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Li Y, Liu X, Xu X, Zhu G, Xiang D, Liu P. Identification and characterization of the RcTCP gene family and its expression in response to abiotic stresses in castor bean. BMC Genomics 2024; 25:670. [PMID: 38965476 PMCID: PMC11223397 DOI: 10.1186/s12864-024-10347-6] [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: 11/28/2023] [Accepted: 04/25/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND The TCP (teosinte branched1/cincinnata/proliferating cell factor) family plays a prominent role in plant development and stress responses. However, TCP family genes have thus far not been identified in castor bean, and therefore an understanding of the expression and functional aspects of castor bean TCP genes is lacking. To identify the potential biological functions of castor bean (RcTCP) TCP members, the composition of RcTCP family members, their basic physicochemical properties, subcellular localizations, interacting proteins, miRNA target sites, and gene expression patterns under stress were assessed. RESULTS The presence of 20 RcTCP genes on the nine chromosomes of castor bean was identified, all of which possess TCP domains. Phylogenetic analysis indicated a close relationship between RcTCP genes and Arabidopsis AtTCP genes, suggesting potential functional similarity. Subcellular localization experiments confirmed that RcTC01/02/03/10/16/18 are all localized in the nucleus. Protein interaction analysis revealed that the interaction quantity of RcTCP03/06/11 proteins is the highest, indicating a cascade response in the functional genes. Furthermore, it was found that the promoter region of RcTCP genes contains a large number of stress-responsive elements and hormone-induced elements, indicating a potential link between RcTCP genes and stress response functions. qRT-PCR showed that all RcTCP genes exhibit a distinct tissue-specific expression pattern and their expression is induced by abiotic stress (including low temperature, abscisic acid, drought, and high salt). Among them, RcTCP01/03/04/08/09/10/14/15/18/19 genes may be excellent stress-responsive genes. CONCLUSION We discovered that RcTCP genes play a crucial role in various activities, including growth and development, the stress response, and transcription. This study provides a basis for studying the function of RcTCP gene in castor.
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Affiliation(s)
- Yanxiao Li
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyang Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyuan Xu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Guishuang Zhu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Dianjun Xiang
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
| | - Peng Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
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2
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Shahzad N, Nabi HG, Qiao L, Li W. The Molecular Mechanism of Cold-Stress Tolerance: Cold Responsive Genes and Their Mechanisms in Rice ( Oryza sativa L.). BIOLOGY 2024; 13:442. [PMID: 38927322 PMCID: PMC11200503 DOI: 10.3390/biology13060442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Rice (Oryza sativa L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change.
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Affiliation(s)
- Nida Shahzad
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (N.S.); (L.Q.)
| | - Hafiz Ghulam Nabi
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Lei Qiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (N.S.); (L.Q.)
| | - Wenqiang Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (N.S.); (L.Q.)
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3
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Sun X, Wang E, Yu L, Liu S, Liu T, Qin J, Jiang P, He S, Cai X, Jing S, Song B. TCP transcription factor StAST1 represses potato tuberization by regulating tuberigen complex activity. PLANT PHYSIOLOGY 2024; 195:1347-1364. [PMID: 38488068 DOI: 10.1093/plphys/kiae138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/01/2024] [Indexed: 06/02/2024]
Abstract
Potato (Solanum tuberosum L.) is cultivated worldwide for its underground tubers, which provide an important part of human nutrition and serve as a model system for belowground storage organ formation. Similar to flowering, stolon-expressed FLOWERING LOCUS T-like (FT-like) protein SELF-PRUNING 6A (StSP6A) plays an instrumental role in tuberization by binding to the bZIP transcription factors StABI5-like 1 (StABL1) and StFD-like 1 (StFDL1), causing transcriptional reprogramming at the stolon subapical apices. However, the molecular mechanism regulating the widely conserved FT-bZIP interactions remains largely unexplored. Here, we identified a TCP transcription factor StAST1 (StABL1 and StSP6A-associated TCP protein 1) binding to both StSP6A and StABL1. StAST1 is specifically expressed in the vascular tissue of leaves and developing stolons. Silencing of StAST1 leads to accelerated tuberization and a shortened life cycle. Molecular dissection reveals that the interaction of StAST1 with StSP6A and StABL1 attenuates the formation of the alternative tuberigen activation complex (aTAC). We also observed StAST1 directly activates the expression of potato GA 20-oxidase gene (StGA20ox1) to regulate GA responses. These results demonstrate StAST1 functions as a tuberization repressor by regulating plant hormone levels; our findings also suggest a mechanism by which the widely conserved FT-FD genetic module is fine-tuned.
