48. [PMID: 30159808 PMCID: PMC6115326 DOI: 10.1186/s12284-018-0241-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 08/10/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Root hairs are valuable in taking up nutrients and water from the rhizosphere and serving as sites of interactions with soil microorganisms. By increasing the external surface area of the roots or interacting with rhizobacteria, root hairs directly and indirectly promote plant growth and yield. Transcriptome data can be used to understand root-hair development in rice. RESULT We performed Agilent 44 K microarray experiments with enriched root-hair samples and identified 409 root hair-preferential genes in rice. The expression patterns of six genes were confirmed using a GUS reporter system and quantitative RT-PCR analysis. Gene Ontology (GO) analysis demonstrated that 13 GO terms, including oxygen transport and cell wall generation, were highly over-represented in those genes. Although comparative analysis between rice and Arabidopsis revealed a large proportion of orthologous pairs, their spatial expression patterns were not conserved. To investigate the molecular network associated with root hair-preferential genes in rice, we analyzed the PPI network as well as coexpression data. Subsequently, we developed a refined network consisting of 24 interactions between 10 genes and 18 of their interactors. CONCLUSION Identification of root hair-preferential genes and in depth analysis of those genes will be a useful reference to accelerate the understanding of root-hair development in rice.
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Affiliation(s)
- Sunok Moon
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Anil Kumar Nalini Chandran
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Gynheung An
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Chanhui Lee
- Department of Plant and Environmental New Resources, Kyung Hee University, Yongin, 17104, Korea.
| | - Ki-Hong Jung
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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32
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Shirai K, Matsuda F, Nakabayashi R, Okamoto M, Tanaka M, Fujimoto A, Shimizu M, Shinozaki K, Seki M, Saito K, Hanada K. A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions. Mol Biol Evol 2018; 34:3111-3122. [PMID: 28961930 DOI: 10.1093/molbev/msx234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication events contribute to the diversity of specialized metabolites within species. We identified metabolome quantitative trait genes (mQTGs) associated with quantitative metabolite variations and examined the relationship between mQTGs and CNVs. We obtained 1,335 specialized metabolite signals from 53 worldwide A. thaliana accessions using liquid chromatography-quadrupole time-of-flight mass spectrometry. In this study, genes associated with specialized metabolites were inferred by either a generally authorized genome-wide association study (GWAS) approach or a novel analysis of the association between gene expression and metabolite accumulation. Genes qualified by both analyses are defined to be mQTGs. The integrated method enabled us to detect mQTGs with a low false positive rate (=5.71 × 10-4). We also identified 5,654 genes associated with 1,335 specialized metabolites. Of these genes, 4.4% were affected by CNVs, which was more than expected (χ2 test: P < 0.01). This result suggests that CNVs contribute to variations in specialized metabolites within a species. To assess the contribution of CNVs to adaptive evolution in A. thaliana, we examined the selective sweeps around the mQTGs. We observed that the mQTGs with CNVs tended to undergo selective sweeps. These observations imply that variations in specialized metabolites caused by CNVs contribute to the adaptive evolution of A. thaliana.
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Affiliation(s)
- Kazumasa Shirai
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Fukuoka, Japan
| | - Fumio Matsuda
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Ryo Nakabayashi
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Masanori Okamoto
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Akihiro Fujimoto
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Minami Shimizu
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Kazuo Shinozaki
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Kazuki Saito
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Kousuke Hanada
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Fukuoka, Japan.,Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
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33
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Iwayama K, Aisaka Y, Kutsuna N, Nagano AJ. FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions. Bioinformatics 2018; 33:1672-1680. [PMID: 28158396 PMCID: PMC5447243 DOI: 10.1093/bioinformatics/btx049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/28/2017] [Indexed: 12/31/2022] Open
Abstract
Motivation Considerable attention has been given to the quantification of environmental effects on organisms. In natural conditions, environmental factors are continuously changing in a complex manner. To reveal the effects of such environmental variations on organisms, transcriptome data in field environments have been collected and analyzed. Nagano et al. proposed a model that describes the relationship between transcriptomic variation and environmental conditions and demonstrated the capability to predict transcriptome variation in rice plants. However, the computational cost of parameter optimization has prevented its wide application. Results We propose a new statistical model and efficient parameter optimization based on the previous study. We developed and released FIT, an R package that offers functions for parameter optimization and transcriptome prediction. The proposed method achieves comparable or better prediction performance within a shorter computational time than the previous method. The package will facilitate the study of the environmental effects on transcriptomic variation in field conditions. Availability and Implementation Freely available from CRAN (https://cran.r-project.org/web/packages/FIT/). Supplementary information Supplementary data are available at Bioinformatics online
