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Zhou S, Wu T, Li X, Wang S, Hu B. Identification of candidate genes controlling cold tolerance at the early seedling stage from Dongxiang wild rice by QTL mapping, BSA-Seq and RNA-Seq. BMC PLANT BIOLOGY 2024; 24:649. [PMID: 38977989 PMCID: PMC11232298 DOI: 10.1186/s12870-024-05369-x] [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: 10/23/2023] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
Abstract
BACKGROUND The cold tolerance of rice is closely related to its production and geographic distribution. The identification of cold tolerance-related genes is of important significance for developing cold-tolerant rice. Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) is well-adapted to the cold climate of northernmost-latitude habitats ever found in the world, and is one of the most valuable rice germplasms for cold tolerance improvement. RESULTS Transcriptome analysis revealed genes differentially expressed between Xieqingzao B (XB; a cold sensitive variety) and 19H19 (derived from an interspecific cross between DXWR and XB) in the room temperature (RT), low temperature (LT), and recovery treatments. The results demonstrated that chloroplast genes might be involved in the regulation of cold tolerance in rice. A high-resolution SNP genetic map was constructed using 120 BC5F2 lines derived from a cross between 19H19 and XB based on the genotyping-by-sequencing (GBS) technique. Two quantitative trait loci (QTLs) for cold tolerance at the early seedling stage (CTS), qCTS12 and qCTS8, were detected. Moreover, a total of 112 candidate genes associated with cold tolerance were identified based on bulked segregant analysis sequencing (BSA-seq). These candidate genes were divided into eight functional categories, and the expression trend of candidate genes related to 'oxidation-reduction process' and 'response to stress' differed between XB and 19H19 in the RT, LT and recovery treatments. Among these candidate genes, the expression level of LOC_Os12g18729 in 19H19 (related to 'response to stress') decreased in the LT treatment but restored and enhanced during the recovery treatment whereas the expression level of LOC_Os12g18729 in XB declined during recovery treatment. Additionally, XB contained a 42-bp deletion in the third exon of LOC_Os12g18729, and the genotype of BC5F2 individuals with a survival percentage (SP) lower than 15% was consistent with that of XB. Weighted gene coexpression network analysis (WGCNA) and modular regulatory network learning with per gene information (MERLIN) algorithm revealed a gene interaction/coexpression network regulating cold tolerance in rice. In the network, differentially expressed genes (DEGs) related to 'oxidation-reduction process', 'response to stress' and 'protein phosphorylation' interacted with LOC_Os12g18729. Moreover, the knockout mutant of LOC_Os12g18729 decreased cold tolerance in early rice seedling stage signifcantly compared with that of wild type. CONCLUSIONS In general, study of the genetic basis of cold tolerance of rice is important for the development of cold-tolerant rice varieties. In the present study, QTL mapping, BSA-seq and RNA-seq were integrated to identify two CTS QTLs qCTS8 and qCTS12. Furthermore, qRT-PCR, genotype sequencing and knockout analysis indicated that LOC_Os12g18729 could be the candidate gene of qCTS12. These results are expected to further exploration of the genetic mechanism of CTS in rice and improve cold tolerance of cultivated rice by introducing the cold tolerant genes from DXWR through marker-assisted selection.
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Affiliation(s)
- Shiqi Zhou
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, No. 602 Nanlian Road, Qingyunpu District, Nanchang, 330000, China
| | - Ting Wu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, No. 602 Nanlian Road, Qingyunpu District, Nanchang, 330000, China
| | - Xia Li
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, No. 602 Nanlian Road, Qingyunpu District, Nanchang, 330000, China
| | - Shilin Wang
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, No. 602 Nanlian Road, Qingyunpu District, Nanchang, 330000, China
| | - Biaolin Hu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, No. 602 Nanlian Road, Qingyunpu District, Nanchang, 330000, China.
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Tossounian MA, Zhao Y, Yu BYK, Markey SA, Malanchuk O, Zhu Y, Cain A, Gout I. Low-molecular-weight thiol transferases in redox regulation and antioxidant defence. Redox Biol 2024; 71:103094. [PMID: 38479221 PMCID: PMC10950700 DOI: 10.1016/j.redox.2024.103094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 03/24/2024] Open
Abstract
Low-molecular-weight (LMW) thiols are produced in all living cells in different forms and concentrations. Glutathione (GSH), coenzyme A (CoA), bacillithiol (BSH), mycothiol (MSH), ergothioneine (ET) and trypanothione T(SH)2 are the main LMW thiols in eukaryotes and prokaryotes. LMW thiols serve as electron donors for thiol-dependent enzymes in redox-mediated metabolic and signaling processes, protect cellular macromolecules from oxidative and xenobiotic stress, and participate in the reduction of oxidative modifications. The level and function of LMW thiols, their oxidized disulfides and mixed disulfide conjugates in cells and tissues is tightly controlled by dedicated oxidoreductases, such as peroxiredoxins, glutaredoxins, disulfide reductases and LMW thiol transferases. This review provides the first summary of the current knowledge of structural and functional diversity of transferases for LMW thiols, including GSH, BSH, MSH and T(SH)2. Their role in maintaining redox homeostasis in single-cell and multicellular organisms is discussed, focusing in particular on the conjugation of specific thiols to exogenous and endogenous electrophiles, or oxidized protein substrates. Advances in the development of new research tools, analytical methodologies, and genetic models for the analysis of known LMW thiol transferases will expand our knowledge and understanding of their function in cell growth and survival under oxidative stress, nutrient deprivation, and during the detoxification of xenobiotics and harmful metabolites. The antioxidant function of CoA has been recently discovered and the breakthrough in defining the identity and functional characteristics of CoA S-transferase(s) is soon expected.
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Affiliation(s)
- Maria-Armineh Tossounian
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Yuhan Zhao
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Bess Yi Kun Yu
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Samuel A Markey
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Oksana Malanchuk
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom; Department of Cell Signaling, Institute of Molecular Biology and Genetics, Kyiv, 143, Ukraine
| | - Yuejia Zhu
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Amanda Cain
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Ivan Gout
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom; Department of Cell Signaling, Institute of Molecular Biology and Genetics, Kyiv, 143, Ukraine.
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Shen Y, Wang G, Ran J, Li Y, Wang H, Ding Q, Li Y, Hou X. Regulation of the trade-off between cold stress and growth by glutathione S-transferase phi class 10 (BcGSTF10) in non-heading Chinese cabbage. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1887-1902. [PMID: 38079376 DOI: 10.1093/jxb/erad494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/10/2023] [Indexed: 03/28/2024]
Abstract
Cold stress is a serious threat to global crop production and food security, but plant cold resistance is accompanied by reductions in growth and yield. In this study, we determined that the novel gene BcGSTF10 in non-heading Chinese cabbage [NHCC; Brassica campestris (syn. Brassica rapa) ssp. chinensis] is implicated in resistance to cold stress. Biochemical and genetic analyses demonstrated that BcGSTF10 interacts with BcICE1 to induce C-REPEAT BINDING FACTOR (CBF) genes that enhance freezing tolerance in NHCC and in Arabidopsis. However, BcCBF2 represses BcGSTF10 and the latter promotes growth in NHCC and Arabidopsis. This dual function of BcGSTF10 indicates its pivotal role in balancing cold stress and growth, and this important understanding has the potential to inform the future development of strategies to breed crops that are both climate-resilient and high-yielding.