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Affiliation(s)
- Xiaomeng Sun
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Enshuang Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Liu Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shengxuan Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Tiantian Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jun Qin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Peng Jiang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shuangshuang He
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xingkui Cai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shenglin Jing
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan 610101, China
| | - Botao Song
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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4
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Lang X, Zhao X, Zhao J, Ren T, Nie L, Zhao W. MicroRNA Profiling Revealed the Mechanism of Enhanced Cold Resistance by Grafting in Melon ( Cucumis melo L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1016. [PMID: 38611545 PMCID: PMC11013280 DOI: 10.3390/plants13071016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Grafting is widely used to improve the resistance to abiotic stresses in cucurbit plants, but the effect and molecular mechanism of grafting on cold stress are still unknown in melon. In this study, phenotypic characteristics, physiological indexes, small-RNA sequencing and expression analyses were performed on grafted plants with pumpkin rootstock (PG) and self-grafted plants (SG) to explore the mechanism of changed cold tolerance by grafting in melon. Compared with SG plants, the cold tolerance was obviously enhanced, the malondialdehyde (MDA) content was significantly decreased and the activities of antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; peroxidase, POD) were significantly increased in PG plants. Depend on differentially expressed miRNA (DEM) identification and expression pattern analyses, cme-miR156b, cme-miR156f and chr07_30026 were thought to play a key role in enhancing low-temperature resistance resulting from grafting. Subsequently, 24, 37 and 17 target genes of cme-miR156b, cme-miR156f and chr07_30026 were respectively predicted, and 21 target genes were co-regulated by cme-miR156b and cme-miR156f. Among these 57 unique target genes, the putative promoter of 13 target genes contained the low-temperature responsive (LTR) cis-acting element. The results of qRT-PCR indicated that six target genes (MELO3C002370, MELO3C009217, MELO3C018972, MELO3C016713, MELO3C012858 and MELO3C000732) displayed the opposite expression pattern to their corresponding miRNAs. Furthermore, MELO3C002370, MELO3C016713 and MELO3C012858 were significantly downregulated in cold-resistant cultivars and upregulated in cold-sensitive varieties after cold stimulus, and they acted as the key negative regulators of low-temperature response in melon. This study revealed three key miRNAs and three putative target genes involved in the cold tolerance of melon and provided a molecular basis underlying how grafting improved the low-temperature resistance of melon plants.
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Affiliation(s)
- Xinmei Lang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Xuan Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Jiateng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Tiantian Ren
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
| | - Lanchun Nie
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding 071000, China
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding 071000, China
| | - Wensheng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (X.L.); (X.Z.); (J.Z.); (T.R.)