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Affiliation(s)
- Koji Iwayama
- Research Institute for Food and Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | | | - Natsumaro Kutsuna
- LPixel Inc, Hongo, Bunkyo-ku, Tokyo, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Atsushi J Nagano
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan.,Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.,JST PRESTO, Kawaguchi, Saitama, Japan
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Zhang L, Kong H, Ma H, Yang J. Phylogenomic detection and functional prediction of genes potentially important for plant meiosis. Gene 2018; 643:83-97. [PMID: 29223357 DOI: 10.1016/j.gene.2017.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/18/2017] [Accepted: 12/04/2017] [Indexed: 11/17/2022]
Abstract
Meiosis is a specialized type of cell division necessary for sexual reproduction in eukaryotes. A better understanding of the cytological procedures of meiosis has been achieved by comprehensive cytogenetic studies in plants, while the genetic mechanisms regulating meiotic progression remain incompletely understood. The increasing accumulation of complete genome sequences and large-scale gene expression datasets has provided a powerful resource for phylogenomic inference and unsupervised identification of genes involved in plant meiosis. By integrating sequence homology and expression data, 164, 131, 124 and 162 genes potentially important for meiosis were identified in the genomes of Arabidopsis thaliana, Oryza sativa, Selaginella moellendorffii and Pogonatum aloides, respectively. The predicted genes were assigned to 45 meiotic GO terms, and their functions were related to different processes occurring during meiosis in various organisms. Most of the predicted meiotic genes underwent lineage-specific duplication events during plant evolution, with about 30% of the predicted genes retaining only a single copy in higher plant genomes. The results of this study provided clues to design experiments for better functional characterization of meiotic genes in plants, promoting the phylogenomic approach to the evolutionary dynamics of the plant meiotic machineries.
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Affiliation(s)
- Luoyan Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong Ma
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.
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Wei K, Chen H. Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice. BMC Genomics 2018; 19:35. [PMID: 29320982 PMCID: PMC5764023 DOI: 10.1186/s12864-017-4425-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 12/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cytochrome P450 monooxygenases (CYP450, CYP, P450) catalyze numerous monooxygenation/hydroxylation reactions in biochemical pathways. Although CYP superfamily has been systematically studied in a few species, the genome-scale research about it in rice has not been done. RESULTS In this study, a total of 355 CYPs encoded by 326 genes were identified in japonica genome. The OsCYP genes are classified into 10 clans including 45 families according to phylogenetic analysis. More than half of the genes are distributed in 53 tandem duplicated gene clusters. Intron-exon structure of OsCYPs exhibits highly conserved and specificity within a family, and divergences of duplicate genes in gene structure result in non-functionalization, neo-functionalization or sub-functionalization. Selection pressure analysis showed that rice CYPs are under purifying selection. The microarray data analysis shows that some genes are tissue-specific expression, such as OsCYP710A5 and OsCYP71X14 in endosperm, OsCYP99A3 and OsCYP78A16 in root and OsCYP93G2 and OsCYP97D7 in leaf. Analysis of RNA-seq data derived from rice leaf developmental gradient indicates that some OsCYPs exhibit zone-specific expression patterns. OsCYP87C2, OsCYP96B5, OsCYP96B8 and OsCYP84A5 were specifically expressed in leaf base and transitional zone. The transcripts of lineages II and IV-1 members were highly abundant in maturing zone. Eighty three OsCYPs are differentially expressed in response to drought stress, of which OsCYP51G3, OsCYP709C9, OsCYP709C5, OsCYP81A6, OsCYP72A18 and OsCYP704A5 are strongly induced and OsCYP78A16, OsCYP89C9 and OsCYP704A5 are down-regulated significantly, and some of the results were validated by qPCR. And 23 up-regulated and 17 down-regulated genes are specific to Osbhlh148 mutation under drought stress. Compared to those in wild type, the changes in transcript levels of several genes are slight in the mutant, such as OsCYP51G3, OsCYP94C2, OsCYP709C9 and OsCYP709C5. CONCLUSION The whole-genomic analysis of rice P450 superfamily provides a clue to understanding biological function of OsCYPs in development regulation and drought stress response, and is helpful to rice molecular breeding.
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, 36 Xian-Qian-Zhi Street, Zhangzhou, Fujian, 363000, China.
| | - Huiqin Chen
- School of Biological Sciences and Biotechnology, Minnan Normal University, 36 Xian-Qian-Zhi Street, Zhangzhou, Fujian, 363000, China.