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Affiliation(s)
- Yunlou Shen
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangpeng Wang
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiajun Ran
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiran Li
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiyu Wang
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiang Ding
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China
- Nanjing Suman Plasma Engineering Research Institute Co., Ltd., Nanjing 211162, China
| | - Xilin Hou
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China
- Nanjing Suman Plasma Engineering Research Institute Co., Ltd., Nanjing 211162, China
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Zaman S, Shen J, Wang S, Song D, Wang H, Ding S, Pang X, Wang M, Wang Y, Ding Z. Effect of Shading on Physiological Attributes and Proteomic Analysis of Tea during Low Temperatures. PLANTS (BASEL, SWITZERLAND) 2023; 13:63. [PMID: 38202371 PMCID: PMC10780538 DOI: 10.3390/plants13010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Shading is an important technique to protect tea plantations under abiotic stresses. In this study, we analyzed the effect of shading (SD60% shade vs. SD0% no-shade) on the physiological attributes and proteomic analysis of tea leaves in November and December during low temperatures. The results revealed that shading protected the tea plants, including their soil plant analysis development (SPAD), photochemical efficiency (Fv/Fm), and nitrogen content (N), in November and December. The proteomics analysis of tea leaves was determined using tandem mass tags (TMT) technology and a total of 7263 proteins were accumulated. Further, statistical analysis and the fold change of significant proteins (FC < 0.67 and FC > 1.5 p < 0.05) revealed 14 DAPs, 11 increased and 3 decreased, in November (nCK_vs_nSD60), 20 DAPs, 7 increased and 13 decreased, in December (dCK_vs_dSD60), and 12 DAPs, 3 increased and 9 decreased, in both November and December (nCK_vs_nSD60). These differentially accumulated proteins (DAPs) were dehydrins (DHNs), late-embryogenesis abundant (LEA), thaumatin-like proteins (TLPs), glutathione S-transferase (GSTs), gibberellin-regulated proteins (GAs), proline-rich proteins (PRPs), cold and drought proteins (CORA-like), and early light-induced protein 1, which were found in the cytoplasm, nucleus, chloroplast, extra cell, and plasma membrane, and functioned in catalytic, cellular, stimulus-response, and metabolic pathways. In conclusion, the proliferation of key proteins was triggered by translation and posttranslational modifications, which might sustain membrane permeability in tea cellular compartments and could be responsible for tea protection under shading during low temperatures. This study aimed to investigate the impact of the conventional breeding technique (shading) and modern molecular technologies (proteomics) on tea plants, for the development and protection of new tea cultivars.
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Affiliation(s)
- Shah Zaman
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (S.Z.); (J.S.); (S.W.)
- School of Tea and Coffee & School of Bioinformatics and Engineering, Pu’er University, 6 Xueyuan Road, Pu’er 665000, China
- International Joint Laboratory of Digital Protection and Germplasm Innovation and Application of China-Laos Tea Tree Resources in Yunnan Province, Pu’er University, 6 Xueyuan Road, Pu’er 665000, China
| | - Jiazhi Shen
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (S.Z.); (J.S.); (S.W.)
| | - Shuangshuang Wang
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (S.Z.); (J.S.); (S.W.)
| | - Dapeng Song
- Rizhao Tea Research Institute, Rizhao 276800, China; (D.S.); (H.W.); (S.D.); (X.P.); (M.W.)
| | - Hui Wang
- Rizhao Tea Research Institute, Rizhao 276800, China; (D.S.); (H.W.); (S.D.); (X.P.); (M.W.)
| | - Shibo Ding
- Rizhao Tea Research Institute, Rizhao 276800, China; (D.S.); (H.W.); (S.D.); (X.P.); (M.W.)
| | - Xu Pang
- Rizhao Tea Research Institute, Rizhao 276800, China; (D.S.); (H.W.); (S.D.); (X.P.); (M.W.)
| | - Mengqi Wang
- Rizhao Tea Research Institute, Rizhao 276800, China; (D.S.); (H.W.); (S.D.); (X.P.); (M.W.)
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China;
| | - Zhaotang Ding
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (S.Z.); (J.S.); (S.W.)
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5
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Li J, Meng L, Ren S, Jia C, Liu R, Jiang H, Chen J. OsGSTU17, a Tau Class Glutathione S-Transferase Gene, Positively Regulates Drought Stress Tolerance in Oryza sativa. PLANTS (BASEL, SWITZERLAND) 2023; 12:3166. [PMID: 37687412 PMCID: PMC10490428 DOI: 10.3390/plants12173166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
As a great threat to the normal growth of rice, drought not only restricts the growth of rice, but also affects its yield. Glutathione S-transferases (GSTs) have antioxidant and detoxification functions. In rice, GSTs can not only effectively cope with biological stress, but also play a defense role against abiotic stress. In this study, we selected OsGSTU17, a member gene that was induced by drought, to explore the role of GSTs and analyze their physiological mechanisms that are involved in rice drought tolerance. With the CRISPR/Cas9 knockout system techniques, we obtained two independent mutant lines of osgstu17. After 14 days of drought stress treatment, and then re-supply of the water for 10 days, the survival rate of the osgstu17 mutant lines was significantly reduced compared to the wild-type (WT). Similarly, with the 10% (w/v) PEG6000 hydroponics experiment at the seedling stage, we also found that compared with the WT, the shoot and root biomass of osgstu17 mutant lines decreased significantly. In addition, both the content of the MDA and H2O2, which are toxic to plants, increased in the osgtu17 mutant lines. On the other hand, chlorophyll and proline decreased by about 20%. The activity of catalase and superoxide dismutase, which react with peroxides, also decreased by about 20%. Under drought conditions, compared with the WT, the expressions of the drought stress-related genes OsNAC10, OsDREB2A, OsAP37, OsP5CS1, OsRAB16C, OsPOX1, OsCATA, and OsCATB in the osgtu17 mutant lines were significantly decreased. Finally, we concluded that knocking out OsGSTU17 significantly reduced the drought tolerance of rice; OsGSTU17 could be used as a candidate gene for rice drought-tolerant cultivation. However, the molecular mechanism of OsGSTU17 involved in rice drought resistance needs to be further studied.
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Affiliation(s)
- Jinyan Li
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (S.R.); (C.J.)
| | - Lijun Meng
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528225, China;
| | - Shuohan Ren
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (S.R.); (C.J.)
| | - Chunying Jia
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (S.R.); (C.J.)
| | - Ruifang Liu
- The High School Affiliated to Renmin University of China, Shenzhen 518119, China;
| | - Hongzhen Jiang
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (S.R.); (C.J.)
| | - Jingguang Chen
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (S.R.); (C.J.)
