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Xue G, He A, Yang H, Song L, Li H, Wu C, Ruan J. Genome-wide identification, abiotic stress, and expression analysis of PYL family in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) during grain development. BMC PLANT BIOLOGY 2024; 24:725. [PMID: 39080537 PMCID: PMC11287990 DOI: 10.1186/s12870-024-05447-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/22/2024] [Indexed: 08/03/2024]
Abstract
BACKGROUND Abscisic acid (ABA) is a plant hormone that plays an important role in plant resistance to drought, salinity, cold, and pathogens. It is also important for regulating plant growth and development. Pyrabactin resistance/pyr1-like/regulatory components of the ABA receptor (PYL/RCAR) are ABA receptor proteins in plants and the core of ABA signal transduction pathways in plant regulatory factors. At present, there are no reports on the PYL family of Tartary buckwheat. RESULTS In this study, 19 paralogous form PYL genes in buckwheat were identified at the whole-genome level and named FtPYL1-FtPYL19 according to their positions on chromosomes. We further analyzed the gene structure, conserved motifs, cis-acting elements, gene duplication, phylogenetic relationships, and expression patterns under different stress treatments and during grain development of the 19 paralogous form PYL genes in Tartary buckwheat. The FtPYL gene exhibits a single exonic gene structure for about 68.4% of the duplicated forms from the total paralogous forms. The remaining subfamilies, such as I and II, contain three exons and two exons (e.g., FtPYL19), respectively. Nineteen FtPYL genes were evenly distributed across the eight chromosomes, with at least one FtPYL gene on each chromosome. In the FtPYL gene family, there was one tandem repeat event and five gene duplication events. We investigated the gene expression levels of FtPYL gene under four abiotic stresses and different stages of grain development. Under drought stress (PEG6000), the relative expression levels of FtPYL14 and FtPYL15 increased by fourfold. Under high temperature stress (38℃), the relative expression level of FtPYL16 dropped to 0.12, and that of FtPYL17 fell to 0.22. At different stages of grain development, the gene expression level of FtPY15 is extremely high at 19 D. The relative expression level of FtPYL7 in roots and stems reaches up to approximately 450, and the relative expression level of FtPYL10 in 13 D also reaches up to 248. In this study, the PYL gene family of Tartary buckwheat was identified and analyzed based on the whole genome, and 19 paralogous form FtPYL genes of Tartary buckwheat were bioinformatically analyzed. The expression patterns of 19 paralogous form FtPYL genes in Tartary buckwheat cultivars under different stress treatments and during grain development were analyzed. It was found that the FtPYL gene played an important role in grain development.
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Affiliation(s)
- Guoxing Xue
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Ailing He
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Haizhu Yang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Lincao Song
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Huan Li
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Chengpeng Wu
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China.
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Huang Z, Huang P, Chen S, Hu M, Yu H, Guo H, Shahid MQ, Liu X, Wu J. Comparative Cytological and Gene Expression Analysis Reveals That a Common Wild Rice Inbred Line Showed Stronger Drought Tolerance Compared with the Cultivar Rice. Int J Mol Sci 2024; 25:7134. [PMID: 39000241 PMCID: PMC11241580 DOI: 10.3390/ijms25137134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Common wild rice (Oryza rufipogon Griff.) is an important germplasm resource containing valuable genes. Our previous analysis reported a stable wild rice inbred line, Huaye3, which derives from the common wild rice of Guangdong Province. However, there was no information about its drought tolerance ability. Here, we assessed the germination characteristics and seedling growth between the Dawennuo and Huaye3 under five concentrations of PEG6000 treatment (0, 5%, 10%, 15%, and 20%). Huaye3 showed a stronger drought tolerance ability, and its seed germination rate still reached more than 52.50% compared with Dawennuo, which was only 25.83% under the 20% PEG6000 treatment. Cytological observations between the Dawennuo and Huaye3 indicated the root tip elongation zone and buds of Huaye3 were less affected by the PEG6000 treatment, resulting in a lower percentage of abnormalities of cortical cells, stele, and shrinkage of epidermal cells. Using the re-sequencing analysis, we detected 13,909 genes that existed in the genetic variation compared with Dawennuo. Of these genes, 39 were annotated as drought stress-related genes and their variance existed in the CDS region. Our study proved the strong drought stress tolerance ability of Huaye3, which provides the theoretical basis for the drought resistance germplasm selection in rice.
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Affiliation(s)
- Zijuan Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (P.H.); (S.C.); (M.H.); (H.Y.); (H.G.); (M.Q.S.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Peishan Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (P.H.); (S.C.); (M.H.); (H.Y.); (H.G.); (M.Q.S.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Shihui Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (P.H.); (S.C.); (M.H.); (H.Y.); (H.G.); (M.Q.S.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Mengzhu Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (P.H.); (S.C.); (M.H.); (H.Y.); (H.G.); (M.Q.S.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (P.H.); (S.C.); (M.H.); (H.Y.); (H.G.); (M.Q.S.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Haibin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (P.H.); (S.C.); (M.H.); (H.Y.); (H.G.); (M.Q.S.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (P.H.); (S.C.); (M.H.); (H.Y.); (H.G.); (M.Q.S.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (P.H.); (S.C.); (M.H.); (H.Y.); (H.G.); (M.Q.S.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (P.H.); (S.C.); (M.H.); (H.Y.); (H.G.); (M.Q.S.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Zhai Z, Ao Q, Yang L, Lu F, Cheng H, Fang Q, Li C, Chen Q, Yan J, Wei Y, Jiang YQ, Yang B. Rapeseed PP2C37 Interacts with PYR/PYL Abscisic Acid Receptors and Negatively Regulates Drought Tolerance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12445-12458. [PMID: 38771652 DOI: 10.1021/acs.jafc.4c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Global water deficit is a severe abiotic stress threatening the yielding and quality of crops. Abscisic acid (ABA) is a phytohormone that mediates drought tolerance. Protein kinases and phosphatases function as molecular switches in eukaryotes. Protein phosphatases type 2C (PP2Cs) are a major family that play essential roles in ABA signaling and stress responses. However, the role and underlying mechanism of PP2C in rapeseed (Brassica napus L.) mediating drought response has not been reported yet. Here, we characterized a PP2C family member, BnaPP2C37, and its expression level was highly induced by ABA and dehydration treatments. It negatively regulates drought tolerance in rapeseed. We further identified that BnaPP2C37 interacted with multiple PYR/PYL receptors and a drought regulator BnaCPK5 (calcium-dependent protein kinase 5) through yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Specifically, BnaPYL1 and BnaPYL9 repress BnaPP2C37 phosphatase activity. Moreover, the pull-down assay and phosphatase assays show BnaPP2C37 interacts with BnaCPK5 to dephosphorylate BnaCPK5 and its downstream BnaABF3. Furthermore, a dual-luciferase assay revealed BnaPP2C37 transcript level was enhanced by BnaABF3 and BnaABF4, forming a negative feedback regulation to ABA response. In summary, we identified that BnaPP2C37 functions negatively in drought tolerance of rapeseed, and its phosphatase activity is repressed by BnaPYL1/9 whereas its transcriptional level is upregulated by BnaABF3/4.
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Affiliation(s)
- Zengkang Zhai
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Qianqian Ao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Liuqing Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Fangxiao Lu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Haokun Cheng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Qinxin Fang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Chun Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Qinqin Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jingli Yan
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, Henan Province, People's Republic of China
| | - Yongsheng Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yuan-Qing Jiang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Bo Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
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Liu M, Liu Y, Hu W, Yin B, Liang B, Li Z, Zhang X, Xu J, Zhou S. Transcriptome and metabolome analyses reveal the regulatory role of MdPYL9 in drought resistance in apple. BMC PLANT BIOLOGY 2024; 24:452. [PMID: 38789915 PMCID: PMC11118111 DOI: 10.1186/s12870-024-05146-w] [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: 02/25/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND The mechanisms by which the apple MdPYL9 gene mediates the response to drought stress remain unclear. Here, transcriptome and metabolome analyses of apple plants under drought were used to investigate the mechanisms by which MdPYL9 regulates the response to drought stress in apple. MdPYL9-overexpressed transgenic and non-transgenic apple histoculture seedlings were rooted, transplanted, and subjected to drought treatments to clarify the mechanisms underlying the responses of apples to drought stress through phenotypic observations, physiological and biochemical index measurements, and transcriptomic and metabolomic analyses. RESULTS Under drought stress treatment, transgenic plants were less affected by drought stress than non-transgenic plants. Decreases in the net photosynthetic rate, stomatal conductance, and transpiration rate of transgenic apple plants were less pronounced in transgenic plants than in non-transgenic plants, and increases in the intercellular CO2 concentration were less pronounced in transgenic plants than in non-transgenic plants. The relative electrical conductivity and content of malondialdehyde, superoxide anion, and hydrogen peroxide were significantly lower in transgenic plants than in non-transgenic plants, and the chlorophyll content and activities of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) were significantly higher in transgenic plants than in non-transgenic plants. The number of differentially expressed genes (DEGs) involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and the most significant and highly annotated DEGs in the transgenic plants were involved in the flavonoid biosynthesis pathway, and the most significant and highly annotated DEGs in control plants were involved in the phytohormone signal transduction pathway. The number of differentially accumulated metabolites involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and up-regulated metabolites were significantly enriched in apigenin-7-O-glucoside in transgenic plants and in abscisic acid in non-transgenic plants. In the flavonoid biosynthetic pathway, the expression of genes encoding chalcone synthase (CHS) and chalcone isomerase (CHI) was more significantly down-regulated in non-transgenic plants than in transgenic plants, and the expression of the gene encoding 4-coumarate-CoA ligase (4CL) was more significantly up-regulated in transgenic plants than in non-transgenic plants, which resulted in the significant up-regulation of apigenin-7-O-glucoside in transgenic plants. CONCLUSIONS The above results indicated that the over-expression of MdPYL9 increased the drought resistance of plants under drought stress by attenuating the down-regulation of the expression of genes encoding CHS and CHI and enhancing the up-regulated expression of the gene encoding 4CL, which enhanced the content of apigenin-7-O-glucoside.
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Affiliation(s)
- Mingxiao Liu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Yitong Liu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Wei Hu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Baoying Yin
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Bowen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Zhongyong Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Xueying Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Jizhong Xu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Shasha Zhou
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China.
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Li C, He YQ, Yu J, Kong JR, Ruan CC, Yang ZK, Zhuang JJ, Wang YX, Xu JH. The rice LATE ELONGATED HYPOCOTYL enhances salt tolerance by regulating Na +/K + homeostasis and ABA signalling. PLANT, CELL & ENVIRONMENT 2024; 47:1625-1639. [PMID: 38282386 DOI: 10.1111/pce.14835] [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: 08/01/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 01/30/2024]
Abstract
The circadian clock plays multiple functions in the regulation of plant growth, development and response to various abiotic stress. Here, we showed that the core oscillator component late elongated hypocotyl (LHY) was involved in rice response to salt stress. The mutations of OsLHY gene led to reduced salt tolerance in rice. Transcriptomic analyses revealed that the OsLHY gene regulates the expression of genes related to ion homeostasis and the abscisic acid (ABA) signalling pathway, including genes encoded High-affinity K+ transporters (OsHKTs) and the stress-activated protein kinases (OsSAPKs). We demonstrated that OsLHY directly binds the promoters of OsHKT1;1, OsHKT1;4 and OsSAPK9 to regulate their expression. Moreover, the ossapk9 mutants exhibited salt tolerance under salt stress. Taken together, our findings revealed that OsLHY integrates ion homeostasis and the ABA pathway to regulate salt tolerance in rice, providing insights into our understanding of how the circadian clock controls rice response to salt stress.