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Minhas AP, Tuli R, Puri S. Pathway Editing Targets for Thiamine Biofortification in Rice Grains. FRONTIERS IN PLANT SCIENCE 2018; 9:975. [PMID: 30042775 PMCID: PMC6048418 DOI: 10.3389/fpls.2018.00975] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has been partially elucidated and the effect of overexpression of a few genes such as thi1 and thiC, on thiamine accumulation in rice has been reported. Based on current knowledge, this review focuses on the potential of gene editing in metabolic engineering of thiamine biosynthesis pathway to improve thiamine in rice grains. Candidate genes, suitable for modification of the structural part to evolve more efficient versions of enzymes in the pathway, are discussed. For example, adjacent cysteine residues may be introduced in the catalytic domain of thi4 to improve the turn over activity of thiamine thiazole synthase 2. Motif specific editing to modify promoter regulatory regions of genes is discussed to modulate gene expression. Editing cis acting regulatory elements in promoter region can shift the expression of transporters and thiamine binding proteins to endosperm. This can enhance dietary availability of thiamine from rice grains. Differential transcriptomics on rice varieties with contrasting grain thiamine and functional genomic studies will identify more strategic targets for editing in future. Developing functionally enhanced foods by biofortification is a sustainable approach to make diets wholesome.
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Töpfer N, Fuchs LM, Aharoni A. The PhytoClust tool for metabolic gene clusters discovery in plant genomes. Nucleic Acids Res 2017; 45:7049-7063. [PMID: 28486689 PMCID: PMC5499548 DOI: 10.1093/nar/gkx404] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 05/01/2017] [Indexed: 01/26/2023] Open
Abstract
The existence of Metabolic Gene Clusters (MGCs) in plant genomes has recently raised increased interest. Thus far, MGCs were commonly identified for pathways of specialized metabolism, mostly those associated with terpene type products. For efficient identification of novel MGCs, computational approaches are essential. Here, we present PhytoClust; a tool for the detection of candidate MGCs in plant genomes. The algorithm employs a collection of enzyme families related to plant specialized metabolism, translated into hidden Markov models, to mine given genome sequences for physically co-localized metabolic enzymes. Our tool accurately identifies previously characterized plant MGCs. An exhaustive search of 31 plant genomes detected 1232 and 5531 putative gene cluster types and candidates, respectively. Clustering analysis of putative MGCs types by species reflected plant taxonomy. Furthermore, enrichment analysis revealed taxa- and species-specific enrichment of certain enzyme families in MGCs. When operating through our web-interface, PhytoClust users can mine a genome either based on a list of known cluster types or by defining new cluster rules. Moreover, for selected plant species, the output can be complemented by co-expression analysis. Altogether, we envisage PhytoClust to enhance novel MGCs discovery which will in turn impact the exploration of plant metabolism.
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Affiliation(s)
- Nadine Töpfer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lisa-Maria Fuchs
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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Lee S, Jeong H, Lee S, Lee J, Kim SJ, Park JW, Woo HR, Lim PO, An G, Nam HG, Hwang D. Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice. Sci Rep 2017; 7:8792. [PMID: 28821707 PMCID: PMC5562787 DOI: 10.1038/s41598-017-07035-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/21/2017] [Indexed: 01/31/2023] Open
Abstract
Flag leaves (FL) and second leaves (SL) in rice show differential aging patterns during monocarpic senescence. Coordination of aging programs between FL and SL is important for grain yield and quality. However, the molecular bases for differential aging programs between FL and SL have not been systematically explored in rice. Here, we performed mRNA-sequencing of FL and SL at six time points during grain-filling and identified four molecular bases for differential aging programs between FL and SL: phenylpropanoid biosynthesis, photosynthesis, amino acid (AA) transport, and hormone response. Of them, photosynthesis (carbon assimilation) and AA transport (nitrogen remobilization) predominantly occurred in FL and SL, respectively, during grain-filling. Unlike other molecular bases, AA transport showed consistent differential expression patterns between FL and SL in independent samples. Moreover, long-distance AA transporters showed invariant differential expression patterns between FL and SL after panicle removal, which was consistent to invariant differential nitrogen contents between FL and SL after panicle removal. Therefore, our results suggest that the supplies of carbon and nitrogen to seeds is functionally segregated between FL and SL and that long-distance AA transport is an invariant core program for high nitrogen remobilization in SL.
