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Liu D, Luo S, Li Z, Liang G, Guo Y, Xu Y, Chong K. COG3 confers the chilling tolerance to mediate OsFtsH2-D1 module in rice. THE NEW PHYTOLOGIST 2024; 241:2143-2157. [PMID: 38173177 DOI: 10.1111/nph.19514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024]
Abstract
The chilling stress induced by the global climate change harms rice production, especially at seedling and booting stage, which feed half the population of the world. Although there are key quantitative trait locus genes identified in the individual stage, few genes have been reported and functioned at both stages. Utilizing chromosome segment substitution lines (CSSLs) and a combination of map-based cloning and phenotypes of the mutants and overexpression lines, we identified the major gene Chilling-tolerance in Geng/japonica rice 3 (COG3) of q chilling-tolerance at the booting and seedling stage 11 (qCTBS11) conferred chilling tolerance at both seedling and booting stages. COG3 was significantly upregulated in Nipponbare under chilling treatment compared with its expression in 93-11. The loss-of-function mutants cog3 showed a reduced chilling tolerance. On the contrary, overexpression enhanced chilling tolerance. Genome evolution and genetic analysis suggested that COG3 may have undergone strong selection in temperate japonica during domestication. COG3, a putative calmodulin-binding protein, physically interacted with OsFtsH2 at chloroplast. In cog3-1, OsFtsH2-mediated D1 degradation was impaired under chilling treatment compared with wild-type. Our results suggest that COG3 is necessary for maintaining OsFtsH2 protease activity to regulate chilling tolerance at the booting and seedling stage.
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Affiliation(s)
- Dongfeng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shengtao Luo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhitao Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guohua Liang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Zhao Y, Chen Y, Gao M, Wang Y. Alcohol dehydrogenases regulated by a MYB44 transcription factor underlie Lauraceae citral biosynthesis. PLANT PHYSIOLOGY 2024; 194:1674-1691. [PMID: 37831423 DOI: 10.1093/plphys/kiad553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023]
Abstract
Lineage-specific terpenoids have arisen throughout the evolution of land plants and are believed to play a role in interactions between plants and the environment. Species-specific gene clusters in plants have provided insight on the evolution of secondary metabolism. Lauraceae is an ecologically important plant family whose members are also of considerable economic value given their monoterpene contents. However, the gene cluster responsible for the biosynthesis of monoterpenes remains yet to be elucidated. Here, a Lauraceae-specific citral biosynthetic gene cluster (CGC) was identified and investigated using a multifaceted approach that combined phylogenetic, collinearity, and biochemical analyses. The CGC comprises MYB44 as a regulator and 2 alcohol dehydrogenases (ADHs) as modifying enzymes, which derived from species-specific tandem and proximal duplication events. Activity and substrate divergence of the ADHs has resulted in the fruit of mountain pepper (Litsea cubeba), a core Lauraceae species, consisting of more than 80% citral. In addition, MYB44 negatively regulates citral biosynthesis by directly binding to the promoters of the ADH-encoding genes. The aggregation of citral biosynthetic pathways suggests that they may form the basis of important characteristics that enhance adaptability. The findings of this study provide insights into the evolution of and the regulatory mechanisms involved in plant terpene biosynthesis.
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Affiliation(s)
- Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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Cai P, Lan Y, Gong F, Li C, Xia F, Li Y, Fang C. Identification and Molecular Characterization of the CAMTA Gene Family in Solanaceae with a Focus on the Expression Analysis of Eggplant Genes under Cold Stress. Int J Mol Sci 2024; 25:2064. [PMID: 38396743 PMCID: PMC10888690 DOI: 10.3390/ijms25042064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Calmodulin-binding transcription activator (CAMTA) is an important calmodulin-binding protein with a conserved structure in eukaryotes which is widely involved in plant stress response, growth and development, hormone signal transduction, and other biological processes. Although CAMTA genes have been identified and characterized in many plant species, a systematic and comprehensive analysis of CAMTA genes in the Solanaceae genome is performed for the first time in this study. A total of 28 CAMTA genes were identified using bioinformatics tools, and the biochemical/physicochemical properties of these proteins were investigated. CAMTA genes were categorized into three major groups according to phylogenetic analysis. Tissue-expression profiles indicated divergent spatiotemporal expression patterns of SmCAMTAs. Furthermore, transcriptome analysis of SmCAMTA genes showed that exposure to cold induced differential expression of many eggplant CAMTA genes. Yeast two-hybrid and bimolecular fluorescent complementary assays suggested an interaction between SmCAMTA2 and SmERF1, promoting the transcription of the cold key factor SmCBF2, which may be an important mechanism for plant cold resistance. In summary, our results provide essential information for further functional research on Solanaceae family genes, and possibly other plant families, in the determination of the development of plants.
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Affiliation(s)
- Peng Cai
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Yanhong Lan
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Fangyi Gong
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Chun Li
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Feng Xia
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Yifan Li
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Chao Fang
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
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Shrestha AMS, Gonzales MEM, Ong PCL, Larmande P, Lee HS, Jeung JU, Kohli A, Chebotarov D, Mauleon RP, Lee JS, McNally KL. RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci. Gigascience 2024; 13:giae013. [PMID: 38832465 PMCID: PMC11148593 DOI: 10.1093/gigascience/giae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources. RESULTS We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs. CONCLUSIONS RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf.