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Affiliation(s)
- Chao Li
- Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong, China
| | - Yi-Qin He
- Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Sanya, China
| | - Jie Yu
- Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Sanya, China
| | - Jia-Rui Kong
- Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Cheng-Cheng Ruan
- Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhen-Kun Yang
- Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Sanya, China
| | - Jun-Jie Zhuang
- Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Yu-Xiao Wang
- Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Sanya, China
| | - Jian-Hong Xu
- Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong, China
- Hainan Institute, Zhejiang University, Sanya, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Sanya, China
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Kim JS, Kidokoro S, Yamaguchi-Shinozaki K, Shinozaki K. Regulatory networks in plant responses to drought and cold stress. PLANT PHYSIOLOGY 2024; 195:170-189. [PMID: 38514098 PMCID: PMC11060690 DOI: 10.1093/plphys/kiae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
Drought and cold represent distinct types of abiotic stress, each initiating unique primary signaling pathways in response to dehydration and temperature changes, respectively. However, a convergence at the gene regulatory level is observed where a common set of stress-responsive genes is activated to mitigate the impacts of both stresses. In this review, we explore these intricate regulatory networks, illustrating how plants coordinate distinct stress signals into a collective transcriptional strategy. We delve into the molecular mechanisms of stress perception, stress signaling, and the activation of gene regulatory pathways, with a focus on insights gained from model species. By elucidating both the shared and distinct aspects of plant responses to drought and cold, we provide insight into the adaptive strategies of plants, paving the way for the engineering of stress-resilient crop varieties that can withstand a changing climate.
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Affiliation(s)
- June-Sik Kim
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045Japan
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046Japan
| | - Satoshi Kidokoro
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8502Japan
| | - Kazuko Yamaguchi-Shinozaki
- Research Institute for Agriculture and Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502Japan
- Graduate School of Agriculture and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045Japan
- Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601Japan
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Zhang D, Zhao R, Xian G, Kou Y, Ma W. A new model construction based on the knowledge graph for mining elite polyphenotype genes in crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1361716. [PMID: 38571713 PMCID: PMC10987776 DOI: 10.3389/fpls.2024.1361716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Identifying polyphenotype genes that simultaneously regulate important agronomic traits (e.g., plant height, yield, and disease resistance) is critical for developing novel high-quality crop varieties. Predicting the associations between genes and traits requires the organization and analysis of multi-dimensional scientific data. The existing methods for establishing the relationships between genomic data and phenotypic data can only elucidate the associations between genes and individual traits. However, there are relatively few methods for detecting elite polyphenotype genes. In this study, a knowledge graph for traits regulating-genes was constructed by collecting data from the PubMed database and eight other databases related to the staple food crops rice, maize, and wheat as well as the model plant Arabidopsis thaliana. On the basis of the knowledge graph, a model for predicting traits regulating-genes was constructed by combining the data attributes of the gene nodes and the topological relationship attributes of the gene nodes. Additionally, a scoring method for predicting the genes regulating specific traits was developed to screen for elite polyphenotype genes. A total of 125,591 nodes and 547,224 semantic relationships were included in the knowledge graph. The accuracy of the knowledge graph-based model for predicting traits regulating-genes was 0.89, the precision rate was 0.91, the recall rate was 0.96, and the F1 value was 0.94. Moreover, 4,447 polyphenotype genes for 31 trait combinations were identified, among which the rice polyphenotype gene IPA1 and the A. thaliana polyphenotype gene CUC2 were verified via a literature search. Furthermore, the wheat gene TraesCS5A02G275900 was revealed as a potential polyphenotype gene that will need to be further characterized. Meanwhile, the result of venn diagram analysis between the polyphenotype gene datasets (consists of genes that are predicted by our model) and the transcriptome gene datasets (consists of genes that were differential expression in response to disease, drought or salt) showed approximately 70% and 54% polyphenotype genes were identified in the transcriptome datasets of Arabidopsis and rice, respectively. The application of the model driven by knowledge graph for predicting traits regulating-genes represents a novel method for detecting elite polyphenotype genes.
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Affiliation(s)
- Dandan Zhang
- Agricultural Information Institute of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruixue Zhao
- Agricultural Information Institute of Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agricultural Integration Publishing Knowledge Mining and Knowledge Service, National Press and Publication Administration, Beijing, China
| | - Guojian Xian
- Agricultural Information Institute of Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agricultural Big Data, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yuantao Kou
- Agricultural Information Institute of Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agricultural Integration Publishing Knowledge Mining and Knowledge Service, National Press and Publication Administration, Beijing, China
| | - Weilu Ma
- Agricultural Information Institute of Chinese Academy of Agricultural Sciences, Beijing, China
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Wang Z, Zhou J, Zou J, Yang J, Chen W. Characterization of PYL gene family and identification of HaPYL genes response to drought and salt stress in sunflower. PeerJ 2024; 12:e16831. [PMID: 38464756 PMCID: PMC10924776 DOI: 10.7717/peerj.16831] [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: 07/03/2023] [Accepted: 01/04/2024] [Indexed: 03/12/2024] Open
Abstract
In the context of global climate change, drought and soil salinity are some of the most devastating abiotic stresses affecting agriculture today. PYL proteins are essential components of abscisic acid (ABA) signaling and play critical roles in responding to abiotic stressors, including drought and salt stress. Although PYL genes have been studied in many species, their roles in responding to abiotic stress are still unclear in the sunflower. In this study, 19 HaPYL genes, distributed on 15 of 17 chromosomes, were identified in the sunflower. Fragment duplication is the main cause of the expansion of PYL genes in the sunflower genome. Based on phylogenetic analysis, HaPYL genes were divided into three subfamilies. Members in the same subfamily share similar protein motifs and gene exon-intron structures, except for the second subfamily. Tissue expression patterns suggested that HaPYLs serve different functions when responding to developmental and environmental signals in the sunflower. Exogenous ABA treatment showed that most HaPYLs respond to an increase in the ABA level. Among these HaPYLs, HaPYL2a, HaPYL4d, HaPYL4g, HaPYL8a, HaPYL8b, HaPYL8c, HaPYL9b, and HaPYL9c were up-regulated with PEG6000 treatment and NaCl treatment. This indicates that they may play a role in resisting drought and salt stress in the sunflower by mediating ABA signaling. Our findings provide some clues to further explore the functions of PYL genes in the sunflower, especially with regards to drought and salt stress resistance.
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Affiliation(s)
- Zhaoping Wang
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Jiayan Zhou
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Jian Zou
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Jun Yang
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Weiying Chen
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
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9
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Sun Y, Zhao N, Sun H, Xu S, Lu Y, Xi H, Guo Z, Shi H. Transcriptome Profiling Reveals Molecular Responses to Salt Stress in Common Vetch ( Vicia sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:714. [PMID: 38475559 DOI: 10.3390/plants13050714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Common vetch (Vicia sativa L.) is an important annual diploid leguminous forage. In the present study, transcriptomic profiling in common vetch in response to salt stress was conducted using a salt-tolerant line (460) and a salt-sensitive line (429). The common responses in common vetch and the specific responses associated with salt tolerance in 460 were analyzed. Several KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, including plant hormone and MAPK (mitogen-activated protein kinase) signaling, galactose metabolism, and phenylpropanoid phenylpropane biosynthesis, were enriched in both lines, though some differentially expressed genes (DEGs) showed distinct expression patterns. The roots in 460 showed higher levels of lignin than in 429. α-linolenic acid metabolism, carotenoid biosynthesis, the photosynthesis-antenna pathway, and starch and sucrose metabolism pathways were specifically enriched in salt-tolerant line 460, with higher levels of accumulated soluble sugars in the leaves. In addition, higher transcript levels of genes involved in ion homeostasis and reactive oxygen species (ROS) scavenging were observed in 460 than in 429 in response to salt stress. The transcriptomic analysis in common vetch in response to salt stress provides useful clues for further investigations on salt tolerance mechanism in the future.
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Affiliation(s)
- Yanmei Sun
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Na Zhao
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongjian Sun
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Shan Xu
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiwen Lu
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Haojie Xi
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenfei Guo
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Haifan Shi
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
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10
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Li P, Wang Z, Wang X, Liu F, Wang H. Changes in Phytohormones and Transcriptomic Reprogramming in Strawberry Leaves under Different Light Qualities. Int J Mol Sci 2024; 25:2765. [PMID: 38474012 DOI: 10.3390/ijms25052765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Strawberry plants require light for growth, but the frequent occurrence of low-light weather in winter can lead to a decrease in the photosynthetic rate (Pn) of strawberry plants. Light-emitting diode (LED) systems could be used to increase Pn. However, the changes in the phytohormones and transcriptomic reprogramming in strawberry leaves under different light qualities are still unclear. In this study, we treated strawberry plants with sunlight, sunlight covered with a 50% sunshade net, no light, blue light (460 nm), red light (660 nm), and a 50% red/50% blue LED light combination for 3 days and 7 days. Our results revealed that the light quality has an effect on the contents of Chl a and Chl b, the minimal fluorescence (F0), and the Pn of strawberry plants. The light quality also affected the contents of abscisic acid (ABA), auxin (IAA), trans-zeatin-riboside (tZ), jasmonic acid (JA), and salicylic acid (SA). RNA sequencing (RNA-seq) revealed that differentially expressed genes (DEGs) are significantly enriched in photosynthesis antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolisms, carotenoid biosynthesis, tryptophan metabolism, phenylalanine metabolism, zeatin biosynthesis, and linolenic acid metabolism. We then selected the key DEGs based on the results of a weighted gene co-expression network analysis (WGCNA) and drew nine metabolic heatmaps and protein-protein interaction networks to map light regulation.
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Affiliation(s)
- Peng Li
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Zhiqiang Wang
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Xiaodi Wang
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Fengzhi Liu
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Haibo Wang
- Institute of Pomology of CAAS, Xingcheng 125100, China
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11
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Geng A, Lian W, Wang Y, Liu M, Zhang Y, Wang X, Chen G. Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice. Int J Mol Sci 2024; 25:1185. [PMID: 38256261 PMCID: PMC10817035 DOI: 10.3390/ijms25021185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.
