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Ercoli MF, Ramos PZ, Jain R, Pilotte J, Dong OX, Thompson T, Wells CI, Elkins JM, Edwards AM, Couñago RM, Drewry DH, Ronald PC. An open source plant kinase chemogenomics set. PLANT DIRECT 2022; 6:e460. [PMID: 36447653 PMCID: PMC9694430 DOI: 10.1002/pld3.460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
One hundred twenty-nine protein kinases, selected to represent the diversity of the rice (Oryza sativa) kinome, were cloned and tested for expression in Escherichia coli. Forty of these rice kinases were purified and screened using differential scanning fluorimetry (DSF) against 627 diverse kinase inhibitors, with a range of structures and activities targeting diverse human kinases. Thirty-seven active compounds were then tested for their ability to modify primary root development in Arabidopsis. Of these, 14 compounds caused a significant reduction of primary root length compared with control plants. Two of these inhibitory compounds bind to the predicted orthologue of Arabidopsis PSKR1, one of two receptors for PSK, a small sulfated peptide that positively controls root development. The reduced root length phenotype could not be rescued by the exogenous addition of the PSK peptide, suggesting that chemical treatment may inhibit both PSKR1 and its closely related receptor PSKR2. Six of the compounds acting as root growth inhibitors in Arabidopsis conferred the same effect in rice. Compound RAF265 (CHIR-265), previously shown to bind the human kinase BRAF (B-Raf proto-oncogene, serine/threonine kinase), also binds to nine highly conserved rice kinases tested. The binding of human and rice kinases to the same compound suggests that human kinase inhibitor sets will be useful for dissecting the function of plant kinases.
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Affiliation(s)
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - Rashmi Jain
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Joseph Pilotte
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Oliver Xiaoou Dong
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Ty Thompson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Carrow I. Wells
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Jonathan M. Elkins
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
- Centre for Medicines DiscoveryUniversity of OxfordOxfordUK
| | - Aled M. Edwards
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - David H. Drewry
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
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Qiu J, Xie J, Chen Y, Shen Z, Shi H, Naqvi NI, Qian Q, Liang Y, Kou Y. Warm temperature compromises JA-regulated basal resistance to enhance Magnaporthe oryzae infection in rice. MOLECULAR PLANT 2022; 15:723-739. [PMID: 35217224 DOI: 10.1016/j.molp.2022.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/24/2022] [Accepted: 02/20/2022] [Indexed: 05/20/2023]
Abstract
Changes in global temperatures profoundly affect the occurrence of plant diseases. It is well known that rice blast can easily become epidemic in relatively warm weather. However, the molecular mechanism remains unclear. In this study, we show that enhanced blast development at a warm temperature (22°C) compared with the normal growth temperature (28°C) is rice plant-determined. Comparative transcriptome analysis revealed that jasmonic acid (JA) biosynthesis and signaling genes in rice could be effectively induced by Magnaporthe oryzae at 28°C but not at 22°C. Phenotypic analyses of the osaoc1 and osmyc2 mutants, OsCOI1 RNAi lines, and OsMYC2-OE plants further demonstrated that compromised M. oryzae-induced JA biosynthesis and signaling lead to enhanced blast susceptibility at the warm temperature. Consistent with these results, we found that exogenous application of methyl jasmonate served as an effective strategy for improving blast resistance under the warm environmental conditions. Furthermore, decreased activation of JA signaling resulted in the downregulated expression of some key basal resistance genes at 22°C when compared with 28°C. Among these affected genes, OsCEBiP (chitin elicitor-binding protein precursor) was found to be directly regulated by OsMYB22 and its interacting protein OsMYC2, a key component of JA signaling, and this contributed to temperature-modulated blast resistance. Taken together, these results suggest that warm temperature compromises basal resistance in rice and enhances M. oryzae infection by reducing JA biosynthesis and signaling, providing potential new strategies for managing rice blast disease under warm climate conditions.