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding 071000, China
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding 071000, China
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5
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Shi C, Zou W, Zhu Y, Zhang J, Teng C, Wei H, He H, He W, Liu X, Zhang B, Zhang H, Leng Y, Guo M, Wang X, Chen W, Zhang Z, Qian H, Cui Y, Jiang H, Chen Y, Fei Q, Meyers BC, Liang W, Qian Q, Shang L. mRNA cleavage by 21-nucleotide phasiRNAs determines temperature-sensitive male sterility in rice. PLANT PHYSIOLOGY 2024; 194:2354-2371. [PMID: 38060676 DOI: 10.1093/plphys/kiad654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/15/2023] [Indexed: 04/02/2024]
Abstract
Temperature-sensitive male sterility is one of the core components for hybrid rice (Oryza sativa) breeding based on the 2-line system. We previously found that knockout of ARGONAUTE 1d (AGO1d) causes temperature-sensitive male sterility in rice by influencing phased small interfering RNA (phasiRNA) biogenesis and function. However, the specific phasiRNAs and their targets underlying the temperature-sensitive male sterility in the ago1d mutant remain unknown. Here, we demonstrate that the ago1d mutant displays normal female fertility but complete male sterility at low temperature. Through a multiomics analysis of small RNA (sRNA), degradome, and transcriptome, we found that 21-nt phasiRNAs account for the greatest proportion of the 21-nt sRNA species in rice anthers and are sensitive to low temperature and markedly downregulated in the ago1d mutant. Moreover, we found that 21-nt phasiRNAs are essential for the mRNA cleavage of a set of fertility- and cold tolerance-associated genes, such as Earlier Degraded Tapetum 1 (EDT1), Tapetum Degeneration Retardation (TDR), OsPCF5, and OsTCP21, directly or indirectly determined by AGO1d-mediated gene silencing. The loss of function of 21-nt phasiRNAs can result in upregulation of their targets and causes varying degrees of defects in male fertility and grain setting. Our results highlight the essential functions of 21-nt phasiRNAs in temperature-sensitive male sterility in rice and suggest their promising application in 2-line hybrid rice breeding in the future.
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Affiliation(s)
- Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Wenli Zou
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Yiwang Zhu
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Jie Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chong Teng
- Donald Danforth Plant Science Center, Saint Louis, MI 63132, USA
| | - Hua Wei
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Xiangpei Liu
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Hong Zhang
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Yue Leng
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Mingliang Guo
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Xianmeng Wang
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Wu Chen
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Zhipeng Zhang
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Hongge Qian
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Yan Cui
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Hongshuang Jiang
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Ying Chen
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for 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
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis, MI 63132, USA
- Division of Plant Sciences and Technology, University of Missouri-Columbia, Columbia, MI 65211, USA
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory for 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
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
- Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for 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
- Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China
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Zhang H, Zhang J, Xu P, Li M, Li Y. Insertion of a miniature inverted-repeat transposable element into the promoter of OsTCP4 results in more tillers and a lower grain size in rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1421-1436. [PMID: 37988625 DOI: 10.1093/jxb/erad467] [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: 06/06/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023]
Abstract
A class I PCF type protein, TCP4, was identified as a transcription factor associated with both grain size and tillering through a DNA pull-down-MS assay combined with a genome-wide association study. This transcription factor was found to have a significant role in the variations among the 533 rice accessions, dividing them into two main subspecies. A Tourist-like miniature inverted-repeat transposable element (MITE) was discovered in the promoter of TCP4 in japonica/geng accessions (TCP4M+), which was found to suppress the expression of TCP4 at the transcriptional level. The MITE-deleted haplotype (TCP4M-) was mainly found in indica/xian accessions. ChIP-qPCR and EMSA demonstrated the binding of TCP4 to promoters of grain reservoir genes such as SSIIa and Amy3D in vivo and in vitro, respectively. The introduction of the genomic sequence of TCP4M+ into different TCP4M- cultivars was found to affect the expression of TCP4 in the transgenic rice, resulting in decreased expression of its downstream target gene SSIIa, increased tiller number, and decreased seed length. This study revealed that a Tourist-like MITE contributes to subspecies divergence by regulating the expression of TCP4 in response to environmental pressure, thus influencing source-sink balance by regulating starch biosynthesis in rice.