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Affiliation(s)
- Anjing Geng
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Wenli Lian
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yihan Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Minghao Liu
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yue Zhang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Guang Chen
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
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12
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Tayade R, Imran M, Ghimire A, Khan W, Nabi RBS, Kim Y. Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1195210. [PMID: 38034572 PMCID: PMC10684784 DOI: 10.3389/fpls.2023.1195210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
Soybean (Glycine max L. Merr.) is a crucial oilseed cash crop grown worldwide and consumed as oil, protein, and food by humans and feed by animals. Comparatively, soybean seed yield is lower than cereal crops, such as maize, rice, and wheat, and the demand for soybean production does not keep up with the increasing consumption level. Therefore, increasing soybean yield per unit area is the most crucial breeding objective and is challenging for the scientific community. Moreover, yield and associated traits are extensively researched in cereal crops, but little is known about soybeans' genetics, genomics, and molecular regulation of yield traits. Soybean seed yield is a complex quantitative trait governed by multiple genes. Understanding the genetic and molecular processes governing closely related attributes to seed yield is crucial to increasing soybean yield. Advances in sequencing technologies have made it possible to conduct functional genomic research to understand yield traits' genetic and molecular underpinnings. Here, we provide an overview of recent progress in the genetic regulation of seed size in soybean, molecular, genetics, and genomic bases of yield, and related key seed yield traits. In addition, phytohormones, such as auxin, gibberellins, cytokinins, and abscisic acid, regulate seed size and yield. Hence, we also highlight the implications of these factors, challenges in soybean yield, and seed trait improvement. The information reviewed in this study will help expand the knowledge base and may provide the way forward for developing high-yielding soybean cultivars for future food demands.
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Affiliation(s)
- Rupesh Tayade
- Upland Field Machinery Research Center, Kyungpook National University, Daegu, Republic of Korea
| | - Muhammad Imran
- Division of Biosafety, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Jeollabul-do, Republic of Korea
| | - Amit Ghimire
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Waleed Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Rizwana Begum Syed Nabi
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Yoonha Kim
- Upland Field Machinery Research Center, Kyungpook National University, Daegu, Republic of Korea
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
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13
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Liao Z, Zhang Y, Yu Q, Fang W, Chen M, Li T, Liu Y, Liu Z, Chen L, Yu S, Xia H, Xue HW, Yu H, Luo L. Coordination of growth and drought responses by GA-ABA signaling in rice. THE NEW PHYTOLOGIST 2023; 240:1149-1161. [PMID: 37602953 DOI: 10.1111/nph.19209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/26/2023] [Indexed: 08/22/2023]
Abstract
The drought caused by global warming seriously affects the crop growth and agricultural production. Plants have evolved distinct strategies to cope with the drought environment. Under drought stress, energy and resources should be diverted from growth toward stress management. However, the molecular mechanism underlying coordination of growth and drought response remains largely elusive. Here, we discovered that most of the gibberellin (GA) metabolic genes were regulated by water scarcity in rice, leading to the lower GA contents and hence inhibited plant growth. Low GA contents resulted in the accumulation of more GA signaling negative regulator SLENDER RICE 1, which inhibited the degradation of abscisic acid (ABA) receptor PYL10 by competitively binding to the co-activator of anaphase-promoting complex TAD1, resulting in the enhanced ABA response and drought tolerance. These results elucidate the synergistic regulation of crop growth inhibition and promotion of drought tolerance and survival, and provide useful genetic resource in breeding improvement of crop drought resistance.
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Affiliation(s)
- Zhigang Liao
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Yunchao Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Qing Yu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weicong Fang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meiyao Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tianfei Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Yi Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Zaochang Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Liang Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Shunwu Yu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Hui Xia
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Hong-Wei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lijun Luo
- Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
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14
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Mi W, Liu K, Liang G, Jia Z, Ma X, Ju Z, Liu W. Genome-wide identification and characterization of ABA receptor pyrabactin resistance 1-like protein (PYL) family in oat. PeerJ 2023; 11:e16181. [PMID: 37810776 PMCID: PMC10552766 DOI: 10.7717/peerj.16181] [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: 04/14/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
Abscisic acid (ABA) is a phytohormone that plays an important role in plant growth and development. Meanwhile, ABA also plays a key role in the plant response to abiotic stressors such as drought and high salinity. The pyrabactin resistance 1-like (PYR/PYL) protein family of ABA receptors is involved in the initial step of ABA signal transduction. However, no systematic studies of the PYL family in "Avena sativa, a genus Avena in the grass family Poaceae," have been conducted to date. Thus, in this study, we performed a genome-wide screening to identify PYL genes in oat and characterized their responses to drought stress. A total of 12 AsPYL genes distributed on nine chromosomes were identified. The phylogenetic analysis divided these AsPYLs into three subfamilies, based on structural and functional similarities. Gene and motif structure analysis of AsPYLs revealed that members of each subfamily share similar gene and motif structure. Segmental duplication appears to be the driving force for the expansion of PYLs, Furthermore, stress-responsive AsPYLs were detected through RNA-seq analysis. The qRT-PCR analysis of 10 AsPYL genes under drought, salt, and ABA stress revealed that AsPYL genes play an important role in stress response. These data provide a reference for further studies on the oat PYL gene family and its function.
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Affiliation(s)
- Wenbo Mi
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Kaiqiang Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Guoling Liang
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Zhifeng Jia
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Xiang Ma
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Zeliang Ju
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
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15
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Long Q, Qiu S, Man J, Ren D, Xu N, Luo R. OsAAI1 Increases Rice Yield and Drought Tolerance Dependent on ABA-Mediated Regulatory and ROS Scavenging Pathway. RICE (NEW YORK, N.Y.) 2023; 16:35. [PMID: 37535208 PMCID: PMC10400514 DOI: 10.1186/s12284-023-00650-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/22/2023] [Indexed: 08/04/2023]
Abstract
In this study, we investigated the function of OsAAI1 in yield and drought tolerance by constructing overexpression line OE-OsAAI1 and mutant line osaai1. Bioinformatics analysis showed that the AAI gene-OsAAI1- belongs to the HPS_like subfamily of the AAI_LTSS superfamily, and OsAAI1 was localized in the nucleus. The expression of OsAAI1 was significantly induced by ABA and drought stress. OsAAI1 overexpression (OE19) significantly increased, and gene mutant (osaai1-1) repressed plant height, primary root length, lateral root number, grain size and yield in rice. Moreover, physiological and biochemical analyses showed that osaai1 was sensitive to drought stress, while OE19 enhanced the drought tolerance in rice. DAB and NBT staining revealed that under drought treatment, osaai1 accumulated a large amount of ROS compared with the wild type, while OE19 accumulated the least, and CAT, APX, GPX, GR activities were higher in OE19 and lower in osaai1, suggesting that OE19 improves rice tolerance to drought stress by enhancing ROS scavenging ability. OE19 also induce the expression of ABA-mediated regulatory pathway genes and enhance accumulation of ABA content in rice seedling. Predictably, OE19 displayed enhanced sensitivity to ABA, and ROS accumulation was significantly higher than in wild type and osaai1 under 3 µM ABA treatment. Thus, these results suggest that OsAAI1 is a positive regulator of rice yield and drought tolerance dependent on the ABA-mediated regulatory and ROS scavenging pathway.
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Affiliation(s)
- Qing Long
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Shichun Qiu
- Chongqing Three Gorges Academy of Agricultural Sciences, Wanzhou, Chongqing City, 404155, China
| | - Jianmin Man
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Denghong Ren
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Ning Xu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Rui Luo
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China.
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16
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Zhang L, Song W, Xin G, Zhu M, Meng X. Comparative Analysis of the PYL Gene Family in Three Ipomoea Species and the Expression Profiling of IbPYL Genes during Abiotic Stress Response in Sweetpotato. Genes (Basel) 2023; 14:1471. [PMID: 37510375 PMCID: PMC10379866 DOI: 10.3390/genes14071471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Abscisic acid (ABA), a critical phytohormone that regulates plant development and stress response, is sensed by the ABA receptors PYR/PYL/RCAR (PYLs). The PYL genes have been widely studied in multiple plant species, while a systematic analysis of PYL genes in the genus Ipomoea remains unperformed. Here, a total of 13, 14, and 14 PYLs were identified in Ipomoea batatas, Ipomoea trifida, and Ipomoea triloba, respectively. Fragment duplication was speculated to play prominent roles in Ipomoea PYL gene expansions. These Ipomoea PYLs were classified into three subfamilies via phylogenetic analysis, which was supported by exon-intron structures and conserved motif analyses. Additionally, the interspecies collinearity analysis further depicted a potential evolutionary relationship between them. Moreover, qRT-PCR analysis showed that multiple IbPYLs are highly and differentially responsive to abiotic stress treatments, suggesting their potential roles in sweetpotato stress responses. Taken together, these data provide valuable insights into the PYLs in the genus Ipomoea, which may be useful for their further functional analysis of their defense against environmental changes.
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Affiliation(s)
- Lei Zhang
- Yantai Academy of Agricultural Sciences, Yantai 261417, China
| | - Weihan Song
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou 221131, China
| | - Guosheng Xin
- Yantai Academy of Agricultural Sciences, Yantai 261417, China
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Xiaoqing Meng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
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17
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Hassan MA, Dahu N, Hongning T, Qian Z, Yueming Y, Yiru L, Shimei W. Drought stress in rice: morpho-physiological and molecular responses and marker-assisted breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1215371. [PMID: 37534289 PMCID: PMC10391551 DOI: 10.3389/fpls.2023.1215371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023]
Abstract
Rice (Oryza Sativa L.) is an essential constituent of the global food chain. Drought stress significantly diminished its productivity and threatened global food security. This review concisely discussed how drought stress negatively influenced the rice's optimal growth cycle and altered its morpho-physiological, biochemical, and molecular responses. To withstand adverse drought conditions, plants activate their inherent drought resistance mechanism (escape, avoidance, tolerance, and recovery). Drought acclimation response is characterized by many notable responses, including redox homeostasis, osmotic modifications, balanced water relations, and restored metabolic activity. Drought tolerance is a complicated phenomenon, and conventional breeding strategies have only shown limited success. The application of molecular markers is a pragmatic technique to accelerate the ongoing breeding process, known as marker-assisted breeding. This review study compiled information about quantitative trait loci (QTLs) and genes associated with agronomic yield-related traits (grain size, grain yield, harvest index, etc.) under drought stress. It emphasized the significance of modern breeding techniques and marker-assisted selection (MAS) tools for introgressing the known QTLs/genes into elite rice lines to develop drought-tolerant rice varieties. Hence, this study will provide a solid foundation for understanding the complex phenomenon of drought stress and its utilization in future crop development programs. Though modern genetic markers are expensive, future crop development programs combined with conventional and MAS tools will help the breeders produce high-yielding and drought-tolerant rice varieties.