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Xia C, Liang G, Chong K, Xu Y. The COG1-OsSERL2 complex senses cold to trigger signaling network for chilling tolerance in japonica rice. Nat Commun 2023; 14:3104. [PMID: 37248220 PMCID: PMC10227007 DOI: 10.1038/s41467-023-38860-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/17/2023] [Indexed: 05/31/2023] Open
Abstract
Improvement of chilling tolerance is a key strategy to face potential menace from abnormal temperature in rice production, which depends on the signaling network triggered by receptors. However, little is known about the QTL genes encoding membrane complexes for sensing cold. Here, Chilling-tolerance in Gengdao/japonica rice 1 (COG1) is isolated from a chromosome segment substitution line containing a QTL (qCS11-jap) for chilling sensitivity. The major gene COG1 is found to confer chilling tolerance in japonica rice. In natural rice populations, only the haplogroup1 encodes a functional COG1. Evolutionary analysis show that COG1 originates from Chinese O. Rufipogon and is fixed in japonica rice during domestication. COG1, a membrane-localized LRR-RLP, targets and activates the kinase OsSERL2 in a cold-induced manner, promoting chilling tolerance. Furthermore, the cold signal transmitted by COG1-OsSERL2 activates OsMAPK3 in the cytoplasm. Our findings reveal a cold-sensing complex, which mediates signaling network for the chilling defense in rice.
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Affiliation(s)
- Changxuan Xia
- The 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
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Kang Chong
- The 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.
| | - Yunyuan Xu
- The 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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Yang L, Lei L, Wang J, Zheng H, Xin W, Liu H, Zou D. qCTB7 positively regulates cold tolerance at booting stage in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:135. [PMID: 37222778 DOI: 10.1007/s00122-023-04388-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/12/2023] [Indexed: 05/25/2023]
Abstract
KEY MESSAGE LOC_Os07g07690 on qCTB7 is associated with cold tolerance at the booting stage in rice, and analysis of transgenic plants demonstrated that qCTB7 influenced cold tolerance by altering the morphology and cytoarchitecture of anthers and pollen. Cold tolerance at the booting stage (CTB) in rice can significantly affect yield in high-latitude regions. Although several CTB genes have been isolated, their ability to induce cold tolerance is insufficient to ensure adequate rice yields in cold regions at high latitudes. Here, we identified the PHD-finger domain-containing protein gene qCTB7 using QTL-seq and linkage analysis through systematic measurement of CTB differences and the spike fertility of the Longjing31 and Longdao3 cultivars, resulting in the derivation of 1570 F2 progeny under cold stress. We then characterized the function of qCTB7 in rice. It was found that overexpression of qCTB7 promoted CTB and the same yield as Longdao3 under normal growing conditions while the phenotype of qctb7 knockout showed anther and pollen failure under cold stress. When subjected to cold stress, the germination of qctb7 pollen on the stigma was reduced, resulting in lower spike fertility. These findings indicate that qCTB7 regulates the appearance, morphology, and cytoarchitecture of the anthers and pollen. Three SNPs in the promoter region and coding region of qCTB7 were identified as recognition signals for CTB in rice and could assist breeding efforts to improve cold tolerance for rice production in high latitudes.
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Affiliation(s)
- Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Lei Lei
- Institute of Crop Cultivation and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Xin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
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Usman B, Derakhshani B, Jung KH. Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2019. [PMID: 37653936 PMCID: PMC10221523 DOI: 10.3390/plants12102019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.
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Affiliation(s)
- Babar Usman
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Behnam Derakhshani
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Ki-Hong Jung
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
- Research Center for Plant Plasticity, Kyung Hee University, Yongin 17104, Republic of Korea
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Feng J, Li Z, Luo W, Liang G, Xu Y, Chong K. COG2 negatively regulates chilling tolerance through cell wall components altered in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:19. [PMID: 36680595 DOI: 10.1007/s00122-023-04261-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/10/2022] [Indexed: 06/17/2023]
Abstract
Chilling-tolerant QTL gene COG2 encoded an extensin and repressed chilling tolerance by affecting the compositions of cell wall. Rice as a major crop is susceptible to chilling stress. Chilling tolerance is a complex trait controlled by multiple quantitative trait loci (QTLs). Here, we identify a QTL gene, COG2, that negatively regulates cold tolerance at seedling stage in rice. COG2 overexpression transgenic plants are sensitive to cold, whereas knockout transgenic lines enhance chilling tolerance. Natural variation analysis shows that Hap1 is a specific haplotype in japonica/Geng rice and correlates with chilling tolerance. The SNP1 in COG2 promoter is a specific divergency and leads to the difference in the expression level of COG2 between japonica/Geng and indica/Xian cultivars. COG2 encodes a cell wall-localized extensin and affects the compositions of cell wall, including pectin and cellulose, to defense the chilling stress. The results extend the understanding of the adaptation to the environment and provide an editing target for molecular design breeding of cold tolerance in rice.
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Affiliation(s)
- Jinglei Feng
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhitao Li
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Luo
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yunyuan Xu
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Kang Chong
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100093, China.
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Khatab AA, Li J, Hu L, Yang J, Fan C, Wang L, Xie G. Global identification of quantitative trait loci and candidate genes for cold stress and chilling acclimation in rice through GWAS and RNA-seq. PLANTA 2022; 256:82. [PMID: 36103054 DOI: 10.1007/s00425-022-03995-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
Associated analysis of GWAS with RNA-seq had detected candidate genes responsible for cold stress and chilling acclimation in rice. Haplotypes of two candidate genes and geographic distribution were analyzed. To explore new candidate genes and genetic resources for cold tolerance improvement in rice, genome-wide association study (GWAS) mapping experiments with 351 rice core germplasms was performed for three traits (survival rate, shoot length and chlorophyll content) under three temperature conditions (normal temperature, cold stress and chilling acclimation), yielding a total of 134 QTLs, of which 54, 59 and 21 QTLs were responsible for normal temperature, cold stress and chilling acclimation conditions, respectively. Integrated analysis of significant SNPs in 134 QTLs further identified 116 QTLs for three temperature treatments, 53, 43 and 18 QTLs responsible for normal temperature, cold stress and chilling acclimation, respectively, and 2 QTLs were responsible for both cold stress and chilling acclimation. Matching differentially expressed genes from RNA-seq to 43 and 18 QTLs for cold stress and chilling acclimation, we identified 69 and 44 trait-associated candidate genes, respectively, to be classified into six and five groups, particularly involved in metabolisms, reactive oxygen species scavenging and hormone signaling. Interestingly, two candidate genes LOC_Os01g04814, encoding a vacuolar protein sorting-associating protein 4B, and LOC_Os01g48440, encoding glycosyltransferase family 43 protein, showed the highest expression levels under chilling acclimation. Haplotype analysis revealed that both genes had a distinctive differentiation with subpopulation. Haplotypes of both genes with more japonica accessions have higher latitude distribution and higher chilling tolerance than the chilling sensitive indica accessions. These findings reveal the new insight into the molecular mechanism and candidate genes for cold stress and chilling acclimation in rice.