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Affiliation(s)
- Hui Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Juncheng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Pengkun Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
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7
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Dong Z, Hao Y, Zhao Y, Tang W, Wang X, Li J, Wang L, Hu Y, Guan X, Gu F, Liu Z, Zhang Z. Genome-Wide Analysis of the TCP Transcription Factor Gene Family in Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:641. [PMID: 38475487 DOI: 10.3390/plants13050641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
TCP transcription factors play a key role in regulating various developmental processes, particularly in shoot branching, flower development, and leaf development, and these factors are exclusively found in plants. However, comprehensive studies investigating TCP transcription factors in pepper (Capsicum annuum L.) are lacking. In this study, we identified 27 CaTCP members in the pepper genome, which were classified into Class I and Class II through phylogenetic analysis. The motif analysis revealed that CaTCPs in the same class exhibit similar numbers and distributions of motifs. We predicted that 37 previously reported miRNAs target 19 CaTCPs. The expression levels of CaTCPs varied in various tissues and growth stages. Specifically, CaTCP16, a member of Class II (CIN), exhibited significantly high expression in flowers. Class I CaTCPs exhibited high expression levels in leaves, while Class II CaTCPs showed high expression in lateral branches, especially in the CYC/TB1 subclass. The expression profile suggests that CaTCPs play specific roles in the developmental processes of pepper. We provide a theoretical basis that will assist in further functional validation of the CaTCPs.
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Affiliation(s)
- Zeyu Dong
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Yupeng Hao
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Yongyan Zhao
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Wenchen Tang
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Xueqiang Wang
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Jun Li
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Luyao Wang
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Yan Hu
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Xueying Guan
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Fenglin Gu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya 572000, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572000, China
| | - Ziji Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Haikou 571101, China
| | - Zhiyuan Zhang
- Hainan Institute, Zhejiang University, Sanya 572000, China
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8
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Yadav A, Mathan J, Dubey AK, Singh A. The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling. Noncoding RNA 2024; 10:13. [PMID: 38392968 PMCID: PMC10893181 DOI: 10.3390/ncrna10010013] [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: 12/11/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.
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Affiliation(s)
- Amit Yadav
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Jyotirmaya Mathan
- Sashi Bhusan Rath Government Autonomous Women’s College, Brahmapur 760001, India;
| | - Arvind Kumar Dubey
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Anuradha Singh
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA
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9
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Wang Y, Wang J, Sarwar R, Zhang W, Geng R, Zhu KM, Tan XL. Research progress on the physiological response and molecular mechanism of cold response in plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1334913. [PMID: 38352650 PMCID: PMC10861734 DOI: 10.3389/fpls.2024.1334913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Low temperature is a critical environmental stress factor that restricts crop growth and geographical distribution, significantly impacting crop quality and yield. When plants are exposed to low temperatures, a series of changes occur in their external morphology and internal physiological and biochemical metabolism. This article comprehensively reviews the alterations and regulatory mechanisms of physiological and biochemical indices, such as membrane system stability, redox system, fatty acid content, photosynthesis, and osmoregulatory substances, in response to low-temperature stress in plants. Furthermore, we summarize recent research on signal transduction and regulatory pathways, phytohormones, epigenetic modifications, and other molecular mechanisms mediating the response to low temperatures in higher plants. In addition, we outline cultivation practices to improve plant cold resistance and highlight the cold-related genes used in molecular breeding. Last, we discuss future research directions, potential application prospects of plant cold resistance breeding, and recent significant breakthroughs in the research and application of cold resistance mechanisms.