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Affiliation(s)
- Muhammad A. Hassan
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ni Dahu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Tong Hongning
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhu Qian
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yi Yueming
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Li Yiru
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Wang Shimei
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
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Woźniak A, Kęsy J, Glazińska P, Glinkowski W, Narożna D, Bocianowski J, Rucińska-Sobkowiak R, Mai VC, Krzesiński W, Samardakiewicz S, Borowiak-Sobkowiak B, Labudda M, Jeandet P, Morkunas I. The Influence of Lead and Acyrthosiphon pisum (Harris) on Generation of Pisum sativum Defense Signaling Molecules and Expression of Genes Involved in Their Biosynthesis. Int J Mol Sci 2023; 24:10671. [PMID: 37445848 PMCID: PMC10341517 DOI: 10.3390/ijms241310671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/04/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
The main aim of this study was to understand the regulation of the biosynthesis of phytohormones as signaling molecules in the defense mechanisms of pea seedlings during the application of abiotic and biotic stress factors. It was important to identify this regulation at the molecular level in Pisum sativum L. seedlings under the influence of various concentrations of lead-i.e., a low concentration increasing plant metabolism, causing a hormetic effect, and a high dose causing a sublethal effect-and during feeding of a phytophagous insect with a piercing-sucking mouthpart-i.e., pea aphid (Acyrthosiphon pisum (Harris)). The aim of the study was to determine the expression level of genes encoding enzymes of the biosynthesis of signaling molecules such as phytohormones-i.e., jasmonates (JA/MeJA), ethylene (ET) and abscisic acid (ABA). Real-time qPCR was applied to analyze the expression of genes encoding enzymes involved in the regulation of the biosynthesis of JA/MeJA (lipoxygenase 1 (LOX1), lipoxygenase 2 (LOX2), 12-oxophytodienoate reductase 1 (OPR1) and jasmonic acid-amido synthetase (JAR1)), ET (1-aminocyclopropane-1-carboxylate synthase 3 (ACS3)) and ABA (9-cis-epoxycarotenoid dioxygenase (NCED) and aldehyde oxidase 1 (AO1)). In response to the abovementioned stress factors-i.e., abiotic and biotic stressors acting independently or simultaneously-the expression of the LOX1, LOX2, OPR1, JAR1, ACS3, NCED and AO1 genes at both sublethal and hormetic doses increased. Particularly high levels of the relative expression of the tested genes in pea seedlings growing at sublethal doses of lead and colonized by A. pisum compared to the control were noticeable. A hormetic dose of lead induced high expression levels of the JAR1, OPR1 and ACS3 genes, especially in leaves. Moreover, an increase in the concentration of phytohormones such as jasmonates (JA and MeJA) and aminococyclopropane-1-carboxylic acid (ACC)-ethylene (ET) precursor was observed. The results of this study indicate that the response of pea seedlings to lead and A. pisum aphid infestation differed greatly at both the gene expression and metabolic levels. The intensity of these defense responses depended on the organ, the metal dose and direct contact of the stress factor with the organ.
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Affiliation(s)
- Agnieszka Woźniak
- Department of Plant Physiology, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Wołyńska 35, 60-637 Poznan, Poland;
| | - Jacek Kęsy
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Torun, Poland; (J.K.); (P.G.); (W.G.)
| | - Paulina Glazińska
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Torun, Poland; (J.K.); (P.G.); (W.G.)
| | - Wojciech Glinkowski
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Torun, Poland; (J.K.); (P.G.); (W.G.)
| | - Dorota Narożna
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland;
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznan, Poland;
| | - Renata Rucińska-Sobkowiak
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznan, Poland;
| | - Van Chung Mai
- Department of Biology and Application, Faculty of Biology, Vinh University, Le Duan 182, 43108 Vinh, Nghe An Province, Vietnam;
| | - Włodzimierz Krzesiński
- Department of Vegetable Crops, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Dąbrowskiego 159, 60-594 Poznan, Poland;
| | - Sławomir Samardakiewicz
- Laboratory of Electron and Confocal Microscopy, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznan, Poland;
| | - Beata Borowiak-Sobkowiak
- Department of Entomology and Environmental Protection, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Dąbrowskiego 159, 60-594 Poznan, Poland;
| | - Mateusz Labudda
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland;
| | - Philippe Jeandet
- Research Unit “Induced Resistance and Plant Bioprotection”, RIBP USC-INRAe 1488, University of Reims, 51100 Reims, France;
| | - Iwona Morkunas
- Department of Plant Physiology, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Wołyńska 35, 60-637 Poznan, Poland;
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Zhang J, Zhang X, Liu X, Pai Q, Wang Y, Wu X. Molecular Network for Regulation of Seed Size in Plants. Int J Mol Sci 2023; 24:10666. [PMID: 37445843 DOI: 10.3390/ijms241310666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The size of seeds is particularly important for agricultural development, as it is a key trait that determines yield. It is controlled by the coordinated development of the integument, endosperm, and embryo. Large seeds are an important way of improving the ultimate "sink strength" of crops, providing more nutrients for early plant growth and showing certain tolerance to abiotic stresses. There are several pathways for regulating plant seed size, including the HAIKU (IKU) pathway, ubiquitin-proteasome pathway, G (Guanosine triphosphate) protein regulatory pathway, mitogen-activated protein kinase (MAPK) pathway, transcriptional regulators pathway, and phytohormone regulatory pathways including the auxin, brassinosteroid (BR), gibberellin (GA), jasmonic acid (JA), cytokinin (CK), Abscisic acid (ABA), and microRNA (miRNA) regulatory pathways. This article summarizes the seed size regulatory network and prospective ways of improving yield. We expect that it will provide a valuable reference to researchers in related fields.
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Affiliation(s)
- Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuan Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xueman Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiaofeng Pai
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Yahui Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
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Wang Y, Zhang G, Zhou H, Yin S, Li Y, Ma C, Chen P, Sun L, Hao F. GhPYL9-5D and GhPYR1-3 A positively regulate Arabidopsis and cotton responses to ABA, drought, high salinity and osmotic stress. BMC PLANT BIOLOGY 2023; 23:310. [PMID: 37296391 DOI: 10.1186/s12870-023-04330-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Abscisic acid (ABA) receptor pyrabactin resistance 1/PYR1-like/regulatory components of ABA receptor proteins (PYR/PYL/RCARs) have been demonstrated to play pivotal roles in ABA signaling and in response to diverse environmental stimuli including drought, salinity and osmotic stress in Arabidopsis. However, whether and how GhPYL9-5D and GhPYR1-3A, the homologues of Arabidopsis PYL9 and PYR1 in cotton, function in responding to ABA and abiotic stresses are still unclear. RESULTS GhPYL9-5D and GhPYR1-3A were targeted to the cytoplasm and nucleus. Overexpression of GhPYL9-5D and GhPYR1-3A in Arabidopsis wild type and sextuple mutant pyr1pyl1pyl2pyl4pyl5pyl8 plants resulted in ABA hypersensitivity in terms of seed germination, root growth and stomatal closure, as well as seedling tolerance to water deficit, salt and osmotic stress. Moreover, the VIGS (Virus-induced gene silencing) cotton plants, in which GhPYL9-5D or GhPYR1-3A were knocked down, showed clearly reduced tolerance to polyethylene glycol 6000 (PEG)-induced drought, salinity and osmotic stresses compared with the controls. Additionally, transcriptomic data revealed that GhPYL9-5D was highly expressed in the root, and GhPYR1-3A was strongly expressed in the fiber and stem. GhPYL9-5D, GhPYR1-3A and their homologs in cotton were highly expressed after treatment with PEG or NaCl, and the two genes were co-expressed with redox signaling components, transcription factors and auxin signal components. These results suggest that GhPYL9-5D and GhPYR1-3A may serve important roles through interplaying with hormone and other signaling components in cotton adaptation to salt or osmotic stress. CONCLUSIONS GhPYL9-5D and GhPYR1-3A positively regulate ABA-mediated seed germination, primary root growth and stomatal closure, as well as tolerance to drought, salt and osmotic stresses likely through affecting the expression of multiple downstream stress-associated genes in Arabidopsis and cotton.
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Affiliation(s)
- Yibin Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Gaofeng Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Huimin Zhou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Shanshan Yin
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Yunxiang Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Caixia Ma
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Pengyun Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Lirong Sun
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Fushun Hao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China.
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Jing Y, Yang Z, Yang R, Zhang Y, Qiao W, Zhou Y, Sun J. PKL is stabilized by MMS21 to negatively regulate Arabidopsis drought tolerance through directly repressing AFL1 transcription. THE NEW PHYTOLOGIST 2023. [PMID: 37209253 DOI: 10.1111/nph.18972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/20/2023] [Indexed: 05/22/2023]
Abstract
Drought stress causes substantial losses in crop production per year worldwide, threatening global food security. Identification of the genetic components underlying drought tolerance in plants is of great importance. In this study, we report that loss-of-function of the chromatin-remodeling factor PICKLE (PKL), which is involved in repression of transcription, enhances drought tolerance of Arabidopsis. At first, we find that PKL interacts with ABI5 to regulate seed germination, but PKL regulates drought tolerance independently of ABI5. Then, we find that PKL is necessary for repressing the drought-tolerant gene AFL1, which is responsible for the drought-tolerant phenotype of pkl mutant. Genetic complementation tests demonstrate that the Chromo domain and ATPase domain but not the PHD domain are required for the function of PKL in regulating drought tolerance. Interestingly, we find that the DNA-binding domain (DBD) is essential for the protein stability of PKL. Furthermore, we demonstrate that the SUMO E3 ligase MMS21 interacts with and enhances the protein stability of PKL. Genetic interaction analysis shows that MMS21 and PKL additively regulate plant drought tolerance. Collectively, our findings uncover a MMS21-PKL-AFL1 module in regulating plant drought tolerance and offer insights into a novel strategy to improve crop drought tolerance.
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Affiliation(s)
- Yexing Jing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ziyi Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruizhen Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunwei Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weihua Qiao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, 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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23
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Lu J, Zheng D, Li M, Fu M, Zhang X, Wan X, Zhang S, Chen Q. A hierarchical model of ABA-mediated signal transduction in tea plant revealed by systematic genome mining analysis and interaction validation. TREE PHYSIOLOGY 2023; 43:867-878. [PMID: 36694977 DOI: 10.1093/treephys/tpad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/20/2022] [Accepted: 01/19/2023] [Indexed: 05/13/2023]
Abstract
As a critical signaling molecule, ABA plays an important role in plant growth, development and stresses response. However, tea plant [Camellia sinensis (L.)], an important economical perennial woody plant, has not been systematically reported in response to ABA signal transduction in vivo. In this study, we mined and identified the gene structure of CsPYL/CsPP2C-A/CsSnRK gene families in the ABA signal transduction pathway through the genome-wide analysis of tea plants. Spatiotemporal expression and stress response (drought, salt, chilling) expression patterns were characterized. The results showed that most members of CsPYLs were conserved, and the gene structures of members of A-type CsPP2Cs were highly similar, whereas the gene structure of CsSnRK2s was highly variable. The transcription levels of different family members were differentially expressed with plant growth and development, and their response to stress signal patterns was highly correlated. The expression patterns of CsPYL/CsPP2C-A/CsSnRK2 gene family members in different tissues of tea plant cuttings after exogenous ABA treatment were detected by qRT-PCR, and the hierarchical model of ABA signaling was constructed by correlation analysis to preliminarily obtain three potential ABA-dependent signaling transduction pathways. Subsequently, the protein interaction of the CsPYL4/7-CsPP2C-A2-CsSnRK2.8 signaling pathway was verified by yeast two-hybrid and surface plasmon resonance experiments, indicating that there is specific selectivity in the ABA signaling pathway. Our results provided novel insights into the ABA-dependent signal transduction model in tea plant and information for future functional characterizations of stress tolerance genes in tea plant.