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Affiliation(s)
- Shinyoung Lee
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Hyobin Jeong
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Sichul Lee
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Jinwon Lee
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Sun-Ji Kim
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Ji-Won Park
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Pyung Ok Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Hong Gil Nam
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea. .,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea.
| | - Daehee Hwang
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea. .,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea.
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Jain P, Singh PK, Kapoor R, Khanna A, Solanke AU, Krishnan SG, Singh AK, Sharma V, Sharma TR. Understanding Host-Pathogen Interactions with Expression Profiling of NILs Carrying Rice-Blast Resistance Pi9 Gene. FRONTIERS IN PLANT SCIENCE 2017; 8:93. [PMID: 28280498 PMCID: PMC5322464 DOI: 10.3389/fpls.2017.00093] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/16/2017] [Indexed: 05/03/2023]
Abstract
Magnaporthe oryzae infection causes rice blast, a destructive disease that is responsible for considerable decrease in rice yield. Development of resistant varieties via introgressing resistance genes with marker-assisted breeding can eliminate pesticide use and minimize crop losses. Here, resistant near-isogenic line (NIL) of Pusa Basmati-1(PB1) carrying broad spectrum rice blast resistance gene Pi9 was used to investigate Pi9-mediated resistance response. Infected and uninfected resistant NIL and susceptible control line were subjected to RNA-Seq. With the exception of one gene (Pi9), transcriptional signatures between the two lines were alike, reflecting basal similarities in their profiles. Resistant and susceptible lines possessed 1043 (727 up-regulated and 316 down-regulated) and 568 (341 up-regulated and 227 down-regulated) unique and significant differentially expressed loci (SDEL), respectively. Pathway analysis revealed higher transcriptional activation of kinases, WRKY, MYB, and ERF transcription factors, JA-ET hormones, chitinases, glycosyl hydrolases, lipid biosynthesis, pathogenesis and secondary metabolism related genes in resistant NIL than susceptible line. Singular enrichment analysis demonstrated that blast resistant NIL is significantly enriched with genes for primary and secondary metabolism, response to biotic stimulus and transcriptional regulation. The co-expression network showed proteins of genes in response to biotic stimulus interacted in a manner unique to resistant NIL upon M. oryzae infection. These data suggest that Pi9 modulates genome-wide transcriptional regulation in resistant NIL but not in susceptible PB1. We successfully used transcriptome profiling to understand the molecular basis of Pi9-mediated resistance mechanisms, identified potential candidate genes involved in early pathogen response and revealed the sophisticated transcriptional reprogramming during rice-M. oryzae interactions.
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Affiliation(s)
- Priyanka Jain
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
- Department of Bioscience & Biotechnology, Banasthali UniversityTonk, India
| | - Pankaj K. Singh
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
- Department of Bioscience & Biotechnology, Banasthali UniversityTonk, India
| | - Ritu Kapoor
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Apurva Khanna
- ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | | | | | - Ashok K. Singh
- ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Vinay Sharma
- Department of Bioscience & Biotechnology, Banasthali UniversityTonk, India
| | - Tilak R. Sharma
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
- *Correspondence: Tilak R. Sharma ;
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40
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Yu N, Liang Y, Peng X, Hou X. Molecular and Bioinformatic Characterization of the Rice ROOT UV-B SENSITIVE Gene Family. RICE (NEW YORK, N.Y.) 2016; 9:55. [PMID: 27730518 PMCID: PMC5059228 DOI: 10.1186/s12284-016-0127-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/01/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND ROOT UV-B SENSITIVE (RUS) genes exist in most eukaryotic organisms, and encode proteins that contain a DUF647 (domain of unknown function 647). Although the RUS genes are known to play essential roles in Arabidopsis seedling development, their precise functions are not well understood in other plants, including rice. FINDINGS In this study, six OsRUS genes were cloned from rice root and leaf cDNA libraries. Our analysis showed that the sequence and open reading frame of cloned OsRUS3 cDNA differs from the predictions reported in the RAP-DB and RGAP databases. Public microarray, MPSS, and EST databases were used to analyze the expression profiles of the six OsRUS genes. Expression profiles for all OsRUS genes at different rice developmental stages were also analyzed by qRT-PCR. The signal peptide, GPI-anchor, transmembrane domain and subcellular localization of OsRUS proteins were predicted by various bioinformatics tools. Furthermore OsRUS1 was determined to be localized to the chloroplast by a protoplast experiment. CONCLUSIONS All the characterization of the OsRUS family generated from this study will provide a crucial foundation from which to further dissect how OsRUS genes function in rice development.