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Affiliation(s)
- Jiehua Qiu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Junhui Xie
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Ya Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhenan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Huanbin Shi
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Naweed I Naqvi
- Temasek Life Sciences Laboratory, and Department of Biological Sciences, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yan Liang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yanjun Kou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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3
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Hong WJ, Jiang X, Choi SH, Kim YJ, Kim ST, Jeon JS, Jung KH. A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity. PLANTS 2021; 10:plants10081690. [PMID: 34451735 PMCID: PMC8401045 DOI: 10.3390/plants10081690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 02/01/2023]
Abstract
Carbohydrate metabolism is an important biochemical process related to developmental growth and yield-related traits. Due to global climate change and rapid population growth, increasing rice yield has become vital. To understand whole carbohydrate metabolism pathways and find related clues for enhancing yield, genes in whole carbohydrate metabolism pathways were systemically dissected using meta-transcriptome data. This study identified 866 carbohydrate genes from the MapMan toolkit and the Kyoto Encyclopedia of Genes and Genomes database split into 11 clusters of different anatomical expression profiles. Analysis of functionally characterized carbohydrate genes revealed that source activity and eating quality are the most well-known functions, and they each have a strong correlation with tissue-preferred clusters. To verify the transcriptomic dissection, three pollen-preferred cluster genes were used and found downregulated in the gori mutant. Finally, we summarized carbohydrate metabolism as a conceptual model in gene clusters associated with morphological traits. This systemic analysis not only provided new insights to improve rice yield but also proposed novel tissue-preferred carbohydrate genes for future research.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Xu Jiang
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Seok-Hyun Choi
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea
| | - Sun-Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
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Norvienyeku J, Lin L, Waheed A, Chen X, Bao J, Aliyu SR, Lin L, Shabbir A, Batool W, Zhong Z, Zhou J, Lu G, Wang Z. Bayogenin 3-O-cellobioside confers non-cultivar-specific defence against the rice blast fungus Pyricularia oryzae. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:589-601. [PMID: 33043566 PMCID: PMC7955875 DOI: 10.1111/pbi.13488] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 09/27/2020] [Indexed: 05/06/2023]
Abstract
Rice cultivars from japonica and indica lineage possess differential resistance against blast fungus as a result of genetic divergence. Whether different rice cultivars also show distinct metabolomic changes in response to P. oryzae, and their role in host resistance, are poorly understood. Here, we examine the responses of six different rice cultivars from japonica and indica lineage challenged with P. oryzae. Both susceptible and resistant rice cultivars expressed several metabolites exclusively during P. oryzae infection, including the saponin Bayogenin 3-O-cellobioside. Bayogenin 3-O-cellobioside level in infected rice directly correlated with their resistant attributes. These findings reveal, for the first time to our knowledge that besides oat, other grass plants including rice produces protective saponins. Our study provides insight into the role of pathogen-mediated metabolomics reprogramming in host immunity. The correlation between Bayogenin 3-O-Cellobioside levels and blast resistance suggests that engineering saponin expression in cereal crops represents attractive and sustainable disease management.
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Affiliation(s)
- Justice Norvienyeku
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Abdul Waheed
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaomin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiandong Bao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Sami Rukaiya Aliyu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ammarah Shabbir
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Wajjiha Batool
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jie Zhou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
- Institute of OceanographyMinjiang UniversityFuzhouChina
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Yoo YH, Kim YJ, Moon S, Gho YS, Hong WJ, Kim EJ, Jiang X, Jung KH. Fast Track to Discover Novel Promoters in Rice. PLANTS 2020; 9:plants9010125. [PMID: 31963727 PMCID: PMC7020180 DOI: 10.3390/plants9010125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/04/2022]
Abstract
Promoters are key components for the application of biotechnological techniques in crop plants. Reporter genes such as GUS or GFP have been used to test the activity of promoters for diverse applications. A huge number of T-DNAs carrying promoterless GUS near their right borders have been inserted into the rice genome, and 105,739 flanking sequence tags from rice lines with this T-DNA insertion have been identified, establishing potential promoter trap lines for 20,899 out of 55,986 genes in the rice genome. Anatomical meta-expression data and information on abiotic stress related to these promoter trap lines enable us to quickly identify new promoters associated with various expression patterns. In the present report, we introduce a strategy to identify new promoters in a very short period of time using a combination of meta-expression analysis and promoter trap lines.