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Affiliation(s)
- Jing Lu
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, China
| | - Dongqiao Zheng
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, China
| | - Mengshuang Li
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, China
| | - Maoyin Fu
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, China
| | - Xianchen Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036 , China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, China
| | - Shihua Zhang
- College of Life Science and Health, Wuhan University of Science and Technology, 947 Peace Avenue, Wuhan 430081, China
| | - Qi Chen
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, China
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24
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Liu L, Zhang Y, Tang C, Shen Q, Fu J, Wang Q. Maize Transcription Factor ZmHsf28 Positively Regulates Plant Drought Tolerance. Int J Mol Sci 2023; 24:ijms24098079. [PMID: 37175787 PMCID: PMC10179534 DOI: 10.3390/ijms24098079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Identification of central genes governing plant drought tolerance is fundamental to molecular breeding and crop improvement. Here, maize transcription factor ZmHsf28 is identified as a positive regulator of plant drought responses. ZmHsf28 exhibited inducible gene expression in response to drought and other abiotic stresses. Overexpression of ZmHsf28 diminished drought effects in Arabidopsis and maize. Gene silencing of ZmHsf28 via the technology of virus-induced gene silencing (VIGS) impaired maize drought tolerance. Overexpression of ZmHsf28 increased jasmonate (JA) and abscisic acid (ABA) production in transgenic maize and Arabidopsis by more than two times compared to wild-type plants under drought conditions, while it decreased reactive oxygen species (ROS) accumulation and elevated stomatal sensitivity significantly. Transcriptomic analysis revealed extensive gene regulation by ZmHsf28 with upregulation of JA and ABA biosynthesis genes, ROS scavenging genes, and other drought related genes. ABA treatment promoted ZmHsf28 regulation of downstream target genes. Specifically, electrophoretic mobility shift assays (EMSA) and yeast one-hybrid (Y1H) assay indicated that ZmHsf28 directly bound to the target gene promoters to regulate their gene expression. Taken together, our work provided new and solid evidence that ZmHsf28 improves drought tolerance both in the monocot maize and the dicot Arabidopsis through the implication of JA and ABA signaling and other signaling pathways, shedding light on molecular breeding for drought tolerance in maize and other crops.
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Affiliation(s)
- Lijun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Chen Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Qinqin Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingye Fu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
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Prakash V, Nihranz CT, Casteel CL. The Potyviral Protein 6K2 from Turnip Mosaic Virus Increases Plant Resilience to Drought. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:189-197. [PMID: 36534062 DOI: 10.1094/mpmi-09-22-0183-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Virus infection can increase drought tolerance of infected plants compared with noninfected plants; however, the mechanisms mediating virus-induced drought tolerance remain unclear. In this study, we demonstrate turnip mosaic virus (TuMV) infection increases Arabidopsis thaliana survival under drought compared with uninfected plants. To determine if specific TuMV proteins mediate drought tolerance, we cloned the coding sequence for each of the major viral proteins and generated transgenic A. thaliana that constitutively express each protein. Three TuMV proteins, 6K1, 6K2, and NIa-Pro, enhanced drought tolerance of A. thaliana when expressed constitutively in plants compared with controls. While in the control plant, transcripts related to abscisic acid (ABA) biosynthesis and ABA levels were induced under drought, there were no changes in ABA or related transcripts in plants expressing 6K2 under drought compared with well-watered conditions. Expression of 6K2 also conveyed drought tolerance in another host plant, Nicotiana benthamiana, when expressed using a virus overexpression construct. In contrast to ABA, 6K2 expression enhanced salicylic acid (SA) accumulation in both Arabidopsis and N. benthamiana. These results suggest 6K2-induced drought tolerance is mediated through increased SA levels and SA-dependent induction of plant secondary metabolites, osmolytes, and antioxidants that convey drought tolerance. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Ved Prakash
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, U.S.A
| | - Chad T Nihranz
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, U.S.A
| | - Clare L Casteel
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, U.S.A
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Beye A, Billot C, Ronfort J, McNally KL, Diouf D, Glaszmann JC. Traces of Introgression from cAus into Tropical Japonica Observed in African Upland Rice Varieties. RICE (NEW YORK, N.Y.) 2023; 16:12. [PMID: 36853402 PMCID: PMC9975138 DOI: 10.1186/s12284-023-00625-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Asian rice Oryza sativa, first domesticated in East Asia, has considerable success in African fields. When and where this introduction occurred is unclear. Rice varieties of Asian origin may have evolved locally during and after migration to Africa, resulting in unique adaptations, particularly in relation to upland cultivation as frequently practiced in Africa. METHODS We investigated the genetic differentiation between Asian and African varieties using the 3000 Rice Genomes SNP dataset. African upland cultivars were first characterized using principal component analysis among 292 tropical Japonica accessions from Africa and Asia. The particularities of African accessions were then explored using two inference techniques, PCA-KDE for supervised classification and chromosome painting, and ELAI for individual allelic dosage monitoring. KEY RESULTS Ambiguities of local differentiation between Japonica and other groups pointed at genomic segments that potentially resulted from genetic exchange. Those specific to West African upland accessions were concentrated on chromosome 6 and featured several cAus introgression signals, including a large one between 17.9 and 21.7 Mb. We found iHS statistics in support of positive selection in this region and we provide a list of candidate genes enriched in GO terms that have regulatory functions involved in stress responses that could have facilitated adaptation to harsh upland growing conditions.
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Affiliation(s)
- Abdoulaye Beye
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, 10700, Dakar-Fann, Dakar, Senegal
| | - Claire Billot
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France
| | - Joëlle Ronfort
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France
| | - Kenneth L McNally
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, The Philippines
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, 10700, Dakar-Fann, Dakar, Senegal
| | - Jean Christophe Glaszmann
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France.
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France.
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Li Q, Shen C, Zhang Y, Zhou Y, Niu M, Wang HL, Lian C, Tian Q, Mao W, Wang X, Liu C, Yin W, Xia X. PePYL4 enhances drought tolerance by modulating water-use efficiency and ROS scavenging in Populus. TREE PHYSIOLOGY 2023; 43:102-117. [PMID: 36074523 DOI: 10.1093/treephys/tpac106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Drought is one of the major limiting factors in the growth of terrestrial plants. Abscisic acid (ABA) and pyrabactin resistance 1/prabactin resistance-1 like/regulatory components of ABA receptors (PYR/PYL/RCARs) play a key role in response to drought stress. However, the underlying mechanisms of this control remain largely elusive in trees. In this study, PePYL4, a potential ortholog of the PYR/PYL/RCARs gene, was cloned from Populus euphratica. It was localized in the cytoplasm and nucleus, induced by ABA, osmotic and dehydration treatments. To study the potential biological functions of PePYL4, transgenic triploid white poplars (Populus tomentosa 'YiXianCiZhu B38') overexpressing PePYL4 were generated. PePYL4 overexpression significantly increased ABA sensitivity and reduced stomatal aperture. Compared with wild-type plants, transgenic plants had higher water-use efficiency (WUE) and lower transpiration. When exposed to drought stress, PePYL4 overexpression plants maintained higher photosynthetic activity and accumulated more biomass. Moreover, overexpression of PePYL4 improved antioxidant enzyme activity and ascorbate content to accelerate reactive oxygen species scavenging. Meanwhile, upregulation expression of the stress-related genes also contributed to improving the drought tolerance of transgenic plants. In conclusion, our data suggest that PePYL4 is a promising gene target for regulating WUE and drought tolerance in Populus.
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Affiliation(s)
- Qing Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Chao Shen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yue Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yangyan Zhou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Mengxue Niu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hou-Ling Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Conglong Lian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qianqian Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wei Mao
- Salver Academy of Botany, Rizhao 262305, China
| | | | - Chao Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Weilun Yin
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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Yang Y, Yu J, Qian Q, Shang L. Enhancement of Heat and Drought Stress Tolerance in Rice by Genetic Manipulation: A Systematic Review. RICE (NEW YORK, N.Y.) 2022; 15:67. [PMID: 36562861 PMCID: PMC9789292 DOI: 10.1186/s12284-022-00614-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 12/13/2022] [Indexed: 05/11/2023]
Abstract
As a result of global warming, plants are subjected to ever-increasing abiotic stresses including heat and drought. Drought stress frequently co-occurs with heat stress as a result of water evaporation. These stressors have adverse effects on crop production, which in turn affects human food security. Rice is a major food resource grown widely in crop-producing regions throughout the world. However, increasingly common heat and drought stresses in growth regions can have negative impacts on seedling morphogenesis, reproductive organ establishment, overall yield, and quality. This review centers on responses to heat and drought stress in rice. Current knowledge of molecular regulation mechanisms is summarized. We focus on approaches to cope with heat and drought stress, both at the genetic level and from an agricultural practice perspective. This review establishes a basis for improving rice stress tolerance, grain quality, and yield for human benefit.
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Affiliation(s)
- Yingxue Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Jianping Yu
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, 102206 China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- China National Rice Research Institute (CNRRI), Chinese Academy of Agricultural Sciences, Hangzhou, 311401 China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
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Kavi Kishor PB, Tiozon RN, Fernie AR, Sreenivasulu N. Abscisic acid and its role in the modulation of plant growth, development, and yield stability. TRENDS IN PLANT SCIENCE 2022; 27:1283-1295. [PMID: 36100537 DOI: 10.1016/j.tplants.2022.08.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/28/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Abscisic acid (ABA) is known to confer stress tolerance; however, at elevated levels it impairs plant growth under prolonged stress. Paradoxically, at its basal level, ABA plays many vital roles in promoting plant growth and development, including modulation of tillering, flowering, and seed development, as well as seed maturation. In this review, we provide insight into novel discoveries of ABA fluxes, ABA signaling responses, and their impact on yield stability. We discuss ABA homeostasis implicated under pre- and postanthesis drought and its impact on productive tillers, grain number determination, and seed development to address yield stability in cereal crops while considering the new knowledge that emerged from the model plant systems.
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Affiliation(s)
- Polavarapu B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research (Deemed to be University), Vadlamudi, Guntur 522 213, Andhra Pradesh, India
| | - Rhowell N Tiozon
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany; International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany
| | - Nese Sreenivasulu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Transcriptome analysis of response strategy in Hemerocallis fulva under drought stress. Genes Genomics 2022; 45:593-610. [PMID: 36348249 DOI: 10.1007/s13258-022-01335-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Hemerocallis fulva is an important ground cover plant widely used in urban greening. The analysis of the molecular mechanism underlying the drought response of H. fulva can lay a foundation for improving its adaptability and expanding its planting area. OBJECTIVE To reveal the drought response mechanisms of H. fulva, identify candidate unigenes associated with drought response, and lay a foundation for further unigenes functional study and drought resistance improvement of H. fulva via genetic engineering. METHODS RNA was isolated from H. fulva under different experimental conditions. De novo transcriptomic analysis of the samples was performed to screen drought response unigenes. The transcriptional changes of candidate drought response unigenes were verified by quantitative real-time PCR. RESULTS The differentially expressed unigenes and their functions were analyzed after H. fulva treated by PEG-simulated drought stress and rewatering. The candidate unigenes, associated with H. fulva drought response, were identified after transcriptome analysis. Then, the transcription level of drought response unigenes of H. fulva under different conditions was further verified. Abscisic acid, protein phosphorylation, sterol biosynthesis and ion transport were involved in drought response with quick restore in H. fulva. The response unigenes, involved in hormone (ABA, JA, CK and GA) signaling pathways, defense response, high light response, karrikin response and leaf shaping, can maintain at changed expression levels even after stress withdraw. CONCLUSION Hemerocallis fulva has unique drought response mechanism. Negative regulation mechanism may play more important roles in drought response of H. fulva. The analysis of candidate unigenes, associated with drought response, lays a foundation for further drought resistance improvement of H. fulva.