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Affiliation(s)
- Ning Yu
- Research Center of Plant Stress Biology, College of Life Sciences, South-China Agricultural University, Guangzhou, 510642 China
| | - Yaping Liang
- Research Center of Plant Stress Biology, College of Life Sciences, South-China Agricultural University, Guangzhou, 510642 China
| | - Xinxiang Peng
- Research Center of Plant Stress Biology, College of Life Sciences, South-China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Plant Functional Genomics and Biotechnology, Education Department of Guangdong Province, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Xuewen Hou
- Research Center of Plant Stress Biology, College of Life Sciences, South-China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Plant Functional Genomics and Biotechnology, Education Department of Guangdong Province, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
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Matsumoto T, Wu J, Itoh T, Numa H, Antonio B, Sasaki T. The Nipponbare genome and the next-generation of rice genomics research in Japan. RICE (NEW YORK, N.Y.) 2016; 9:33. [PMID: 27447712 PMCID: PMC4958085 DOI: 10.1186/s12284-016-0107-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/03/2016] [Indexed: 05/28/2023]
Abstract
The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits.
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Affiliation(s)
- Takashi Matsumoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takeshi Itoh
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Hisataka Numa
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Baltazar Antonio
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takuji Sasaki
- Nodai Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
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Herath V. Small family, big impact: In silico analysis of DREB2 transcription factor family in rice. Comput Biol Chem 2016; 65:128-139. [PMID: 27816829 DOI: 10.1016/j.compbiolchem.2016.10.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/10/2016] [Accepted: 10/25/2016] [Indexed: 01/15/2023]
Abstract
Dehydration-responsive element- (DREB) proteins are considered as the master regulators of plant abiotic stress responses including drought, salinity and cold. They are also involved in other developmental processes such as embryo and endosperm development. DREB family of transcription factors consist of two sub families namely CBF1/DREB1 and DREB2. In this study, a genome-wide in silico analysis was carried out to dissect the structure and function of DREB2 family transcription factors in the rice genome. Using Arabidopsis DREB2 sequences a total of five rice DREB2 homologs were identified and they were distributed among four chromosomes. All OsDREBs contained the AP2 domain and unique [K/R]GKKGPxN motif characteristic to DREB2 family. During rice growth and development, three OsDREB2s namely OsDREB2A, OsDREB2B and OsABI4 were expressed and their expression was confined to embryo and endosperm tissues. OsDREB2A, OsDREB2B and OsDREB2C were expressed under abiotic stress conditions. OsDREB2B was expressed under drought, salinity and cold stress conditions while OsDREB2A and OsDREB2C were expressed only under drought and salinity conditions. The putative promoter regions of OsDREB2s were enriched with elements related to cellular development, hormonal regulation and stress response validating the observed expression dynamics. Co-expression analysis revealed that embryo development and stress related genes were expressed together with OsDREB2s. Predicted post-translational modifications indicated the fine regulation of OsDREB2s. These findings may shed light in uncovering the complex abiotic stress signaling networks and future genomics studies targeting the development of climate ready crops.
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Affiliation(s)
- Venura Herath
- Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka.
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Lu HP, Pang WQ, Li WX, Tan YY, Wang Q, Zhao HJ, Shu QY. Tissue-specific expression, developmentally and spatially regulated alternative splicing, and protein subcellular localization of OsLpa rice. J Zhejiang Univ Sci B 2016; 17:100-9. [PMID: 26834011 DOI: 10.1631/jzus.b1500205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The OsLpa1 gene (LOC_Os57400) was identified to be involved in phytic acid (PA) metabolism because its knockout and missense mutants reduce PA content in rice grain. However, little is known about the molecular characteristics of OsLpa rice and of its homologues in other plants. In the present study, the spatial pattern of OsLpa1 expression was revealed using OsLpa1 promoter::GUS transgenic plants (GUS: β-glucuronidase); GUS histochemical assay showed that OsLpa1 was strongly expressed in stem, leaf, and root tissues, but in floral organ it is expressed mainly and strongly in filaments. In seeds, GUS staining was concentrated in the aleurone layers; a few blue spots were observed in the outer layers of embryo, but no staining was observed in the endosperm. Three OsLpa1 transcripts (OsLpa1.1, OsLpa1.2, OsLpa1.3) are produced due to alternative splicing; quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) analysis revealed that the abundance of OsLpa1.3 was negligible compared with OsLpa1.1 and OsLpa all tissues. OsLpa1.2 is predominant in germinating seeds (about 5 times that of OsLpa1.1), but its abundance decreases quickly with the development of seedlings and plants, whereas the abundance of OsLpa1.1 rises and falls, reaching its highest level in 45-d-old plants, with abundance greater than that of OsLpa both leaves and roots. In seeds, the abundance of OsLpa1 continuously increases with seed growth, being 27.5 and 15 times greater in 28-DAF (day after flowering) seeds than in 7-DAF seeds for OsLpa1.1 and OsLpa1.2, respectively. Transient expression of chimeric genes with green fluorescence protein (GFP) in rice protoplasts demonstrated that all proteins encoded by the three OsLpa1 transcripts are localized to the chloroplast.