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Affiliation(s)
- Ahmed Adel Khatab
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jiangyi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Chuchuan Fan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lingqiang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China.
| | - Guosheng Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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11
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Lou Q, Guo H, Li J, Han S, Khan NU, Gu Y, Zhao W, Zhang Z, Zhang H, Li Z, Li J. Cold-adaptive evolution at the reproductive stage in Geng/japonica subspecies reveals the role of OsMAPK3 and OsLEA9. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1032-1051. [PMID: 35706359 DOI: 10.1111/tpj.15870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Cold stress at the reproductive stage severely affects the production and geographic distribution of rice. The Geng/japonica subpopulation gradually developed stronger cold adaptation than the Xian/indica subpopulation during the long-term domestication of cultivated rice. However, the evolutionary path and natural alleles underlying the cold adaptability of intra-Geng subspecies remain largely unknown. Here, we identified MITOGEN-ACTIVATED PROTEIN KINASE 3 (OsMAPK3) and LATE EMBRYOGENESIS ABUNDANT PROTEIN 9 (OsLEA9) as two important regulators for the cold adaptation of Geng subspecies from a combination of transcriptome analysis and genome-wide association study. Transgenic validation showed that OsMAPK3 and OsLEA9 confer cold tolerance at the reproductive stage. Selection and evolution analysis suggested that the Geng version of OsMAPK3 (OsMAPK3Geng ) directly evolved from Chinese Oryza rufipogon III and was largely retained in high-latitude and high-altitude regions with low temperatures during domestication. Later, the functional nucleotide polymorphism (FNP-776) in the Kunmingxiaobaigu and Lijiangxiaoheigu version of the OsLEA9 (OsLEA9KL ) promoter originated from novel variation of intra-Geng was selected and predominantly retained in temperate Geng to improve the adaptation of Geng together with OsMAPK3Geng to colder climatic conditions in high-latitude areas. Breeding potential analysis suggested that pyramiding of OsMAPK3Geng and OsLEA9KL enhanced the cold tolerance of Geng and promotes the expansion of cultivated rice to colder regions. This study not only highlights the evolutionary path taken by the cold-adaptive differentiation of intra-Geng, but also provides new genetic resources for rice molecular breeding in low-temperature areas.
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Affiliation(s)
- Qijin Lou
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Haifeng Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jin Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shichen Han
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Najeeb Ullah Khan
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yunsong Gu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Weitong Zhao
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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12
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Sohrabi SS, Ismaili A, Nazarian-Firouzabadi F, Fallahi H, Hosseini SZ. Identification of key genes and molecular mechanisms associated with temperature stress in lentil. Gene 2022; 807:145952. [PMID: 34500049 DOI: 10.1016/j.gene.2021.145952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/24/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023]
Abstract
Extreme temperature is one of the serious threats to crop production in present and future scenarios of global climate changes. Lentil (Lens culinaris) is an important crop, and there is a serious lack of genetic information regarding environmental and temperature stresses responses. This study is the first report of evaluation of key genes and molecular mechanisms related to temperature stresses in lentil using the RNA sequencing technique. De novo transcriptome assembly created 44,673 contigs and differential gene expression analysis revealed 7494 differentially expressed genes between the temperature stresses and control group. Basic annotation of generated transcriptome assembly in our study led to the identification of 2765 novel transcripts that have not been identified yet in lentil genome draft v1.2. In addition, several unigenes involved in mechanisms of temperature sensing, calcium and hormone signaling and DNA-binding transcription factor activity were identified. Also, common mechanisms in response to temperature stresses, including the proline biosynthesis, the photosynthetic light reactions balancing, chaperone activity and circadian rhythms, are determined by the hub genes through the protein-protein interaction networks analysis. Deciphering the mechanisms of extreme temperature tolerance would be a new way for developing crops with enhanced plasticity against climate change. In general, this study has identified set of mechanisms and various genes related to cold and heat stresses which will be useful in better understanding of the lentil's reaction to temperature stresses.
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Affiliation(s)
- Seyed Sajad Sohrabi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Farhad Nazarian-Firouzabadi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran.
| | - Seyedeh Zahra Hosseini
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
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Li J, Zhang Z, Chong K, Xu Y. Chilling tolerance in rice: Past and present. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153576. [PMID: 34875419 DOI: 10.1016/j.jplph.2021.153576] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Rice is generally sensitive to chilling stress, which seriously affects growth and yield. Since early in the last century, considerable efforts have been made to understand the physiological and molecular mechanisms underlying the response to chilling stress and improve rice chilling tolerance. Here, we review the research trends and advances in this field. The phenotypic and biochemical changes caused by cold stress and the physiological explanations are briefly summarized. Using published data from the past 20 years, we reviewed the past progress and important techniques in the identification of quantitative trait loci (QTL), novel genes, and cellular pathways involved in rice chilling tolerance. The advent of novel technologies has significantly advanced studies of cold tolerance, and the characterization of QTLs, key genes, and molecular modules have sped up molecular design breeding for cold tolerance in rice varieties. In addition to gene function studies based on overexpression or artificially generated mutants, elucidating natural allelic variation in specific backgrounds is emerging as a novel approach for the study of cold tolerance in rice, and the superior alleles identified using this approach can directly facilitate breeding.
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Affiliation(s)
- Junhua Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Zeyong Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, 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.
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14
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Dubas E, Żur I, Moravčiková J, Fodor J, Krzewska M, Surówka E, Nowicka A, Gerši Z. Proteins, Small Peptides and Other Signaling Molecules Identified as Inconspicuous but Possibly Important Players in Microspores Reprogramming Toward Embryogenesis. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.745865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this review, we describe and integrate the latest knowledge on the signaling role of proteins and peptides in the stress-induced microspore embryogenesis (ME) in some crop plants with agricultural importance (i.e., oilseed rape, tobacco, barley, wheat, rice, triticale, rye). Based on the results received from the most advanced omix analyses, we have selected some inconspicuous but possibly important players in microspores reprogramming toward embryogenic development. We provide an overview of the roles and downstream effect of stress-related proteins (e.g., β-1,3-glucanases, chitinases) and small signaling peptides, especially cysteine—(e.g., glutathione, γ-thionins, rapid alkalinization factor, lipid transfer, phytosulfokine) and glycine-rich peptides and other proteins (e.g., fasciclin-like arabinogalactan protein) on acclimation ability of microspores and the cell wall reconstruction in a context of ME induction and haploids/doubled haploids (DHs) production. Application of these molecules, stimulating the induction and proper development of embryo-like structures and green plant regeneration, brings significant improvement of the effectiveness of DHs procedures and could result in its wider incorporation on a commercial scale. Recent advances in the design and construction of synthetic peptides–mainly cysteine-rich peptides and their derivatives–have accelerated the development of new DNA-free genome-editing techniques. These new systems are evolving incredibly fast and soon will find application in many areas of plant science and breeding.
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15
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Hu C, Huang L, Chen Y, Liu J, Wang Z, Gao B, Zhu Q, Ren C. Fumarylacetoacetate hydrolase is required for fertility in rice. PLANTA 2021; 253:122. [PMID: 34003383 DOI: 10.1007/s00425-021-03632-1] [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: 10/25/2020] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
The rice OsFAH gene functions identically to that of Arabidopsis SSCD1 encoding FAH. Loss of OsFAH causes rice sterility. Fumarylacetoacetate hydrolase (FAH) is the last enzyme in the tyrosine (Tyr) degradation pathway that is crucial for animals. By genetic analysis of the mutant of Short-day Sensitive Cell Death 1 gene encoding Arabidopsis FAH, we first found the pathway also plays a critical role in plants (Han et al., Plant Physiol 162:1956-1964, 2013). To further understand the role of the Tyr degradation pathway in plants, we investigated a biological function of the rice FAH. Firstly, the cDNA of rice FAH gene (OsFAH) was cloned and confirmed to be able to rescue the Arabidopsis Short-day Sensitive Cell Death 1 mutant defective in the FAH. Then, we identified the OsFAH T-DNA insertion mutant and generated the OsFAH RNA interference lines, and found that loss of OsFAH results in rice sterility. Furthermore, we analyzed expression of the OsFAH gene in roots, stems, leaves and young panicles at booting stage of rice and found that its transcript level was highest in young panicles and lowest in roots. In addition, the expression analysis of β-glucuronidase driven by OsFAH promoter in transgenic Arabidopsis showed that the OsFAH promoter was highly active in aerial tissues in vegetative stage, and sepals, filaments and stigma in reproductive stage. These results suggested that FAH plays an important role in rice fertility.