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A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6534745. [PMID: 31396532 PMCID: PMC6668530 DOI: 10.1155/2019/6534745] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 11/18/2022]
Abstract
Chloroplasts are intracellular semiautonomous organelles central to photosynthesis and are essential for plant growth and yield. The significance of the function of chloroplast-related genes in response to climate change has not been well studied in crops. In the present study, the initial focus was on genes that were predicted to be located in the chloroplast genome in rice, a model crop plant, with genes either preferentially expressed in the leaf or ubiquitously expressed in all organs. The characteristics were analyzed by Gene Ontology (GO) enrichment and MapMan functional classification tools. It was then identified that 110 GO terms (45 for leaf expression and 65 for ubiquitous expression) and 1,695 genes mapped to MapMan overviews were strongly associated with chloroplasts. In particular, the MapMan cellular response overview revealed a close association between heat stress response and chloroplast-related genes in rice. Moreover, features of these genes in response to abiotic stress were analyzed using a large-scale publicly available transcript dataset. Consequently, the expression of 215 genes was found to be upregulated in response to high temperature stress. Conversely, genes that responded to other stresses were extremely limited. In other words, chloroplast-related genes were found to affect abiotic stress response mainly through high temperature response, with little effect on response to drought and salinity stress. These results suggest that genes involved in diurnal rhythm in the leaves participate in the reaction to recognize temperature changes in the environment. Furthermore, the predicted protein–protein interaction network analysis associated with high temperature stress is expected to provide a very important basis for the study of molecular mechanisms by which chloroplasts will respond to future climate changes.
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Bashir K, Matsui A, Rasheed S, Seki M. Recent advances in the characterization of plant transcriptomes in response to drought, salinity, heat, and cold stress. F1000Res 2019; 8:F1000 Faculty Rev-658. [PMID: 31131087 PMCID: PMC6518435 DOI: 10.12688/f1000research.18424.1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/09/2019] [Indexed: 11/28/2022] Open
Abstract
Despite recent advancements in plant molecular biology and biotechnology, providing food security for an increasing world population remains a challenge. Drought (water scarcity), salinity, heat, and cold stress are considered major limiting factors that affect crop production both qualitatively and quantitatively. Therefore, the development of cost-effective and environmentally friendly strategies will be needed to resolve these agricultural problems. This will require a comprehensive understanding of transcriptomic alterations that occur in plants in response to varying levels of environmental stresses, singly and in combination. Here, we briefly discuss the current status and future challenges in plant research related to understanding transcriptional changes that occur in response to drought, salinity, heat, and cold stress.