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Affiliation(s)
| | | | | | | | | | | | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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10
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Zhou B, Zheng B, Wu W. The ncRNAs Involved in the Regulation of Abiotic Stress-Induced Anthocyanin Biosynthesis in Plants. Antioxidants (Basel) 2023; 13:55. [PMID: 38247480 PMCID: PMC10812613 DOI: 10.3390/antiox13010055] [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: 11/24/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
Plants have evolved complicated defense and adaptive systems to grow in various abiotic stress environments such as drought, cold, and salinity. Anthocyanins belong to the secondary metabolites of flavonoids with strong antioxidant activity in response to various abiotic stress and enhance stress tolerance. Anthocyanin accumulation often accompanies the resistance to abiotic stress in plants to scavenge reactive oxygen species (ROS). Recent research evidence showed that many regulatory pathways such as osmoregulation, antioxidant response, plant hormone response, photosynthesis, and respiration regulation are involved in plant adaption to stress. However, the molecular regulatory mechanisms involved in controlling anthocyanin biosynthesis in relation to abiotic stress response have remained obscure. Here, we summarize the current research progress of specific regulators including small RNAs, and lncRNAs involved in the molecular regulation of abiotic stress-induced anthocyanin biosynthesis. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by microRNAs (miRNAs), long non-coding RNAs (lncRNAs), transcription factors, and stress response factors is also discussed. Understanding molecular mechanisms of anthocyanin biosynthesis for ROS scavenging in various abiotic stress responses will benefit us for resistance breeding in crop plants.
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Affiliation(s)
- Bo Zhou
- College of Life Science, Northeast Forestry University, Harbin 150040, China;
| | - Baojiang Zheng
- College of Life Science, Northeast Forestry University, Harbin 150040, China;
| | - Weilin Wu
- Agricultural College, Yanbian University, Yanji 133002, China
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11
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Zhang M, Agassin RH, Huang Z, Wang D, Yao S, Ji K. Transcriptome-Wide Identification of TCP Transcription Factor Family Members in Pinus massoniana and Their Expression in Regulation of Development and in Response to Stress. Int J Mol Sci 2023; 24:15938. [PMID: 37958919 PMCID: PMC10648340 DOI: 10.3390/ijms242115938] [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: 08/31/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Pinus massoniana is an important coniferous tree species for barren mountain afforestation with enormous ecological and economic significance. It has strong adaptability to the environment. TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors (TFs) play crucial roles in plant stress response, hormone signal transduction, and development processes. At present, TCP TFs have been widely studied in multiple plant species, but research in P. massoniana has not been carried out. In this study, 13 PmTCP TFs were identified from the transcriptomes of P. massoniana. The phylogenetic results revealed that these PmTCP members were divided into two categories: Class I and Class II. Each PmTCP TF contained a conserved TCP domain, and the conserved motif types and numbers were similar in the same subgroup. According to the transcriptional profiling analysis under drought stress conditions, it was found that seven PmTCP genes responded to drought treatment to varying degrees. The qRT-PCR results showed that the majority of PmTCP genes were significantly expressed in the needles and may play a role in the developmental stage. Meanwhile, the PmTCPs could respond to several stresses and hormone treatments at different levels, which may be important for stress resistance. In addition, PmTCP7 and PmTCP12 were nuclear localization proteins, and PmTCP7 was a transcriptional suppressor. These results will help to explore the regulatory factors related to the growth and development of P. massoniana, enhance its stress resistance, and lay the foundation for further exploration of the physiological effects on PmTCPs.
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Affiliation(s)
| | | | | | | | | | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry and Grassland Administration, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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12
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Xu P, Zhang W, Wang X, Zhu Y, Liang W, He Y, Yu X. Multiomics analysis reveals a link between Brassica-specific miR1885 and rapeseed tolerance to low temperature. PLANT, CELL & ENVIRONMENT 2023; 46:3405-3419. [PMID: 37564020 DOI: 10.1111/pce.14690] [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: 06/30/2022] [Revised: 06/26/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Brassica crops include various edible vegetable and plant oil crops, and their production is limited by low temperature beyond their tolerant capability. The key regulators of low-temperature resistance in Brassica remain largely unexplored. To identify posttranscriptional regulators of plant response to low temperature, we performed small RNA profiling, and found that 16 known miRNAs responded to cold treatment in Brassica rapa. The cold response of seven of those miRNAs were further confirmed by qRT-PCR and/or northern blot analyses. In parallel, a genome-wide association study of 220 accessions of Brassica napus identified four candidate MIRNA genes, all of which were cold-responsive, at the loci associated with low-temperature resistance. Specifically, these large-scale data analyses revealed a link between miR1885 and the plant response to low temperature in both B. rapa and B. napus. Using 5' rapid amplification of cDNA ends approach, we validated that miR1885 can cleave its putative target gene transcripts, Bn.TIR.A09 and Bn.TNL.A03, in B. napus. Furthermore, overexpression of miR1885 in Semiwinter type B. napus decreased the mRNA abundance of Bn.TIR.A09 and Bn.TNL.A03 and resulted in increased sensitivity to low temperature. Knocking down of miR1885 in Spring type B. napus led to increased mRNA abundance of its targets and improved rapeseed tolerance to low temperature. Together, our results suggested that the loci of miR1885 and its targets could be potential candidates for the molecular breeding of low temperature-tolerant Spring type Brassica crops.