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Affiliation(s)
- Hai-ping Lu
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Wei-qin Pang
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Wen-xu Li
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Yuan-yuan Tan
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Qing Wang
- Wuxi Hupper Bioseed Technology Academy Ltd., Wuxi 214000, China
| | - Hai-jun Zhao
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Qing-yao Shu
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
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Lane T, Best T, Zembower N, Davitt J, Henry N, Xu Y, Koch J, Liang H, McGraw J, Schuster S, Shim D, Coggeshall MV, Carlson JE, Staton ME. The green ash transcriptome and identification of genes responding to abiotic and biotic stresses. BMC Genomics 2016; 17:702. [PMID: 27589953 PMCID: PMC5009568 DOI: 10.1186/s12864-016-3052-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/27/2016] [Indexed: 11/25/2022] Open
Abstract
Background To develop a set of transcriptome sequences to support research on environmental stress responses in green ash (Fraxinus pennsylvanica), we undertook deep RNA sequencing of green ash tissues under various stress treatments. The treatments, including emerald ash borer (EAB) feeding, heat, drought, cold and ozone, were selected to mimic the increasing threats of climate change and invasive pests faced by green ash across its native habitat. Results We report the generation and assembly of RNA sequences from 55 green ash samples into 107,611 putative unique transcripts (PUTs). 52,899 open reading frames were identified. Functional annotation of the PUTs by comparison to the Uniprot protein database identified matches for 63 % of transcripts and for 98 % of transcripts with ORFs. Further functional annotation identified conserved protein domains and assigned gene ontology terms to the PUTs. Examination of transcript expression across different RNA libraries revealed that expression patterns clustered based on tissues regardless of stress treatment. The transcripts from stress treatments were further examined to identify differential expression. Tens to hundreds of differentially expressed PUTs were identified for each stress treatment. A set of 109 PUTs were found to be consistently up or down regulated across three or more different stress treatments, representing basal stress response candidate genes in green ash. In addition, 1956 simple sequence repeats were identified in the PUTs, of which we identified 465 high quality DNA markers and designed flanking PCR primers. Conclusions North American native ash trees have suffered extensive mortality due to EAB infestation, creating a need to breed or select for resistant green ash genotypes. Stress from climate change is an additional concern for longevity of native ash populations. The use of genomics could accelerate management efforts. The green ash transcriptome we have developed provides important sequence information, genetic markers and stress-response candidate genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3052-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Lane
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37966, USA
| | - Teodora Best
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Nicole Zembower
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jack Davitt
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37966, USA
| | - Nathan Henry
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37966, USA
| | - Yi Xu
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, USA.,Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Jennifer Koch
- Northern Research Station, USDA Forest Service, Delaware, OH, 43015, USA
| | - Haiying Liang
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - John McGraw
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Stephan Schuster
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Donghwan Shim
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Mark V Coggeshall
- Department of Forestry, University of Missouri, Columbia, MO, 65211, USA
| | - John E Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37966, USA.
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45
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Harrop TWR, Ud Din I, Gregis V, Osnato M, Jouannic S, Adam H, Kater MM. Gene expression profiling of reproductive meristem types in early rice inflorescences by laser microdissection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:75-88. [PMID: 26932536 DOI: 10.1111/tpj.13147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 02/11/2016] [Accepted: 02/15/2016] [Indexed: 05/05/2023]
Abstract
In rice, inflorescence architecture is established at early stages of reproductive development and contributes directly to grain yield potential. After induction of flowering, the complexity of branching, and therefore the number of seeds on the panicle, is determined by the activity of different meristem types and the timing of transitions between them. Although some of the genes involved in these transitions have been identified, an understanding of the network of transcriptional regulators controlling this process is lacking. To address this we used a precise laser microdissection and RNA-sequencing approach in Oryza sativa ssp. japonica cv. Nipponbare to produce quantitative data that describe the landscape of gene expression in four different meristem types: the rachis meristem, the primary branch meristem, the elongating primary branch meristem (including axillary meristems), and the spikelet meristem. A switch in expression profile between apical and axillary meristem types followed by more gradual changes during transitions in axillary meristem identity was observed, and several genes potentially involved in branching were identified. This resource will be vital for a mechanistic understanding of the link between inflorescence development and grain yield.