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Affiliation(s)
- Chao Hu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lihua Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China
| | - Yancheng Chen
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture, Hunan Rice Research Institute, Changsha, 410125, China
| | - Jinling Liu
- Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China
| | - Zhilong Wang
- Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China
| | - Bida Gao
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Qi Zhu
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Chunmei Ren
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China.
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16
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Abstract
Extensive industrial activities resulted in an increase in chromium (Cr) contamination in the environment. The toxicity of Cr severely affects plant growth and development. Cr is also recognized as a human carcinogen that enters the human body via inhalation or by consuming Cr-contaminated food products. Taking consideration of Cr enrichment in the environment and its toxic effects, US Environmental Protection Agency and Agency for Toxic Substances and Disease Registry listed Cr as a priority pollutant. In nature, Cr exists in various valence states, including Cr(III) and Cr(VI). Cr(VI) is the most toxic and persistent form in soil. Plants uptake Cr through various transporters such as phosphate and sulfate transporters. Cr exerts its effect by generating reactive oxygen species (ROS) and hampering various metabolic and physiological pathways. Studies on genetic and transcriptional regulation of plants have shown the various detoxification genes get up-regulated and confer tolerance in plants under Cr stress. In recent years, the ability of the plant to withstand Cr toxicity by accumulating Cr inside the plant has been recognized as one of the promising bioremediation methods for the Cr contaminated region. This review summarized the Cr occurrence and toxicity in plants, role of detoxification genes in Cr stress response, and various plants utilized for phytoremediation in Cr-contaminated regions.
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Tian CB, Li YY, Huang J, Chu WQ, Wang ZY, Liu H. Comparative Transcriptome and Proteome Analysis of Heat Acclimation in Predatory Mite Neoseiulus barkeri. Front Physiol 2020; 11:426. [PMID: 32411020 PMCID: PMC7201100 DOI: 10.3389/fphys.2020.00426] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 04/07/2020] [Indexed: 11/24/2022] Open
Abstract
In our previous study, we reported a high temperature adapted strain (HTAS) of the predatory mite Neoseiulus barkeri was artificially selected via a long-term heat acclimation (35°C) and frequent heat hardenings. To understand the molecular basis of heat acclimation, 'omics' analyses were performed to compare the differences between HTAS female adults to conventional strain (CS) at transcriptional and translational levels. We obtained a total of 5,374 differentially expressed genes and 500 differentially expressed proteins. Among them, 119 transcripts had concurrent transcription and translation profiles. It's conserved that some processes, such as high expression of heat shock protein (HSP) genes, involved in heat tolerance of transcriptome analyses, while many protective enzymes including glutathione S-transferase, superoxide dismutase, peroxidase, and cytochrome P450 displayed down-regulated expression. KEGG analysis mapped 4,979 and 348 differentially expressed genes and proteins, to 299 and 253 pathways, respectively. The mitogen-activated protein kinases (MAPK) signaling pathway may provide new insights for the investigation of the molecular mechanisms of heat tolerance. Correlation enriched pathways indicated that there were four pathways associated with heat acclimation involving in energy metabolism and immunity. In addition, the expression patterns of ten randomly selected genes including HSP were consistent with the transcriptome results obtained through quantitative real-time PCR. Comparisons between transcriptome and proteome results indicated the upregulation of HSPs and genes participated in ATP production, immunity and energy metabolism process. A majority of antioxidant-related genes and detoxication-related genes were down-regulated suggesting a fitness cost of heat acclimation. Our results demonstrated that heat tolerance during a long-time acclimation of N. barkeri is a fairly complicated process of physiological regulations. These findings also contribute to a better understanding of the mechanisms of thermal responses of phytoseiid mites which could provide useful information for biological control through natural enemies.
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Affiliation(s)
| | | | | | | | | | - Huai Liu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
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19
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Zhao J, Wang S, Qin J, Sun C, Liu F. The lipid transfer protein OsLTPL159 is involved in cold tolerance at the early seedling stage in rice. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:756-769. [PMID: 31469486 PMCID: PMC7004919 DOI: 10.1111/pbi.13243] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 08/03/2019] [Accepted: 08/15/2019] [Indexed: 05/11/2023]
Abstract
Nonspecific lipid transfer proteins (nsLTPs) play critical roles in plant development and response to abiotic stresses. Here, we found that a rice lipid transfer protein, OsLTPL159, was associated with cold tolerance at the early seedling stage. Overexpression of an OsLTPL159IL112 allele from the cold-tolerant introgression line IL112 in either the japonica variety Zhonghua17 (ZH17) or the indica variety Teqing background dramatically enhanced cold tolerance. In addition, down-regulation of the expression of OsLTPL159 in the japonica variety ZH17 by RNA interference (RNAi) significantly decreased cold tolerance. Further transcriptomic, physiological and histological analysis showed that the OsLTPL159IL112 allele likely enhanced the cold tolerance of rice at the early seedling stage by decreasing the toxic effect of reactive oxygen species, enhancing cellulose deposition in the cell wall and promoting osmolyte accumulation, thereby maintaining the integrity of the chloroplasts. Notably, overexpression of another allele, OsLTPL159GC2 , from the recipient parent Guichao 2 (GC2), an indica variety, did not improve cold tolerance, indicating that the variations in the OsLTPL159 coding region of GC2 might disrupt its function for cold tolerance. Further sequence comparison found that all 22 japonica varieties surveyed had an OsLTPL159 haplotype identical to IL112 and were more cold-tolerant than the surveyed indica varieties, implying that the variations in OsLTPL159 might be associated with differential cold tolerance of japonica and indica rice. Therefore, our findings suggest that the OsLTPL159 allele of japonica rice could be used to improve cold tolerance of indica rice through a molecular breeding strategy.
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Affiliation(s)
- Jie Zhao
- State Key Laboratory of Plant Physiology and BiochemistryNational Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Shanshan Wang
- State Key Laboratory of Plant Physiology and BiochemistryNational Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jingjing Qin
- State Key Laboratory of Plant Physiology and BiochemistryNational Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and BiochemistryNational Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Fengxia Liu
- State Key Laboratory of Plant Physiology and BiochemistryNational Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
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20
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Wei J, Xie W, Li R, Wang S, Qu H, Ma R, Zhou X, Jia Z. Analysis of trait heritability in functionally partitioned rice genomes. Heredity (Edinb) 2019; 124:485-498. [PMID: 31253955 DOI: 10.1038/s41437-019-0244-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 06/05/2019] [Accepted: 06/08/2019] [Indexed: 01/10/2023] Open
Abstract
Knowledge of the genetic architecture of importantly agronomical traits can speed up genetic improvement in cultivated rice (Oryza sativa L.). Many recent investigations have leveraged genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs), associated with agronomic traits in various rice populations. The reported trait-relevant SNPs appear to be arbitrarily distributed along the genome, including genic and nongenic regions. Whether the SNPs in different genomic regions play different roles in trait heritability and which region is more responsible for phenotypic variation remains opaque. We analyzed a natural rice population of 524 accessions with 3,616,597 SNPs to compare the genetic contributions of functionally distinct genomic regions for five agronomic traits, i.e., yield, heading date, plant height, grain length, and grain width. An analysis of heritability in the functionally partitioned rice genome showed that regulatory or intergenic regions account for the most trait heritability. A close look at the trait-associated SNPs (TASs) indicated that the majority of the TASs are located in nongenic regions, and the genetic effects of the TASs in nongenic regions are generally greater than those in genic regions. We further compared the predictabilities using the genetic variants from genic regions with those using nongenic regions. The results revealed that nongenic regions play a more important role than genic regions in trait heritability in rice, which is consistent with findings in humans and maize. This conclusion not only offers clues for basic research to disclose genetics behind these agronomic traits, but also provides a new perspective to facilitate genomic selection in rice.