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Affiliation(s)
- Pengfei Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xuan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yantao Zhu
- Hybrid Rape Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuke He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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13
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Jiang Y, Jiang D, Xia M, Gong M, Li H, Xing H, Zhu X, Li HL. Genome-Wide Identification and Expression Analysis of the TCP Gene Family Related to Developmental and Abiotic Stress in Ginger. PLANTS (BASEL, SWITZERLAND) 2023; 12:3389. [PMID: 37836129 PMCID: PMC10574737 DOI: 10.3390/plants12193389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Ginger (Zingiber officinale Roscoe), a widely consumed edible and medicinal plant, possesses significant nutritional and economic value. Abiotic stresses such as drought and low temperatures can impact the growth and development of ginger. The plant-specific transcription factor Teosinte branched1/cycloidea/proliferating cell factor (TCP) has progressively been identified in various plants for its role in regulating plant growth and development as well as conferring resistance to abiotic stresses. However, limited information on the TCP family is available in ginger. In this study, we identified 20 TCP members in the ginger genome, which were randomly distributed across 9 chromosomes. Based on phylogenetic analysis, these ginger TCP were classified into two subfamilies: Class I (PCF) and Class II (CIN, CYC/TB). The classification of the identified ginger TCPs was supported by a multi-species phylogenetic tree and motif structure analysis, suggesting that the amplification of the ginger TCP gene family occurred prior to the differentiation of angiosperms. The promoter region of ginger TCP genes was found to contain numerous cis-acting elements associated with plant growth, development, and abiotic stress response. Among these elements, the stress response element, anaerobic induction, and MYB binding site play a dominant role in drought responsiveness. Additionally, expression pattern analysis revealed variations in the expression of ginger TCP gene among different tissues and in response to diverse abiotic stresses (drought, low temperature, heat, and salt). Our research offers a thorough examination of TCP members within the ginger plant. This analysis greatly contributes to the understanding of how TCP genes regulate tissue development and response to stress, opening up new avenues for further exploration in this field.
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Affiliation(s)
- Yajun Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Dongzhu Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Maoqin Xia
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Min Gong
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Hui Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Haitao Xing
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Xuedong Zhu
- Yudongnan Academy of Agricultural Sciences, Chongqing 408000, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
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14
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Ma Z, Hu L. MicroRNA: A Dynamic Player from Signalling to Abiotic Tolerance in Plants. Int J Mol Sci 2023; 24:11364. [PMID: 37511124 PMCID: PMC10379455 DOI: 10.3390/ijms241411364] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding single-stranded RNA molecules composed of approximately 20-24 nucleotides in plants. They play an important regulatory role in plant growth and development and as a signal in abiotic tolerance. Some abiotic stresses include drought, salt, cold, high temperature, heavy metals and nutritional elements. miRNAs affect gene expression by manipulating the cleavage, translational expression or DNA methylation of target messenger RNAs (mRNAs). This review describes the current progress in the field considering two aspects: (i) the way miRNAs are produced and regulated and (ii) the way miRNA/target genes are used in plant responses to various abiotic stresses. Studying the molecular mechanism of action of miRNAs' downstream target genes could optimize the genetic manipulation of crop growth and development conditions to provide a more theoretically optimized basis for improving crop production. MicroRNA is a novel signalling mechanism in interplant communication relating to abiotic tolerance.