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Affiliation(s)
- Khurram Bashir
- Plant Genomic Network Research Team, CSRS, RIKEN, Yokohama, Tsurumi-ku, Kanagawa, 230-0045, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, CSRS, RIKEN, Yokohama, Tsurumi-ku, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, CPR, RIKEN, Wako, Saitama, 351-0198, Japan
| | - Sultana Rasheed
- Plant Genomic Network Research Team, CSRS, RIKEN, Yokohama, Tsurumi-ku, Kanagawa, 230-0045, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, CSRS, RIKEN, Yokohama, Tsurumi-ku, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, CPR, RIKEN, Wako, Saitama, 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Core Research for Evolutionary Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
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Hong WJ, Kim YJ, Chandran AKN, Jung KH. Infrastructures of systems biology that facilitate functional genomic study in rice. RICE (NEW YORK, N.Y.) 2019; 12:15. [PMID: 30874968 PMCID: PMC6419666 DOI: 10.1186/s12284-019-0276-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 05/08/2023]
Abstract
Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice. In this review, we categorize the resources using six omics levels: genomics, transcriptomics, proteomics, metabolomics, integrated omics, and functional genomics. We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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Hoang GT, Van Dinh L, Nguyen TT, Ta NK, Gathignol F, Mai CD, Jouannic S, Tran KD, Khuat TH, Do VN, Lebrun M, Courtois B, Gantet P. Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase. RICE (NEW YORK, N.Y.) 2019; 12:4. [PMID: 30701393 PMCID: PMC6357217 DOI: 10.1186/s12284-018-0258-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/11/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Drought tolerance is a major challenge in breeding rice for unfavorable environments. In this study, we used a panel of 180 Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers to perform a genome-wide association study (GWAS) for different drought response and recovery traits during the vegetative stage. These landraces originate from different geographical locations and are adapted to different agrosystems characterized by contrasted water regimes. Vietnamese landraces are often underrepresented in international panels used for GWAS, but they can contain original genetic determinants related to drought resistance. RESULTS The panel of 180 rice varieties was phenotyped under greenhouse conditions for several drought-related traits in an experimental design with 3 replicates. Plants were grown in pots for 4 weeks and drought-stressed by stopping irrigation for an additional 4 weeks. Drought sensitivity scores and leaf relative water content were measured throughout the drought stress. The recovery capacity was measured 2 weeks after plant rewatering. Several QTLs associated with these drought tolerance traits were identified by GWAS using a mixed model with control of structure and kinship. The number of detected QTLs consisted of 14 for leaf relative water content, 9 for slope of relative water content, 12 for drought sensitivity score, 3 for recovery ability and 1 for relative crop growth rate. This set of 39 QTLs actually corresponded to a total of 17 different QTLs because 9 were simultaneously associated with two or more traits, which indicates that these common loci may have pleiotropic effects on drought-related traits. No QTL was found in association with the same traits in both the indica and japonica subpanels. The possible candidate genes underlying the quantitative trait loci are reviewed. CONCLUSIONS Some of the identified QTLs contain promising candidate genes with a function related to drought tolerance by osmotic stress adjustment.
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Affiliation(s)
- Giang Thi Hoang
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam.
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam.
| | - Lam Van Dinh
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Thom Thi Nguyen
- IRD, Université de Montpellier, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Nhung Kim Ta
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Floran Gathignol
- IRD, Université de Montpellier, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Chung Duc Mai
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Stefan Jouannic
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam
- IRD, Université de Montpellier, UMR DIADE, 34095, Montpellier, France
| | - Khanh Dang Tran
- Genetic Engineering Division, Agricultural Genetics Institute, Hanoi, 00000, Vietnam
| | - Trung Huu Khuat
- Genetic Engineering Division, Agricultural Genetics Institute, Hanoi, 00000, Vietnam
| | - Vinh Nang Do
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Michel Lebrun
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam
- IRD, Université de Montpellier, LMI RICE-2, Hanoi, 00000, Vietnam
- IRD, Université de Montpellier, UMR LSTM, 34095, Montpellier, France
| | - Brigitte Courtois
- Cirad, UMR-AGAP, F-34398, Montpellier, France
- CIRAD, INRA, Univ Montpellier, Montpellier SupAgro, Montpellier, France
| | - Pascal Gantet
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam.
- IRD, Université de Montpellier, LMI RICE-2, Hanoi, 00000, Vietnam.
- IRD, Université de Montpellier, UMR DIADE, 34095, Montpellier, France.