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Affiliation(s)
- Anish M S Shrestha
- Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, College of Computer Studies, De La Salle University, Manila 1004, Philippines
- International Rice Research Institute (IRRI), Metro Manila 1301, Philippines
| | - Mark Edward M Gonzales
- Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, College of Computer Studies, De La Salle University, Manila 1004, Philippines
| | - Phoebe Clare L Ong
- Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, College of Computer Studies, De La Salle University, Manila 1004, Philippines
| | - Pierre Larmande
- DIADE, Univ Montpellier, Cirad, IRD, 34394 Montpellier, France
| | - Hyun-Sook Lee
- National Institute of Crop Science, Wanju-gun 55365, Republic of Korea
| | - Ji-Ung Jeung
- National Institute of Crop Science, Wanju-gun 55365, Republic of Korea
| | - Ajay Kohli
- International Rice Research Institute (IRRI), Metro Manila 1301, Philippines
| | - Dmytro Chebotarov
- International Rice Research Institute (IRRI), Metro Manila 1301, Philippines
| | - Ramil P Mauleon
- International Rice Research Institute (IRRI), Metro Manila 1301, Philippines
| | - Jae-Sung Lee
- International Rice Research Institute (IRRI), Metro Manila 1301, Philippines
| | - Kenneth L McNally
- International Rice Research Institute (IRRI), Metro Manila 1301, Philippines
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Mai NTP, Nguyen LTT, Tran SG, To HTM. Genome-wide association study reveals useful QTL and genes controlling the fatty acid composition in rice bran oil using Vietnamese rice landraces. Funct Integr Genomics 2023; 23:150. [PMID: 37156920 DOI: 10.1007/s10142-023-01080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/10/2023]
Abstract
In rice (Oryza sativa L.), rice bran contains valuable nutritional constituents, such as high unsaturated fat content, tocotrienols, inositol, γ-oryzanol, and phytosterols, all of which are of nutritional and pharmaceuticals interest. There is now a rising market demand for rice bran oil, which makes research into their content and fatty acid profile an area of interest. As it is evident that lipid content has a substantial impact on the eating, cooking, and storage quality of rice, an understanding of the genetic mechanisms that determine oil content in rice is of great importance, equal to that of rice quality. Therefore, in this study, we performed a genome-wide association study on the composition and oil concentration of 161 Vietnamese rice varieties. Five categories of fatty acids in rice bran were discovered and the bran oil concentration profile in different rice accessions was identified. We also identified 229 important markers related to the fatty acid composition of bran oil, distributed mainly on chromosomes 1 and 7. Seven quantitative trait loci and five potential genes related to unsaturated fatty acid content were detected, including OsKASI, OsFAD, OsARF, OsGAPDH, and OsMADS29. These results provide insights into the genetic basis of rice bran oil composition, which is pivotal to the metabolic engineering of rice plants with desirable bran oil content through candidate genes selection.
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Affiliation(s)
- Nga T P Mai
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Linh Thi Thuy Nguyen
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Son Giang Tran
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Huong Thi Mai To
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam.
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Liu C, Tang D. Comprehensive identification and expression analysis of CAMTA gene family in Phyllostachys edulis under abiotic stress. PeerJ 2023; 11:e15358. [PMID: 37180580 PMCID: PMC10174056 DOI: 10.7717/peerj.15358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/14/2023] [Indexed: 05/16/2023] Open
Abstract
Background Calmodulin-binding transcription factor (CAMTA) is a major transcription factor regulated by calmodulin (CaM) that plays an essential role in plant growth, development and response to biotic and abiotic stresses. The CAMTA gene family has been identified in Arabidopsis thaliana, rice (Oryza sativa) and other model plants, and its gene function in moso bamboo (Phyllostachys edulis) has not been identified. Results In this study, a total of 11 CAMTA genes were identified in P. edulis genome. Conserved domain and multiplex sequence alignment analysis showed that the structure between these genes was highly similar, with all members having CG-1 domains and some members having TIG and IQ domains. Phylogenetic relationship analysis showed that the CAMTA genes were divided into five subfamilies, and gene fragment replication promoted the evolution of this gene family. Promoter analysis revealed a large number of drought stress-related cis-acting elements in PeCAMTAs, and similarly high expression of the CAMTA gene family was found in drought stress response experiments, indicating the involvement of this gene family in drought stress. Gene expression pattern according to transcriptome data revealed participation of the PeCAMTA genes in tissue development. Conclusions Our results present new findings for the P. edulis CAMTA gene family and provide partial experimental evidence for further validation of the function of PeCAMTAs.
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Affiliation(s)
- Ce Liu
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou City, Lin’an, China
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Hangzhou City, Lin’an, China
| | - Dingqin Tang
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou City, Lin’an, China
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Hangzhou City, Lin’an, China
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