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Li F, Liu Y, Zhang X, Liu L, Yan Y, Ji X, Kong F, Zhao Y, Li J, Peng T, Sun H, Du Y, Zhao Q. Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2022; 15:52. [PMID: 36302917 PMCID: PMC9613846 DOI: 10.1186/s12284-022-00600-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development. RESULTS In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation. CONCLUSIONS Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.
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Affiliation(s)
- Fei Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Ye Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Xiaohua Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Lingzhi Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yun Yan
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Xin Ji
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Fanshu Kong
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yafan Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Junzhou Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Ting Peng
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China.
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China.
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Li Q, Zhou L, Chen Y, Xiao N, Zhang D, Zhang M, Wang W, Zhang C, Zhang A, Li H, Chen J, Gao Y. Phytochrome interacting factor regulates stomatal aperture by coordinating red light and abscisic acid. THE PLANT CELL 2022; 34:4293-4312. [PMID: 35929789 PMCID: PMC9614506 DOI: 10.1093/plcell/koac244] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/01/2022] [Indexed: 06/10/2023]
Abstract
Stomata are crucial valves coordinating the fixation of carbon dioxide by photosynthesis and water loss through leaf transpiration. Phytochrome interacting factors (PIFs) are negative regulators of red light responses that belong to the basic helix-loop-helix family of transcription factors. Here, we show that the rice (Oryza sativa) PIF family gene OsPIL15 acts as a negative regulator of stomatal aperture to control transpiration in rice. OsPIL15 reduces stomatal aperture by activating rice ABSCISIC ACID INSENSITIVE 5 (OsABI5), which encodes a critical positive regulator of ABSCISIC ACID (ABA) signaling in rice. Moreover, OsPIL15 interacts with the NIGT1/HRS1/HHO family transcription factor rice HRS1 HOMOLOG 3 (OsHHO3) to possibly enhance the regulation of stomatal aperture. Notably, we discovered that the maize (Zea mays) PIF family genes ZmPIF1 and ZmPIF3, which are homologous to OsPIL15, are also involved in the regulation of stomatal aperture in maize, indicating that PIF-mediated regulation of stomatal aperture may be conserved in the plant lineage. Our findings explain the molecular mechanism by which PIFs play a role in red-light-mediated stomatal opening, and demonstrate that PIFs regulate stomatal aperture by coordinating the red light and ABA signaling pathways.
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Affiliation(s)
| | | | - Yanan Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Ning Xiao
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Dongping Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Mengjiao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Wenguo Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China
| | - Changquan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Anning Zhang
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Hua Li
- Hezhou Academy of Agricultural Sciences, Hezhou 542813, China
| | - Jianmin Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
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Liu Y, Yu T, Li Y, Zheng L, Lu Z, Zhou Y, Chen J, Chen M, Zhang J, Sun G, Cao X, Liu Y, Ma Y, Xu Z. Mitogen-activated protein kinase TaMPK3 suppresses ABA response by destabilising TaPYL4 receptor in wheat. THE NEW PHYTOLOGIST 2022; 236:114-131. [PMID: 35719110 PMCID: PMC9544932 DOI: 10.1111/nph.18326] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 06/10/2022] [Indexed: 06/01/2023]
Abstract
Abscisic acid (ABA) receptors are considered as the targeted manipulation of ABA sensitivity and water productivity in plants. Regulation of their stability or activity will directly affect ABA signalling. Mitogen-activated protein kinase (MAPK) cascades link multiple environmental and plant developmental cues. However, the molecular mechanism of ABA signalling and MAPK cascade interaction remains largely elusive. TaMPK3 overexpression decreases drought tolerance and wheat sensitivity to ABA, significantly weakening ABA's inhibitory effects on growth. Under drought stress, overexpression lines show lower survival rates, shoot fresh weight and proline content, but higher malondialdehyde levels at seedling stage, as well as decreased grain width and 1000 grain weight in both glasshouse and field conditions at the adult stage. TaMPK3-RNAi increases drought tolerance. TaMPK3 interaction with TaPYL4 leads to decreased TaPYL4 levels by promoting its ubiquitin-mediated degradation, whereas ABA treatment diminishes TaMPK3-TaPYL interactions. In addition, the expression of ABA signalling proteins is impaired in TaMPK3-overexpressing wheat plants under ABA treatment. The MPK3-PYL interaction module was found to be conserved across monocots and dicots. Our results suggest that the MPK3-PYL module could serve as a negative regulatory mechanism for balancing appropriate drought stress response with normal plant growth signalling in wheat.
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Affiliation(s)
- Ying Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Tai‐Fei Yu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Yi‐Tong Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Lei Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Zhi‐Wei Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Yong‐Bin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Jin‐Peng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Guo‐Zhong Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Xin‐You Cao
- National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement, Crop Research InstituteShandong Academy of Agricultural SciencesJinan250100China
| | - Yong‐Wei Liu
- Institute of Biotechnology and Food ScienceHebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei ProvinceShijiazhuang050051China
| | - You‐Zhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
| | - Zhao‐Shi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureBeijing100081China
- National Nanfan Research Institute (Sanya)Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed LaboratorySanya572024China
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Wei H, Xu H, Su C, Wang X, Wang L. Rice CIRCADIAN CLOCK ASSOCIATED 1 transcriptionally regulates ABA signaling to confer multiple abiotic stress tolerance. PLANT PHYSIOLOGY 2022; 190:1057-1073. [PMID: 35512208 PMCID: PMC9516778 DOI: 10.1093/plphys/kiac196] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/29/2022] [Indexed: 05/06/2023]
Abstract
The circadian clock facilitates the survival and reproduction of crop plants under harsh environmental conditions such as drought and osmotic and salinity stresses, mainly by reprogramming the endogenous transcriptional landscape. Nevertheless, the genome-wide roles of core clock components in rice (Oryza sativa L.) abiotic stress tolerance are largely uncharacterized. Here, we report that CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1), a vital clock component in rice, is required for tolerance to salinity, osmotic, and drought stresses. DNA affinity purification sequencing coupled with transcriptome analysis identified 692 direct transcriptional target genes of OsCCA1. Among them, the genes involved in abscisic acid (ABA) signaling, including group A protein phosphatase 2C genes and basic region and leucine zipper 46 (OsbZIP46), were substantially enriched. Moreover, OsCCA1 could directly bind the promoters of OsPP108 and OsbZIP46 to activate their expression. Consistently, oscca1 null mutants generated via genome editing displayed enhanced sensitivities to ABA signaling. Together, our findings illustrate that OsCCA1 confers multiple abiotic stress tolerance likely by orchestrating ABA signaling, which links the circadian clock with ABA signaling in rice.
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Affiliation(s)
- Hua Wei
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Xu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Su
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiling Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Wu Y, Sun Z, Qi F, Tian M, Wang J, Zhao R, Wang X, Wu X, Shi X, Liu H, Dong W, Huang B, Zheng Z, Zhang X. Comparative transcriptomics analysis of developing peanut ( Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size. FRONTIERS IN PLANT SCIENCE 2022; 13:958808. [PMID: 36172561 PMCID: PMC9511224 DOI: 10.3389/fpls.2022.958808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
Pod size is one of the most important agronomic features of peanuts, which directly affects peanut yield. Studies on the regulation mechanism underpinning pod size in cultivated peanuts remain hitherto limited compared to model plant systems. To better understand the molecular elements that underpin peanut pod development, we conducted a comprehensive analysis of chronological transcriptomics during pod development in four peanut accessions with similar genetic backgrounds, but varying pod sizes. Several plant transcription factors, phytohormones, and the mitogen-activated protein kinase (MAPK) signaling pathways were significantly enriched among differentially expressed genes (DEGs) at five consecutive developmental stages, revealing an eclectic range of candidate genes, including PNC, YUC, and IAA that regulate auxin synthesis and metabolism, CYCD and CYCU that regulate cell differentiation and proliferation, and GASA that regulates seed size and pod elongation via gibberellin pathway. It is plausible that MPK3 promotes integument cell division and regulates mitotic activity through phosphorylation, and the interactions between these genes form a network of molecular pathways that affect peanut pod size. Furthermore, two variant sites, GCP4 and RPPL1, were identified which are stable at the QTL interval for seed size attributes and function in plant cell tissue microtubule nucleation. These findings may facilitate the identification of candidate genes that regulate pod size and impart yield improvement in cultivated peanuts.
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Affiliation(s)
- Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Ziqi Sun
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Feiyan Qi
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Mengdi Tian
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Juan Wang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruifang Zhao
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiao Wang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaohui Wu
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xinlong Shi
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Hongfei Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Wenzhao Dong
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Bingyan Huang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Zheng Zheng
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
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Zhang Y, Zhao Y, Li T, Ni C, Han L, Du P, Xiao K. TaPYL4, an ABA receptor gene of wheat, positively regulates plant drought adaptation through modulating the osmotic stress-associated processes. BMC PLANT BIOLOGY 2022; 22:423. [PMID: 36050643 PMCID: PMC9434867 DOI: 10.1186/s12870-022-03799-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/12/2022] [Indexed: 05/27/2023]
Abstract
BACKGROUND Abscisic acid receptors (ABR) involve transduction of the ABA signaling in plants, impacting largely on stress-defensive physiological processes and plant osmotic stress response. In this study, we characterized TaPYL4, a gene of ABR family in T. aestivum, in mediating plant drought tolerance given scarcity of functional characterization on wheat ABR members thus far. RESULTS TaPYL4 harbors nine conserved domains shared by its PYL counterparts, targeting onto plasma membrane and nucleus after endoplasmic reticulum assortment. TaPYL4 interacts with TaPP2C2 whereas the latter with TaSnRK2.1, which establish a core module of the ABA signaling pathway. TaPYL4 expression was upregulated in root and aerial tissues upon drought stress. Overexpressing TaPYL4 conferred plants improved growth traits whereas knockdown expression of target gene alleviated growth feature compared with wild type under drought treatment. The TaPYL4-enhanced drought adaptation associates gene function in positively regulating stomata movement, osmolyte biosynthesis, and root system architecture (RSA) establishment. Expression analysis on the P5CS family genes involving proline biosynthesis indicated that TaP5CS1 exerts critical roles in promoting osmolytes accumulation in drought-challenged TaPYL4 lines. TaPIN9, a PIN-FORMED gene modulating cellular auxin translocation, was validated to function as a crucial mediator in defining RSA establishment underlying TaPYL4 regulation. Transcriptome analysis revealed that TaPYL4 controls transcription of numerous genes, which impact on physiological processes associated with 'biological process', 'molecular component', and 'cellular process'. Moreover, the differentially expressed genes mediated by TaPYL4 were closely related to stress defensive pathways. CONCLUSIONS Our investigation suggested that TaPYL4 acts as a positive regulator in plant drought tolerance and a valuable target for engineering drought-tolerant cultivars in T. aestivum.
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Affiliation(s)
- Yanyang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei, 071001, People's Republic of China
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, People's Republic of China
| | - Yingjia Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei, 071001, People's Republic of China
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, People's Republic of China
| | - Tianjiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei, 071001, People's Republic of China
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, People's Republic of China
| | - Chenyang Ni
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei, 071001, People's Republic of China
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, People's Republic of China
| | - Le Han
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei, 071001, People's Republic of China
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, People's Republic of China
| | - Pingping Du
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei, 071001, People's Republic of China
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, People's Republic of China
| | - Kai Xiao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei, 071001, People's Republic of China.