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Affiliation(s)
- Julong Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ruidong Li
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA
| | - Shibo Wang
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA
| | - Han Qu
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA
| | - Renyuan Ma
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA.,Department of Mathematics, Bowdoin College, Brunswick, ME, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Zhenyu Jia
- Department of Botany & Plant Sciences, University of California (Riverside), Riverside, CA, USA.
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21
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Early selection of bZIP73 facilitated adaptation of japonica rice to cold climates. Nat Commun 2018; 9:3302. [PMID: 30120236 PMCID: PMC6098049 DOI: 10.1038/s41467-018-05753-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/08/2018] [Indexed: 12/17/2022] Open
Abstract
Cold stress is a major factor limiting production and geographic distribution of rice (Oryza sativa). Although the growth range of japonica subspecies has expanded northward compared to modern wild rice (O. rufipogon), the molecular basis of the adaptation remains unclear. Here we report bZIP73, a bZIP transcription factor-coding gene with only one functional polymorphism (+511 G>A) between the two subspecies japonica and indica, may have facilitated japonica adaptation to cold climates. We show the japonica version of bZIP73 (bZIP73Jap) interacts with bZIP71 and modulates ABA levels and ROS homeostasis. Evolutionary and population genetic analyses suggest bZIP73 has undergone balancing selection; the bZIP73Jap allele has firstly selected from standing variations in wild rice and likely facilitated cold climate adaptation during initial japonica domestication, while the indica allele bZIP73Ind was subsequently selected for reasons that remain unclear. Our findings reveal early selection of bZIP73Jap may have facilitated climate adaptation of primitive rice germplasms. Japonica rice can grow further north than wild or indica rice and is more tolerant of cold climates. Here, the authors show that bZIP73 likely underwent selection in the early phase of rice domestication to facilitate cold tolerance in japonica by modulating ABA and ROS homeostasis.
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Huang L, Hu C, Cai W, Zhu Q, Gao B, Zhang X, Ren C. Fumarylacetoacetate hydrolase is involved in salt stress response in Arabidopsis. PLANTA 2018; 248:499-511. [PMID: 29785518 DOI: 10.1007/s00425-018-2907-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/26/2018] [Indexed: 05/10/2023]
Abstract
Fumarylacetoacetate hydrolase participates in positive regulation of salt stress in Arabidopsis. Fumarylacetoacetate hydrolase (FAH) catalyzes the hydrolysis of fumarylacetoacetate into fumarate and acetoacetate, the final step in the Tyr degradation pathway that is essential to animals. However, the Tyr degradation pathway is not well understood in plants. Previously, we found that mutation of the SHORT-DAY SENSITIVE CELL DEATH 1 (SSCD1) gene encoding FAH in Arabidopsis causes spontaneous cell death under short day, which first indicated that the Tyr degradation pathway also plays an important role in plants. In this study, we found that the SSCD1 gene was up-regulated by salt stress, and the sscd1 mutant was hypersensitive to salt stress. However, the double mutant of SSCD1 and HOMOGENTISATE DIOXYGENASE, in which intermediates of the Tyr degradation pathway could not be produced, displayed a normal response to salt stress. Furthermore, the sscd1 mutant showed more accumulation of reactive oxygen species (ROS) and less up-regulation of some ROS-scavenging genes such as ASCORBATE PEROXIDASE 2 and COPPER/ZINC SUPEROXIDE DISMUTASE 1 compared with wild type under salt stress. In addition, SSCD1 expression was also up-regulated by H2O2, and the sscd1 mutant exhibited hypersensitivity to oxidative stress compared with wild type. Taken together, we concluded that loss of FAH in sscd1 leads to the accumulation of Tyr degradation intermediates, which impairs the up-regulation of some ROS-scavenging genes under salt stress, causing more accumulation of ROS, resulting in the hypersensitivity of sscd1 to salt stress.
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Affiliation(s)
- Lihua Huang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Chao Hu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Wei Cai
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Qi Zhu
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Bida Gao
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Xuewen Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Chunmei Ren
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China.
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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Kumar S, Trivedi PK. Glutathione S-Transferases: Role in Combating Abiotic Stresses Including Arsenic Detoxification in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:751. [PMID: 29930563 PMCID: PMC5999759 DOI: 10.3389/fpls.2018.00751] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/16/2018] [Indexed: 05/20/2023]
Abstract
Arsenic (As), naturally occurring metalloid and a potential hazardous material, is found in low concentrations in the environment and emerges from natural sources and anthropogenic activities. The presence of As in ground water, which is used for irrigation, is a matter of great concern since it affects crop productivity and contaminates food chain. In plants, As alters various metabolic pathways in cells including the interaction of substrates/enzymes with the sulfhydryl groups of proteins and the replacement of phosphate in ATP for energy. In addition, As stimulates the generation of free radicals and reactive oxygen species (ROS), resulting in oxidative stress. Glutathione S-transferases (GSTs) quench reactive molecules with the addition of glutathione (GSH) and protect the cell from oxidative damage. GSTs are a multigene family of isozymes, known to catalyze the conjugation of GSH to miscellany of electrophilic and hydrophobic substrates. GSTs have been reported to be associated with plant developmental processes and are responsive to multitude of stressors. In past, several studies suggested involvement of plant GST gene family in As response due to the requirement of sulfur and GSH in the detoxification of this toxic metalloid. This review provides updated information about the role of GSTs in abiotic and biotic stresses with an emphasis on As uptake, metabolism, and detoxification in plants. Further, the genetic manipulations that helped in enhancing the understanding of the function of GSTs in abiotic stress response and heavy metal detoxification has been reviewed.
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Comprehensive genome-wide analysis of Glutathione S-transferase gene family in potato (Solanum tuberosum L.) and their expression profiling in various anatomical tissues and perturbation conditions. Gene 2017; 639:149-162. [PMID: 28988961 DOI: 10.1016/j.gene.2017.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/29/2017] [Accepted: 10/05/2017] [Indexed: 12/20/2022]
Abstract
Glutathione S-transferases (GSTs) are ubiquitous enzymes which play versatile functions including cellular detoxification and stress tolerance. In this study, a comprehensive genome-wide identification of GST gene family was carried out in potato (Solanum tuberosum L.). The result demonstrated the presence of at least 90 GST genes in potato which is greater than any other reported species. According to the phylogenetic analyses of Arabidopsis, rice and potato GST members, GSTs could be subdivided into ten different classes and each class is found to be highly conserved. The largest class of potato GST family is tau with 66 members, followed by phi and lambda. The chromosomal localization analysis revealed the highly uneven distribution of StGST genes across the potato genome. Transcript profiling of 55 StGST genes showed the tissue-specific expression for most of the members. Moreover, expression of StGST genes were mainly repressed in response to abiotic stresses, while largely induced in response to biotic and hormonal elicitations. Further analysis of StGST gene's promoter identified the presence of various stress responsive cis-regulatory elements. Moreover, one of the highly stress responsive StGST members, StGSTU46, showed strong affinity towards flurazole with lowest binding energy of -7.6kcal/mol that could be used as antidote to protect crop against herbicides. These findings will facilitate the further functional and evolutionary characterization of GST genes in potato.