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Pei W, Jain A, Ai H, Liu X, Feng B, Wang X, Sun Y, Xu G, Sun S. OsSIZ2 regulates nitrogen homeostasis and some of the reproductive traits in rice. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:51-60. [PMID: 30530203 DOI: 10.1016/j.jplph.2018.11.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
Small ubiquitin-related modifier (SUMO) is a post-translational modification of proteins that has important roles in plant growth and development as well as nutrition study. OsSIZ1, a SUMO E3 ligase in rice (Oryza sativa), exerts regulatory influence on nitrogen (N) homeostasis. Here, we investigated the biological function of OsSIZ2, a paralog of OsSIZ1, in the responses to nitrogen, anther dehiscence, and seed length using a reverse genetics approach. The expression of OsSIZ2 was increased during N deficiency. Under -N condition, total N concentration in the root of OsSIZ2-Ri plants and ossiz2 was significantly increased compared with wild type. Further, 15N-labelled uptake assay revealed the role of OsSIZ2 in acquisition and mobilization of N. Moreover, qRT-PCR analyses revealed that several genes involved in the maintenance of N homeostasis were altered in OsSIZ2 mutants. In addition, ossiz2 indicated obvious defects in anther dehiscence, pollen fertility, and seed set percentage. Interestingly, however, the seed length was longer in the mutant compared with wild type. Overall, these results suggest pivotal roles of OsSIZ2 in regulating homeostasis of N and different agronomic traits including anther and seed development.
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Affiliation(s)
- Wenxia Pei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University, Kant Kalwar NH-11C, Jaipur, India
| | - Hao Ai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Xiuli Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Bing Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Xiaowen Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Yafei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China.
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Zhu K, Liu H, Chen X, Cheng Q, Cheng ZM(M. The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants. BMC PLANT BIOLOGY 2018; 18:199. [PMID: 30227850 PMCID: PMC6145126 DOI: 10.1186/s12870-018-1389-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/14/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Crassulacean acid metabolism (CAM) plants use water 20-80% more efficiently by shifting stomata opening and primary CO2 uptake and fixation to the nighttime. Protein kinases (PKs) play pivotal roles in this biological process. However, few PKs have been functionally analyzed precisely due to their abundance and potential functional redundancy (caused by numerous gene duplications). RESULTS In this study, we systematically identified a total of 758 predicted PK genes in the genome of a CAM plant, pineapple (Ananas comosus). The pineapple kinome was classified into 20 groups and 116 families based on the kinase domain sequences. The RLK was the largest group, containing 480 members, and over half of them were predicted to locate at the plasma membrane. Both segmental and tandem duplications make important contributions to the expansion of pineapple kinome based on the synteny analysis. Ka/Ks ratios showed all of the duplication events were under purifying selection. The global expression analysis revealed that pineapple PKs exhibit different tissue-specific and diurnal expression patterns. Forty PK genes in a cluster performed higher expression levels in green leaf tip than in white leaf base, and fourteen of them had strong differential expression patterns between the photosynthetic green leaf tip and the non-photosynthetic white leaf base tissues. CONCLUSIONS Our findings provide insights into the evolution and biological function of pineapple PKs and a foundation for further functional analysis of PKs in CAM plants. The gene duplication, expression, and coexpression analysis helped us to rapidly identify the key candidates in pineapple kinome, which may play roles in the carbon fixation process in pineapple and help engineering CAM pathway into C3 crops for improved drought tolerance.
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Affiliation(s)
- Kaikai Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Hui Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Qunkang Cheng
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras, OR 97741 USA
| | - Zong-Ming (Max) Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
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Zhu K, Wang X, Liu J, Tang J, Cheng Q, Chen JG, Cheng ZM(M. The grapevine kinome: annotation, classification and expression patterns in developmental processes and stress responses. HORTICULTURE RESEARCH 2018; 5:19. [PMID: 29619230 PMCID: PMC5878832 DOI: 10.1038/s41438-018-0027-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 02/13/2018] [Accepted: 02/22/2018] [Indexed: 05/08/2023]
Abstract
Protein kinases (PKs) have evolved as the largest family of molecular switches that regulate protein activities associated with almost all essential cellular functions. Only a fraction of plant PKs, however, have been functionally characterized even in model plant species. In the present study, the entire grapevine kinome was identified and annotated using the most recent version of the grapevine genome. A total of 1168 PK-encoding genes were identified and classified into 20 groups and 121 families, with the RLK-Pelle group being the largest, with 872 members. The 1168 kinase genes were unevenly distributed over all 19 chromosomes, and both tandem and segmental duplications contributed to the expansion of the grapevine kinome, especially of the RLK-Pelle group. Ka/Ks values indicated that most of the tandem and segmental duplication events were under purifying selection. The grapevine kinome families exhibited different expression patterns during plant development and in response to various stress treatments, with many being coexpressed. The comprehensive annotation of grapevine kinase genes, their patterns of expression and coexpression, and the related information facilitate a more complete understanding of the roles of various grapevine kinases in growth and development, responses to abiotic stress, and evolutionary history.