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, People's Republic of China.
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, People's Republic of China.
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37
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You X, Nasrullah, Wang D, Mei Y, Bi J, Liu S, Xu W, Wang NN. N 7 -SSPP fusion gene improves salt stress tolerance in transgenic Arabidopsis and soybean through ROS scavenging. PLANT, CELL & ENVIRONMENT 2022; 45:2794-2809. [PMID: 35815549 DOI: 10.1111/pce.14392] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/30/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Considerable signal crosstalk exists in the regulatory network of senescence and stress response. Numerous senescence-associated genes are also involved in plant stress tolerance. However, the underlying mechanisms and application potential of these genes in stress-tolerant crop breeding remain poorly explored. We found that overexpression of SENESCENCE-SUPPRESSED PROTEIN PHOSPHATASE (SSPP), a negative regulator of leaf senescence, significantly improved plant salt tolerance by increasing reactive oxygen species (ROS) scavenging in both Arabidopsis and soybean. However, overexpression of SSPP severely suppressed normal plant growth, limiting its direct use in agriculture. We previously revealed that the N-terminal 1-14 residues of ACS7 (termed 'N7 ') negatively regulated its protein stability through the ubiquitin/proteasome pathway, and the N7 -mediated protein degradation was suppressed by environmental and senescence signals. To avoid the adverse effects of SSPP, the N7 element was fused to the N-terminus of SSPP. We demonstrated that N7 -SSPP fusion gene effectively rescued SSPP-induced growth suppression but maintained enhanced salt tolerance in Arabidopsis and soybean. Particularly, N7 -SSPP enhanced tolerance to long-term salt stress and increased seed yield in soybean. These results suggest that N7 -SSPP overcomes the disadvantages of SSPP on plant growth inhibition and effectively improves salt tolerance through enhanced ROS scavenging, providing an effective strategy of using posttranslational regulatory element for salt-tolerant crop breeding.
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Affiliation(s)
- Xiang You
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Nasrullah
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Dan Wang
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Yuanyuan Mei
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Juanjuan Bi
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Sheng Liu
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Wei Xu
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
| | - Ning Ning Wang
- College of Life Sciences, College of Agricultural Sciences, Tianjin Key Laboratory of Protein Sciences, Nankai University, Tianjin, China
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38
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Mao H, Jian C, Cheng X, Chen B, Mei F, Li F, Zhang Y, Li S, Du L, Li T, Hao C, Wang X, Zhang X, Kang Z. The wheat ABA receptor gene TaPYL1-1B contributes to drought tolerance and grain yield by increasing water-use efficiency. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:846-861. [PMID: 34890091 PMCID: PMC9055818 DOI: 10.1111/pbi.13764] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/28/2021] [Accepted: 12/03/2021] [Indexed: 05/14/2023]
Abstract
The role of abscisic acid (ABA) receptors, PYR1/PYL/RCAR (PYLs), is well established in ABA signalling and plant drought response, but limited research has explored the regulation of wheat PYLs in this process, especially the effects of their allelic variations on drought tolerance or grain yield. Here, we found that the overexpression of a TaABFs-regulated PYL gene, TaPYL1-1B, exhibited higher ABA sensitivity, photosynthetic capacity and water-use efficiency (WUE), all contributed to higher drought tolerance than that of wild-type plants. This heightened water-saving mechanism further increased grain yield and protected productivity during water deficit. Candidate gene association analysis revealed that a favourable allele TaPYL1-1BIn-442 , carrying an MYB recognition site insertion in the promoter, is targeted by TaMYB70 and confers enhanced expression of TaPYL1-1B in drought-tolerant genotypes. More importantly, an increase in frequency of the TaPYL1-1BIn-442 allele over decades among modern Chinese cultivars and its association with high thousand-kernel weight together demonstrated that it was artificially selected during wheat improvement efforts. Taken together, our findings illuminate the role of TaPYL1-1B plays in coordinating drought tolerance and grain yield. In particular, the allelic variant TaPYL1-1BIn-442 substantially contributes to enhanced drought tolerance while maintaining high yield, and thus represents a valuable genetic target for engineering drought-tolerant wheat germplasm.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Chao Jian
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Xinxiu Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life ScienceNorthwest A&F UniversityYanglingShaanxi712100China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Xiaojing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life ScienceNorthwest A&F UniversityYanglingShaanxi712100China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
- Yangling Seed Industry Innovation CenterYanglingShaanxi712100China
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39
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Drincovich MF, Maurino VG. Adjustments of carbon allocation and stomatal dynamics by target localized strategies to increase crop productivity under changing climates. JOURNAL OF PLANT PHYSIOLOGY 2022; 272:153685. [PMID: 35364488 DOI: 10.1016/j.jplph.2022.153685] [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: 12/04/2021] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Increasing crop productivity to ensure food security for future generations is one of the greatest challenges in current plant research. This challenge is even greater due to global climate changes, as enhancing crop yields must occur against the backdrop of increasingly changing environments, particularly rising temperatures and water constraints. Global crop yield growth depends on an improved dynamic balance between carbon and water usage. Here we discuss different approaches that highlight the role of vascular tissue and guard cells in attempting to mitigate the carbon-water trade-off. We argue that crop engineering in the future will require the incorporation of a combination of improved traits. Since targeted gene modifications generally produce fewer undesirable pleiotropic effects than constitutive modifications, we envision that modifications of specific cell types, such as phloem companion cells and guard cells, represent an effective approach for adding beneficial gene modifications in the same plant. This approach will enable trait stacking to design future crops with both high yield and resilience to various climate change stresses.
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Affiliation(s)
- Maria F Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina.
| | - Veronica G Maurino
- Molekulare Pflanzenphysiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
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40
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Wang G, Qi K, Gao X, Guo L, Cao P, Li Q, Qiao X, Gu C, Zhang S. Genome-wide identification and comparative analysis of the PYL gene family in eight Rosaceae species and expression analysis of seeds germination in pear. BMC Genomics 2022; 23:233. [PMID: 35337257 PMCID: PMC8957196 DOI: 10.1186/s12864-022-08456-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/08/2022] [Indexed: 11/10/2022] Open
Abstract
Abscisic acid (ABA) is a phytohormone that plays important roles in the regulation of plant growth, seed germination, and stress responses. The pyrabactin resistance 1-like (PYR/PYL) protein, an ABA receptor, was involved in the initial step in ABA signal transduction. However, the evolutionary history and characteristics of PYL genes expression remain unclear in Chinese white pear (Pyrus bretschneideri) or other Rosaceae species. In this study, 67 PYL genes were identified in eight Rosaceae species, and have been classified into three subgroups based on specific motifs and phylogenetic analysis. Intriguingly, we observed that whole-genome duplication (WGD) and dispersed duplication (DSD) have a major contribution to PYL family expansion. Purifying selection was the major force in PYL genes evolution. Expression analysis finds that PYL genes may function in multiple pear tissues. qRT-PCR validation of 11 PbrPYL genes indicates their roles in seed germination and abiotic stress responses. Our study provides a basis for further elucidation of the function of PYL genes and analysis of their expansion, evolution and expression patterns, which helps to understand the molecular mechanism of pear response to seed germination and seedling abiotic stress.
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Affiliation(s)
- Guoming Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Kaijie Qi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xin Gao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lei Guo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Peng Cao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Qionghou Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Chao Gu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
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Chen Z, Wang Y, Huang R, Zhang Z, Huang J, Yu F, Lin Y, Guo Y, Liang K, Zhou Y, Chen F. Integration of transcriptomic and proteomic analyses reveals several levels of metabolic regulation in the excess starch and early senescent leaf mutant lses1 in rice. BMC PLANT BIOLOGY 2022; 22:137. [PMID: 35321646 PMCID: PMC8941791 DOI: 10.1186/s12870-022-03510-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The normal metabolism of transitory starch in leaves plays an important role in ensuring photosynthesis, delaying senescence and maintaining high yield in crops. OsCKI1 (casein kinase I1) plays crucial regulatory roles in multiple important physiological processes, including root development, hormonal signaling and low temperature-treatment adaptive growth in rice; however, its potential role in regulating temporary starch metabolism or premature leaf senescence remains unclear. To reveal the molecular regulatory mechanism of OsCKI1 in rice leaves, physiological, transcriptomic and proteomic analyses of leaves of osckI1 allele mutant lses1 (leaf starch excess and senescence 1) and its wild-type varieties (WT) were performed. RESULTS Phenotypic identification and physiological measurements showed that the lses1 mutant exhibited starch excess in the leaves and an obvious leaf tip withering phenotype as well as high ROS and MDA contents, low chlorophyll content and protective enzyme activities compared to WT. The correlation analyses between protein and mRNA abundance are weak or limited. However, the changes of several important genes related to carbohydrate metabolism and apoptosis at the mRNA and protein levels were consistent. The protein-protein interaction (PPI) network might play accessory roles in promoting premature senescence of lses1 leaves. Comprehensive transcriptomic and proteomic analysis indicated that multiple key genes/proteins related to starch and sugar metabolism, apoptosis and ABA signaling exhibited significant differential expression. Abnormal increase in temporary starch was highly correlated with the expression of starch biosynthesis-related genes, which might be the main factor that causes premature leaf senescence and changes in multiple metabolic levels in leaves of lses1. In addition, four proteins associated with ABA accumulation and signaling, and three CKI potential target proteins related to starch biosynthesis were up-regulated in the lses1 mutant, suggesting that LSES1 may affect temporary starch accumulation and premature leaf senescence through phosphorylation crosstalk ABA signaling and starch anabolic pathways. CONCLUSION The current study established the high correlation between the changes in physiological characteristics and mRNA and protein expression profiles in lses1 leaves, and emphasized the positive effect of excessive starch on accelerating premature leaf senescence. The expression patterns of genes/proteins related to starch biosynthesis and ABA signaling were analyzed via transcriptomes and proteomes, which provided a novel direction and research basis for the subsequent exploration of the regulation mechanism of temporary starch and apoptosis via LSES1/OsCKI1 in rice.
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Affiliation(s)
- Zhiming Chen
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongsheng Wang
- Postdoctoral Station of Biology, School of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Rongyu Huang
- School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Zesen Zhang
- School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Jinpeng Huang
- School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Feng Yu
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yaohai Lin
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuchun Guo
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Kangjing Liang
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuanchang Zhou
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Fangyu Chen
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Liu B, Stevens-Green R, Johal D, Buchanan R, Geddes-McAlister J. Fungal pathogens of cereal crops: Proteomic insights into fungal pathogenesis, host defense, and resistance. JOURNAL OF PLANT PHYSIOLOGY 2022; 269:153593. [PMID: 34915227 DOI: 10.1016/j.jplph.2021.153593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/28/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Fungal infections of cereal crops pose a significant risk to global food security through reduced grain production and quality, as well as contamination of animal feed and human products for consumption. To combat fungal disease, we need to understand how the pathogen adapts and survives within the hostile environment of the host and how the host's defense response can be modulated for protection from disease. Such investigations offer insight into fungal pathogenesis, host immunity, the development of resistance, and mechanisms of action for currently-used control strategies. Mass spectrometry-based proteomics provides a technologically-advanced platform to define differences among fungal pathogens and their hosts at the protein level, supporting the discovery of proteins critical for disease, and uncovering novel host responses driving susceptibly or resistance of the host. In this Review, we explore the role of mass spectrometry-based proteomics in defining the intricate relationship between a pathogen and host during fungal disease of cereal crops with a focus on recent discoveries derived from the globally-devastating diseases of Fusarium head blight, Rice blast, and Powdery mildew. We highlight advances made for each of these diseases and discuss opportunities to extrapolate findings to further our fight against fungal pathogens on a global scale.