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Affiliation(s)
- Thomas W R Harrop
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394, Montpellier, France
| | - Israr Ud Din
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Michela Osnato
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Stefan Jouannic
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394, Montpellier, France
| | - Hélène Adam
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394, Montpellier, France
| | - Martin M Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
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46
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Hu C, Tohge T, Chan SA, Song Y, Rao J, Cui B, Lin H, Wang L, Fernie AR, Zhang D, Shi J. Identification of Conserved and Diverse Metabolic Shifts during Rice Grain Development. Sci Rep 2016; 6:20942. [PMID: 26860358 PMCID: PMC4748235 DOI: 10.1038/srep20942] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/14/2016] [Indexed: 11/26/2022] Open
Abstract
Seed development dedicates to reserve synthesis and accumulation and uncovering its genetic and biochemical mechanisms has been a major research focus. Although proteomic and transcriptomic analyses revealed dynamic changes of genes and enzymes involved, the information regarding concomitant metabolic changes is missing. Here we investigated the dynamic metabolic changes along the rice grain development of two japonica and two indica cultivars using non-targeted metabolomics approach, in which we successfully identified 214 metabolites. Statistical analyses revealed both cultivar and developmental stage dependent metabolic changes in rice grains. Generally, the stage specific metabolic kinetics corresponded well to the physiological status of the developing grains, and metabolic changes in developing rice grain are similar to those of dicot Arabidopsis and tomato at reserve accumulation stage but are different from those of dicots at seed desiccation stage. The remarkable difference in metabolite abundances between japonica and indica rice grain was observed at the reserve accumulation stage. Metabolite-metabolite correlation analysis uncovered potential new pathways for several metabolites. Taken together, this study uncovered both conserved and diverse development associated metabolic kinetics of rice grains, which facilitates further study to explore fundamental questions regarding the evolution of seed metabolic capabilities as well as their potential applications in crop improvement.
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Affiliation(s)
- Chaoyang Hu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
| | - Takayuki Tohge
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | | | - Yue Song
- Agilent Technology, Inc. Shanghai, China
| | - Jun Rao
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
- Jiangxi Cancer Hospital, No. 519 East Beijing Road, Nanchang 330029, China
| | - Bo Cui
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
| | - Hong Lin
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
| | - Lei Wang
- Agilent Technology, Inc. Beijing 100000, China
| | - Alisdair R. Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
- Shanghai Ruifeng Agro-biotechnology Co., Ltd, Room 108, No 233 Rushan Rd., Shanghai 200120, China
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47
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Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters. Nat Commun 2016; 7:10527. [PMID: 26841834 PMCID: PMC4742901 DOI: 10.1038/ncomms10527] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 12/22/2015] [Indexed: 12/24/2022] Open
Abstract
Rice panicle architecture is a key target of selection when breeding for yield and grain quality. However, panicle phenotypes are difficult to measure and susceptible to confounding during genetic mapping due to correlation with flowering and subpopulation structure. Here we quantify 49 panicle phenotypes in 242 tropical rice accessions with the imaging platform PANorama. Using flowering as a covariate, we conduct a genome-wide association study (GWAS), detect numerous subpopulation-specific associations, and dissect multi-trait peaks using panicle phenotype covariates. Ten candidate genes in pathways known to regulate plant architecture fall under GWAS peaks, half of which overlap with quantitative trait loci identified in an experimental population. This is the first study to assess inflorescence phenotypes of field-grown material using a high-resolution phenotyping platform. Herein, we establish a panicle morphocline for domesticated rice, propose a genetic model underlying complex panicle traits, and demonstrate subtle links between panicle size and yield performance. Panicle architecture is an important determinant of crop yield and a target of selection by plant breeders. Here, Crowell et al. combine image-based phenotyping with high-density array-based genotyping to perform a genome-wide association study revealing a number of candidate genes linked to panicle variation in rice.