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Affiliation(s)
- Kaikai Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Xiaolong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Jinyi Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Jun Tang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014 China
| | - Qunkang Cheng
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996 USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Zong-Ming (Max) Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
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13
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Pei W, Jain A, Sun Y, Zhang Z, Ai H, Liu X, Wang H, Feng B, Sun R, Zhou H, Xu G, Sun S. OsSIZ2 exerts regulatory influences on the developmental responses and phosphate homeostasis in rice. Sci Rep 2017; 7:12280. [PMID: 28947784 PMCID: PMC5612973 DOI: 10.1038/s41598-017-10274-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/20/2017] [Indexed: 01/01/2023] Open
Abstract
OsSIZ1, a small ubiquitin-related modifier (SUMO) E3 ligase, exerts regulatory influences on the developmental responses and phosphate (Pi) homeostasis in rice (Oryza sativa). Whether paralogs OsSIZ1 and OsSIZ2 are functionally redundant or the latter regulates these traits independent of the former is not known. To determine this, in this study, OsSIZ2 was functionally characterized by employing reverse genetic approaches. Although the relative expression of OsSIZ2 was spatiotemporally regulated, it showed constitutive expression in root and leaf blade irrespective of Pi regime. Analysis of T-DNA insertion knockout (ossiz2) and RNAi-mediated knockdown (Ri1-3) mutants revealed positive influences on growth and developmental responses including yield-related traits. On the contrary, these mutants exhibited negative effects on the concentrations of Pi and total P in different tissues. The relative expression levels of some of the genes that are involved in Pi sensing and signaling cascades were differentially modulated in the mutants. Further, attenuation in the expression levels of OsSIZ2 in the roots of ossiz1 and relatively similar trend of the effects of the mutation in OsSIZ1 and OsSIZ2 on growth and development and total P concentration in different tissues suggested a prevalence of partial functional redundancy between these paralogs.
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Affiliation(s)
- Wenxia Pei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Ajay Jain
- Amity Centre of Nano Biotechnology and Plant Nutrition, Kant Kalwar, NH-11C, Jaipur, 303002, India
| | - Yafei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhantian Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Hao Ai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiuli Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Huadun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China.,Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Bing Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Rui Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Hongmin Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China.
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Mathur S, Umakanth AV, Tonapi VA, Sharma R, Sharma MK. Sweet sorghum as biofuel feedstock: recent advances and available resources. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:146. [PMID: 28603553 PMCID: PMC5465577 DOI: 10.1186/s13068-017-0834-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/30/2017] [Indexed: 05/08/2023]
Abstract
Sweet sorghum is a promising target for biofuel production. It is a C4 crop with low input requirements and accumulates high levels of sugars in its stalks. However, large-scale planting on marginal lands would require improved varieties with optimized biofuel-related traits and tolerance to biotic and abiotic stresses. Considering this, many studies have been carried out to generate genetic and genomic resources for sweet sorghum. In this review, we discuss various attributes of sweet sorghum that make it an ideal candidate for biofuel feedstock, and provide an overview of genetic diversity, tools, and resources available for engineering and/or marker-assisting breeding of sweet sorghum. Finally, the progress made so far, in identification of genes/quantitative trait loci (QTLs) important for agronomic traits and ongoing molecular breeding efforts to generate improved varieties, has been discussed.
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Affiliation(s)
- Supriya Mathur
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - A. V. Umakanth
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - V. A. Tonapi
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manoj K. Sharma
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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