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Nianiou-Obeidat I, Madesis P, Kissoudis C, Voulgari G, Chronopoulou E, Tsaftaris A, Labrou NE. Plant glutathione transferase-mediated stress tolerance: functions and biotechnological applications. PLANT CELL REPORTS 2017; 36:791-805. [PMID: 28391528 DOI: 10.1007/s00299-017-2139-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/27/2017] [Indexed: 05/07/2023]
Abstract
Plant glutathione transferases (EC 2.5.1.18, GSTs) are an ancient, multimember and diverse enzyme class. Plant GSTs have diverse roles in plant development, endogenous metabolism, stress tolerance, and xenobiotic detoxification. Their study embodies both fundamental aspects and agricultural interest, because of their ability to confer tolerance against biotic and abiotic stresses and to detoxify herbicides. Here we review the biotechnological applications of GSTs towards developing plants that are resistant to biotic and abiotic stresses. We integrate recent discoveries, highlight, and critically discuss the underlying biochemical and molecular pathways involved. We elaborate that the functions of GSTs in abiotic and biotic stress adaptation are potentially a result of both catalytic and non-catalytic functions. These include conjugation of reactive electrophile species with glutathione and the modulation of cellular redox status, biosynthesis, binding, and transport of secondary metabolites and hormones. Their major universal functions under stress underline the potential in developing climate-resilient cultivars through a combination of molecular and conventional breeding programs. We propose that future GST engineering efforts through rational and combinatorial approaches, would lead to the design of improved isoenzymes with purpose-designed catalytic activities and novel functional properties. Concurrent GST-GSH metabolic engineering can incrementally increase the effectiveness of GST biotechnological deployment.
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Affiliation(s)
- Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, 54124, Thessaloniki, Greece.
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis Road, Thermi, P.O. Box 361, 57001, Thessaloniki, Greece
| | - Christos Kissoudis
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, 54124, Thessaloniki, Greece
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Georgia Voulgari
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, 54124, Thessaloniki, Greece
| | - Evangelia Chronopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 11855, Athens, Greece
| | - Athanasios Tsaftaris
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, 54124, Thessaloniki, Greece
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis Road, Thermi, P.O. Box 361, 57001, Thessaloniki, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 11855, Athens, Greece
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Shakiba E, Edwards JD, Jodari F, Duke SE, Baldo AM, Korniliev P, McCouch SR, Eizenga GC. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis. PLoS One 2017; 12:e0172133. [PMID: 28282385 PMCID: PMC5345765 DOI: 10.1371/journal.pone.0172133] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/31/2017] [Indexed: 01/11/2023] Open
Abstract
Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.
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Affiliation(s)
- Ehsan Shakiba
- University of Arkansas, Rice Research and Extension Center, Stuttgart, Arkansas, United States of America
| | - Jeremy D. Edwards
- USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Farman Jodari
- Rice Experiment Station (RES), Biggs, California, United States of America
| | - Sara E. Duke
- USDA/ARS Plains Area, College Station, Texas, United States of America
| | - Angela M. Baldo
- USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Pavel Korniliev
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Susan R. McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, United States of America
| | - Georgia C. Eizenga
- USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
- * E-mail:
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27
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Schläppi MR, Jackson AK, Eizenga GC, Wang A, Chu C, Shi Y, Shimoyama N, Boykin DL. Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection. FRONTIERS IN PLANT SCIENCE 2017; 8:957. [PMID: 28642772 PMCID: PMC5463297 DOI: 10.3389/fpls.2017.00957] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/22/2017] [Indexed: 05/21/2023]
Abstract
Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC) collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association study (GWAS) based quantitative trait loci (QTL) mapping. For young seedling stage indices, japonica and indica subspecies clustered into chilling tolerant and chilling sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. Indica subspecies were shown to have chilling acclimation potential. GWAS mapping uncovered 48 QTL at 39 chromosome regions distributed across all 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 18 QTL and 32 QTL were in regions discovered in previously reported bi-parental and GWAS based QTL mapping studies, respectively. Two novel low temperature seedling survivability (LTSS)-QTL, qLTSS3-4 and qLTSS4-1, were not in a previously reported QTL region. QTL with strong effect alleles identified in this study will be useful for marker assisted breeding efforts to improve chilling tolerance in rice cultivars and enhance gene discovery for chilling tolerance.
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Affiliation(s)
- Michael R. Schläppi
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
- *Correspondence: Michael R. Schläppi,
| | - Aaron K. Jackson
- Dale Bumpers National Rice Research Center, United States Department of Agriculture – Agricultural Research Service, StuttgartAR, United States
| | - Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, United States Department of Agriculture – Agricultural Research Service, StuttgartAR, United States
| | - Aiju Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yao Shi
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
| | - Naoki Shimoyama
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
| | - Debbie L. Boykin
- United States Department of Agriculture – Agricultural Research Service, StonevilleMS, United States
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28
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Dametto A, Sperotto RA, Adamski JM, Blasi ÉAR, Cargnelutti D, de Oliveira LFV, Ricachenevsky FK, Fregonezi JN, Mariath JEA, da Cruz RP, Margis R, Fett JP. Cold tolerance in rice germinating seeds revealed by deep RNAseq analysis of contrasting indica genotypes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:1-12. [PMID: 26259169 DOI: 10.1016/j.plantsci.2015.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 05/10/2023]
Abstract
Rice productivity is largely affected by low temperature, which can be harmful throughout plant development, from germination to grain filling. Germination of indica rice cultivars under cold is slow and not uniform, resulting in irregular emergence and small plant population. To identify and characterize novel genes involved in cold tolerance during the germination stage, two indica rice genotypes (sister lines previously identified as cold-tolerant and cold-sensitive) were used in parallel transcriptomic analysis (RNAseq) under cold treatment (seeds germinating at 13 °C for 7 days). We detected 1,361 differentially expressed transcripts. Differences in gene expression found by RNAseq were confirmed for 11 selected genes using RT-qPCR. Biological processes enhanced in the cold-tolerant seedlings include: cell division and expansion (confirmed by anatomical sections of germinating seeds), cell wall integrity and extensibility, water uptake and membrane transport capacity, sucrose synthesis, generation of simple sugars, unsaturation of membrane fatty acids, wax biosynthesis, antioxidant capacity (confirmed by histochemical staining of H2O2), and hormone and Ca(2+)-signaling. The cold-sensitive seedlings respond to low temperature stress increasing synthesis of HSPs and dehydrins, along with enhanced ubiquitin/proteasome protein degradation pathway and polyamine biosynthesis. Our findings can be useful in future biotechnological approaches aiming to cold tolerance in indica rice.