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48
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Regulatory role of FZP in the determination of panicle branching and spikelet formation in rice. Sci Rep 2016; 6:19022. [PMID: 26744119 PMCID: PMC4705600 DOI: 10.1038/srep19022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/02/2015] [Indexed: 11/22/2022] Open
Abstract
FRIZZLE PANICLE (FZP) and RFL/ABERRANT PANICLE ORGANIZATION 2 (APO2) play important roles in regulating the ABCDE floral organ identity genes. However, the relationships among FZP and these floral identity genes in the regulation of panicle formation remain unclear. Here, we used the novel mutant fzp-11, wild-type and FZP-overexpressing plants to compare the expression of these genes during panicle development by real-time PCR and in situ hybridization. The results indicate that FZP is a major negative regulator of RFL/APO2 and determines the transition from panicle branching to spikelet formation. Moreover, overexpression of FZP severely represses axillary meristem formation in both the vegetative and reproductive phases and the outgrowth of secondary branches in panicle. FZP overexpression positively regulates the expression of a subset of the class B genes, AGL6 genes (OsMADS6 and OsMADS17) as well as class E genes (OsMADS1, OsMADS7 and OsMADS8) in floral meristem (FM). Thus, it suggested that FZP could specify floral organ identity by regulating the related OsMADS-box genes.
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49
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Wei Y, Zeng H, Hu W, Chen L, He C, Shi H. Comparative Transcriptional Profiling of Melatonin Synthesis and Catabolic Genes Indicates the Possible Role of Melatonin in Developmental and Stress Responses in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:676. [PMID: 27242875 PMCID: PMC4870392 DOI: 10.3389/fpls.2016.00676] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/02/2016] [Indexed: 05/17/2023]
Abstract
As a well-known animal hormone, melatonin (N-acetyl-5-methoxytryptamine) is also involved in multiple plant biological processes, especially in various stress responses. Rice is one of the most important crops, and melatonin is taken in by many people everyday from rice. However, the transcriptional profiling of melatonin-related genes in rice is largely unknown. In this study, the expression patterns of 11 melatonin related genes in rice in different periods, tissues, in response to different treatments were synthetically analyzed using published microarray data. These results suggest that the melatonin-related genes may play important and dual roles in rice developmental stages. We highlight the commonly regulation of rice melatonin-related genes by abscisic acid (ABA), jasmonic acid (JA), various abiotic stresses and pathogen infection, indicating the possible role of these genes in multiple stress responses and underlying crosstalks of plant hormones, especially ABA and JA. Taken together, this study may provide insight into the association among melatonin biosynthesis and catabolic pathway, plant development and stress responses in rice. The profile analysis identified candidate genes for further functional characterization in circadian rhythm and specific stress responses.
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Affiliation(s)
- Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHaikou, China
| | - Hongqiu Zeng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHaikou, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Lanzhen Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural SciencesBeijing, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHaikou, China
- *Correspondence: Haitao Shi, ; Chaozu He,
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHaikou, China
- *Correspondence: Haitao Shi, ; Chaozu He,
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50
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Takehisa H, Sato Y, Antonio B, Nagamura Y. Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice. RICE (NEW YORK, N.Y.) 2015; 8:24. [PMID: 26206757 PMCID: PMC4513034 DOI: 10.1186/s12284-015-0059-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND Macronutrients are pivotal elements for proper plant growth and development. Although extensive gene expression profiling revealed a large number of genes differentially expressed under various nutrient deprivation, characterization of these genes has never been fully explored especially in rice. Coexpression network analysis is a useful tool to elucidate the functional relationships of genes based on common expression. Therefore, we performed microarray analysis of rice shoot under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions. Moreover, we conducted a large scale coexpression analysis by integrating the data with previously generated gene expression profiles of organs and tissues at different developmental stages to obtain a global view of gene networks associated with plant response to nutrient deficiency. RESULTS We statistically identified 5400 differentially expressed genes under the nutrient deficiency treatments. Subsequent coexpression analysis resulted in the extraction of 6 modules (groups of highly interconnected genes) with distinct gene expression signatures. Three of these modules comprise mostly of downregulated genes under N deficiency associated with distinct functions such as development of immature organs, protein biosynthesis and photosynthesis in chloroplast of green tissues, and fundamental cellular processes in all organs and tissues. Furthermore, we identified one module containing upregulated genes under N and K deficiency conditions, and a number of genes encoding protein kinase, kinase-like domain containing protein and nutrient transporters. This module might be particularly involved in adaptation to nutrient deficiency via phosphorylation-mediated signal transduction and/or post-transcriptional regulation. CONCLUSIONS Our study demonstrated that large scale coexpression analysis is an efficient approach in characterizing the nutrient response genes based on biological functions and could provide new insights in understanding plant response to nutrient deficiency.
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Affiliation(s)
- Hinako Takehisa
- Genome Resource Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Yutaka Sato
- Genome Resource Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Baltazar Antonio
- Genome Resource Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Yoshiaki Nagamura
- Genome Resource Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
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