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Affiliation(s)
- B Liu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - R Stevens-Green
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - D Johal
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - R Buchanan
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - J Geddes-McAlister
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Canadian Proteomics and Artificial Intelligence Research and Training Consortium, Canada.
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Muhammad Aslam M, Waseem M, Jakada BH, Okal EJ, Lei Z, Saqib HSA, Yuan W, Xu W, Zhang Q. Mechanisms of Abscisic Acid-Mediated Drought Stress Responses in Plants. Int J Mol Sci 2022; 23:ijms23031084. [PMID: 35163008 PMCID: PMC8835272 DOI: 10.3390/ijms23031084] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Drought is one of the major constraints to rain-fed agricultural production, especially under climate change conditions. Plants evolved an array of adaptive strategies that perceive stress stimuli and respond to these stress signals through specific mechanisms. Abscisic acid (ABA) is a premier signal for plants to respond to drought and plays a critical role in plant growth and development. ABA triggers a variety of physiological processes such as stomatal closure, root system modulation, organizing soil microbial communities, activation of transcriptional and post-transcriptional gene expression, and metabolic alterations. Thus, understanding the mechanisms of ABA-mediated drought responses in plants is critical for ensuring crop yield and global food security. In this review, we highlighted how plants adjust ABA perception, transcriptional levels of ABA- and drought-related genes, and regulation of metabolic pathways to alter drought stress responses at both cellular and the whole plant level. Understanding the synergetic role of drought and ABA will strengthen our knowledge to develop stress-resilient crops through integrated advanced biotechnology approaches. This review will elaborate on ABA-mediated drought responses at genetic, biochemical, and molecular levels in plants, which is critical for advancement in stress biology research.
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Affiliation(s)
- Mehtab Muhammad Aslam
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (Z.L.); (W.X.)
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Muhammad Waseem
- Department of Botany, University of Narowal, Narowal 51600, Pakistan;
- College of Horticulture, Hainan University, Haikou 570100, China
| | - Bello Hassan Jakada
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, College of Life Science, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou 350002, China;
| | - Eyalira Jacob Okal
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
| | - Zuliang Lei
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (Z.L.); (W.X.)
| | - Hafiz Sohaib Ahmad Saqib
- Guangdong Provincial Key Laboratory of Marine Biology, College of Science, Shantou University, Shantou 515063, China;
| | - Wei Yuan
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Correspondence: (W.Y.); (Q.Z.)
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (Z.L.); (W.X.)
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qian Zhang
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (Z.L.); (W.X.)
- Correspondence: (W.Y.); (Q.Z.)
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Li R, Su X, Zhou R, Zhang Y, Wang T. Molecular mechanism of mulberry response to drought stress revealed by complementary transcriptomic and iTRAQ analyses. BMC PLANT BIOLOGY 2022; 22:36. [PMID: 35039015 PMCID: PMC8762937 DOI: 10.1186/s12870-021-03410-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND The use of mulberry leaves has long been limited to raising silkworms, but with the continuous improvement of mulberry (Morus alba) resource development and utilization, various mulberry leaf extension products have emerged. However, the fresh leaves of mulberry trees have a specific window of time for picking and are susceptible to adverse factors, such as drought stress. Therefore, exploring the molecular mechanism by which mulberry trees resist drought stress and clarifying the regulatory network of the mulberry drought response is the focus of the current work. RESULTS In this study, natural and drought-treated mulberry grafted seedlings were used for transcriptomic and proteomic analyses (CK vs. DS9), aiming to clarify the molecular mechanism of the mulberry drought stress response. Through transcriptome and proteome sequencing, we identified 9889 DEGs and 1893 DEPs enriched in stress-responsive GO functional categories, such as signal transducer activity, antioxidant activity, and transcription regulator activity. KEGG enrichment analysis showed that a large number of codifferentially expressed genes were enriched in flavonoid biosynthesis pathways, hormone signalling pathways, lignin metabolism and other pathways. Through subsequent cooperation analysis, we identified 818 codifferentially expressed genes in the CK vs. DS9 comparison group, including peroxidase (POD), superoxide dismutase (SOD), aldehyde dehydrogenase (ALDHs), glutathione s-transferase (GST) and other genes closely related to the stress response. In addition, we determined that the mulberry gene MaWRKYIII8 (XP_010104968.1) underwent drought- and abscisic acid (ABA)-induced expression, indicating that it may play an important role in the mulberry response to drought stress. CONCLUSIONS Our research shows that mulberry can activate proline and ABA biosynthesis pathways and produce a large amount of proline and ABA, which improves the drought resistance of mulberry. MaWRKYIII8 was up-regulated and induced by drought and exogenous ABA, indicating that MaWRKYIII8 may be involved in the mulberry response to drought stress. These studies will help us to analyse the molecular mechanism underlying mulberry drought tolerance and provide important gene information and a theoretical basis for improving mulberry drought tolerance through molecular breeding in the future.
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Affiliation(s)
- Ruixue Li
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Xueqiang Su
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Rong Zhou
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Yuping Zhang
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Taichu Wang
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China.
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45
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Zhang Z, Luo S, Liu Z, Wan Z, Gao X, Qiao Y, Yu J, Zhang G. Genome-wide identification and expression analysis of the cucumber PYL gene family. PeerJ 2022; 10:e12786. [PMID: 35047239 PMCID: PMC8759363 DOI: 10.7717/peerj.12786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/21/2021] [Indexed: 01/10/2023] Open
Abstract
Abscisic acid (ABA) is a very important hormone in plants. It regulates growth and development of plants and plays an important role in biotic and abiotic stresses. The Pyrabactin resistance 1-like (PYR/PYL) proteins play a central role in ABA signal transduction pathways. The working system of PYL genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. Through bioinformatics, a total of 14 individual PYL genes were identified in Chinese long '9930' cucumber. Fourteen PYL genes were distributed on six chromosomes of cucumber, and their encoded proteins predicted to be distributed in cytoplasm and nucleus. Based on the phylogenetic analysis, the PYL genes of cucumber, Arabidopsis, rice, apple, Brachypodium distachyon and soybeancould be classified into three groups. Genetic structures and conserved domains analysis revealed that CsPYL genes in the same group have similar exons and conserved domains. By predicting cis-elements in the promoters, we found that all CsPYL members contained hormone and stress-related elements. Additionally, the expression patterns of CsPYL genes were specific in tissues. Finally, we further examined the expression of 14 CsPYL genes under ABA, PEG, salt stress. The qRT-PCR results showed that most PYL gene expression levels were up-regulated. Furthermore, with different treatments about 3h, the relative expression of PYL8 was up-regulated and more than 20 times higher than 0h. It indicated that this gene may play an important role in abiotic stress.
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Affiliation(s)
- Zeyu Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China,College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Shilei Luo
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China,College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zeci Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China,College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zilong Wan
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China,College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Xueqin Gao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China,College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Yali Qiao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China,College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jihua Yu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China,College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Guobin Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China,College of Horticulture, Gansu Agricultural University, Lanzhou, China
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Chen R, Deng Y, Ding Y, Guo J, Qiu J, Wang B, Wang C, Xie Y, Zhang Z, Chen J, Chen L, Chu C, He G, He Z, Huang X, Xing Y, Yang S, Xie D, Liu Y, Li J. Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2022. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Affiliation(s)
- Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bing Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changsheng Wang
- National Center for Gene Research, Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihua Zhang
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Daoxin Xie
- MOE Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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47
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Berrío RT, Nelissen H, Inzé D, Dubois M. Increasing yield on dry fields: molecular pathways with growing potential. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:323-341. [PMID: 34695266 PMCID: PMC7612350 DOI: 10.1111/tpj.15550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/08/2021] [Accepted: 10/19/2021] [Indexed: 05/02/2023]
Abstract
Drought stress constitutes one of the major constraints to agriculture all over the world, and its devastating effect is only expected to increase in the following years due to climate change. Concurrently, the increasing food demand in a steadily growing population requires a proportional increase in yield and crop production. In the past, research aimed to increase plant resilience to severe drought stress. However, this often resulted in stunted growth and reduced yield under favorable conditions or moderate drought. Nowadays, drought tolerance research aims to maintain plant growth and yield under drought conditions. Overall, recently deployed strategies to engineer drought tolerance in the lab can be classified into a 'growth-centered' strategy, which focuses on keeping growth unaffected by the drought stress, and a 'drought resilience without growth penalty' strategy, in which the main aim is still to boost drought resilience, while limiting the side effects on plant growth. In this review, we put the scope on these two strategies and some molecular players that were successfully engineered to generate drought-tolerant plants: abscisic acid, brassinosteroids, cytokinins, ethylene, ROS scavenging genes, strigolactones, and aquaporins. We discuss how these pathways participate in growth and stress response regulation under drought. Finally, we present an overview of the current insights and future perspectives in the development of new strategies to improve drought tolerance in the field.
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Affiliation(s)
- Rubén Tenorio Berrío
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hilde Nelissen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Corresponding Author: Dirk Inzé VIB Center for Plant Systems Biology Ghent University, Department of Plant Biotechnology Technologiepark 71 B-9052 Ghent (Belgium) Tel.: +32 9 3313800; Fax: +32 9 3313809;
| | - Marieke Dubois
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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48
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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49
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Verma V, Vishal B, Kohli A, Kumar PP. Systems-based rice improvement approaches for sustainable food and nutritional security. PLANT CELL REPORTS 2021; 40:2021-2036. [PMID: 34591154 DOI: 10.1007/s00299-021-02790-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
An integrated research approach to ensure sustainable rice yield increase of a crop grown by 25% of the world's farmers in 10% of cropland is essential for global food security. Rice, being a global staple crop, feeds about 56% of the world population and sustains 40% of the world's poor. At ~ $200 billion, it also accounts for 13% of the annual crop value. With hunger and malnutrition rampant among the poor, rice research for development is unique in global food and nutrition security. A systems-based, sustainable increase in rice quantity and quality is imperative for environmental and biodiversity benefits. Upstream 'discovery' through biotechnology, midstream 'development' through breeding and agronomy, downstream 'dissemination and deployment' must be 'demand-driven' for 'distinct socio-economic transformational impacts'. Local agro-ecology and livelihood nexus must drive the research agenda for targeted benefits. This necessitates sustained long-term investments by government, non-government and private sectors to secure the future food, nutrition, environment, prosperity and equity status.
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Affiliation(s)
- Vivek Verma
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, 305817, Rajasthan, India.
| | - Bhushan Vishal
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Republic of Singapore
| | - Ajay Kohli
- Strategic Innovation Platform, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - Prakash P Kumar
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Republic of Singapore.
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50
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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