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Affiliation(s)
- Andressa Dametto
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro Universitário UNIVATES, Lajeado, RS, Brazil
| | - Raul A Sperotto
- Centro de Ciências Biológicas e da Saúde (CCBS), Centro Universitário UNIVATES, Lajeado, RS, Brazil; Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro Universitário UNIVATES, Lajeado, RS, Brazil.
| | - Janete M Adamski
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Édina A R Blasi
- Centro de Ciências Biológicas e da Saúde (CCBS), Centro Universitário UNIVATES, Lajeado, RS, Brazil
| | - Denise Cargnelutti
- Departamento de Agronomia, Universidade Federal da Fronteira Sul (UFFS), Erechim, RS, Brazil
| | - Luiz F V de Oliveira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Felipe K Ricachenevsky
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Jeferson N Fregonezi
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Jorge E A Mariath
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Renata P da Cruz
- Departamento de Plantas de Lavoura, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rogério Margis
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Janette P Fett
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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29
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Tripathi A, Indoliya Y, Tiwari M, Tiwari P, Srivastava D, kumar Verma P, Verma S, Gautam N, Chakrabarty D. Transformed yeast (Schizosaccharomyces pombe) overexpressing rice Tau class glutathione S-transferase (OsGSTU30 and OsGSTU41) shows enhanced resistance to hexavalent chromium. Metallomics 2014; 6:1549-57. [PMID: 24968244 DOI: 10.1039/c4mt00083h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Two Tau class GSTs that are up-regulated in rice roots upon exposure to Cr(vi), showed resistance when expressed in yeast.
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Affiliation(s)
- Ankita Tripathi
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI)
- Lucknow-226001, India
| | - Yuvraj Indoliya
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI)
- Lucknow-226001, India
- Academy of Scientific and Innovative Research (AcSIR)
- Anusandhan Bhawan
- New Delhi-110 001, India
| | - Madhu Tiwari
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI)
- Lucknow-226001, India
| | - Poonam Tiwari
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI)
- Lucknow-226001, India
| | - Dipali Srivastava
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI)
- Lucknow-226001, India
| | - Pankaj kumar Verma
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI)
- Lucknow-226001, India
| | - Shikha Verma
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI)
- Lucknow-226001, India
| | - Neelam Gautam
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI)
- Lucknow-226001, India
- Academy of Scientific and Innovative Research (AcSIR)
- Anusandhan Bhawan
- New Delhi-110 001, India
| | - Debasis Chakrabarty
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI)
- Lucknow-226001, India
- Academy of Scientific and Innovative Research (AcSIR)
- Anusandhan Bhawan
- New Delhi-110 001, India
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30
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Liu D, Liu Y, Rao J, Wang G, Li H, Ge F, Chen C. Overexpression of the glutathione S-transferase gene from Pyrus pyrifolia fruit improves tolerance to abiotic stress in transgenic tobacco plants. Mol Biol 2013. [DOI: 10.1134/s0026893313040109] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Cruz RPD, Sperotto RA, Cargnelutti D, Adamski JM, FreitasTerra T, Fett JP. Avoiding damage and achieving cold tolerance in rice plants. Food Energy Secur 2013. [DOI: 10.1002/fes3.25] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
| | - Raul Antonio Sperotto
- Centro de Ciências Biológicas e da Saúde (CCBS) Programa de Pós‐Graduação em Biotecnologia (PPGBiotec) Centro Universitário UNIVATES Lajeado Rio Grande do Sul Brazil
| | - Denise Cargnelutti
- Universidade Federal da Fronteira Sul (UFFS) Erechim Rio Grande do Sul Brazil
| | - Janete Mariza Adamski
- Departamento de Botânica Universidade Federal do Rio Grande do Sul (UFRGS) Porto Alegre Rio Grande do Sul Brazil
| | - Tatiana FreitasTerra
- Departamento de Botânica Universidade Federal do Rio Grande do Sul (UFRGS) Porto Alegre Rio Grande do Sul Brazil
| | - Janette Palma Fett
- Departamento de Botânica Universidade Federal do Rio Grande do Sul (UFRGS) Porto Alegre Rio Grande do Sul Brazil
- Centro de Biotecnologia Universidade Federal do Rio Grande do Sul (UFRGS) Porto Alegre Rio Grande do Sul Brazil
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32
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Kumar S, Asif MH, Chakrabarty D, Tripathi RD, Dubey RS, Trivedi PK. Differential Expression of Rice Lambda Class GST Gene Family Members During Plant Growth, Development, and in Response to Stress Conditions. PLANT MOLECULAR BIOLOGY REPORTER 2013; 31:569-580. [DOI: 10.1007/s11105-012-0524-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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33
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Kumar S, Asif MH, Chakrabarty D, Tripathi RD, Dubey RS, Trivedi PK. Expression of a rice Lambda class of glutathione S-transferase, OsGSTL2, in Arabidopsis provides tolerance to heavy metal and other abiotic stresses. JOURNAL OF HAZARDOUS MATERIALS 2013; 248-249:228-37. [PMID: 23380449 DOI: 10.1016/j.jhazmat.2013.01.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/12/2012] [Accepted: 01/03/2013] [Indexed: 05/04/2023]
Abstract
Global industrial growth has contaminated the soil and water with many hazardous compounds, including heavy metals. These heavy metals are not only toxic to plants but also cause severe human health hazards when leach out into food chain. One of the approaches employed for the decontamination of environment includes identification and overexpression of genes involved in the detoxification mechanism of plants. Glutathione S-transferases (GSTs) are a superfamily of enzymes, principally known for their role in detoxification reactions. Different classes of GSTs have been used to develop plants with improved detoxification mechanism, but not much information is available for Lambda class of GSTs. Here, we studied expression of OsGSTLs in different rice genotypes under arsenic stress. The study suggests differential expression of these genes in arsenic sensitive and tolerant genotypes. Further, the role of one member of Lambda class OsGSTL2 was studied by expressing in heterologous system, Arabidopsis. Transgenic lines developed were analysed for their response to different abiotic stresses including heavy metals. Analysis suggests that OsGSTL2 provides tolerance for heavy metals and other abiotic stresses like cold, osmotic stress and salt. We conclude that OsGSTLs can be utilized for developing plant varieties tolerant to different abiotic stresses including heavy metals.
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Affiliation(s)
- Smita Kumar
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
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34
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Grativol C, Hemerly AS, Ferreira PCG. Genetic and epigenetic regulation of stress responses in natural plant populations. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:176-85. [PMID: 21914492 DOI: 10.1016/j.bbagrm.2011.08.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 08/25/2011] [Accepted: 08/26/2011] [Indexed: 11/30/2022]
Abstract
Plants have developed intricate mechanisms involving gene regulatory systems to adjust to stresses. Phenotypic variation in plants under stress is classically attributed to DNA sequence variants. More recently, it was found that epigenetic modifications - DNA methylation-, chromatin- and small RNA-based mechanisms - can contribute separately or together to phenotypes by regulating gene expression in response to the stress effect. These epigenetic modifications constitute an additional layer of complexity to heritable phenotypic variation and the evolutionary potential of natural plant populations because they can affect fitness. Natural populations can show differences in performance when they are exposed to changes in environmental conditions, partly because of their genetic variation but also because of their epigenetic variation. The line between these two components is blurred because little is known about the contribution of genotypes and epigenotypes to stress tolerance in natural populations. Recent insights in this field have just begun to shed light on the behavior of genetic and epigenetic variation in natural plant populations under biotic and abiotic stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.
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Affiliation(s)
- Clícia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil
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