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Affiliation(s)
- Ziming Ma
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Lanjuan Hu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
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15
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Kaur S, Seem K, Kumar S, Kaundal R, Mohapatra T. Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought. Genes (Basel) 2023; 14:1390. [PMID: 37510295 PMCID: PMC10379292 DOI: 10.3390/genes14071390] [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: 05/21/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Recurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food security. The root of a plant is primarily responsible to perceive drought stress and acquire sufficient water for the survival/optimal growth of the plant under extreme climatic conditions. Earlier studies reported the involvement/important roles of microRNAs (miRNAs) in plants' responses to environmental/abiotic stresses. A number (738) of miRNAs is known to be expressed in different tissues under varying environmental conditions in rice, but our understanding of the role, mode of action, and target genes of the miRNAs are still elusive. Using contrasting rice [IR-64 (reproductive-stage drought sensitive) and N-22 (drought-tolerant)] cultivars, imposed with terminal (reproductive-stage) drought stress, we demonstrate differential expression of 270 known and 91 novel miRNAs in roots of the contrasting rice cultivars in response to the stress. Among the known miRNAs, osamiR812, osamiR166, osamiR156, osamiR167, and osamiR396 were the most differentially expressed miRNAs between the rice cultivars. In the root of N-22, 18 known and 12 novel miRNAs were observed to be exclusively expressed, while only two known (zero novels) miRNAs were exclusively expressed in the roots of IR-64. The majority of the target gene(s) of the miRNAs were drought-responsive transcription factors playing important roles in flower, grain development, auxin signaling, root development, and phytohormone-crosstalk. The novel miRNAs identified in this study may serve as good candidates for the genetic improvement of rice for terminal drought stress towards developing climate-smart rice for sustainable food production.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
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16
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Edrisi Maryan K, Farrokhi N, Samizadeh Lahiji H. Cold-responsive transcription factors in Arabidopsis and rice: A regulatory network analysis using array data and gene co-expression network. PLoS One 2023; 18:e0286324. [PMID: 37289769 PMCID: PMC10249815 DOI: 10.1371/journal.pone.0286324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
Plant growth and development can be influenced by cold stress. Responses of plants to cold are regulated in part by transcription factors (TFs) and microRNAs, which their determination would be necessary in comprehension of the corresponding molecular cues. Here, transcriptomes of Arabidopsis and rice were analyzed to computationally determine TFs and microRNAs that are differentially responsive to cold treatment, and their co-expression networks were established. Among 181 Arabidopsis and 168 rice differentially expressed TF genes, 37 (26 novel) were up- and 16 (8 novel) were downregulated. Common TF encoding genes were from ERF, MYB, bHLH, NFY, bZIP, GATA, HSF and WRKY families. NFY A4/C2/A10 were the significant hub TFs in both plants. Phytohormone responsive cis-elements such as ABRE, TGA, TCA and LTR were the common cis-elements in TF promoters. Arabidopsis had more responsive TFs compared to rice possibly due to its greater adaptation to ranges geographical latitudes. Rice had more relevant miRNAs probably because of its bigger genome size. The interacting partners and co-expressed genes were different for the common TFs so that of the downstream regulatory networks and the corresponding metabolic pathways. Identified cold-responsive TFs in (A + R) seemed to be more engaged in energy metabolism esp. photosynthesis, and signal transduction, respectively. At post-transcriptional level, miR5075 showed to target many identified TFs in rice. In comparison, the predictions showed that identified TFs are being targeted by diverse groups of miRNAs in Arabidopsis. Novel TFs, miRNAs and co-expressed genes were introduced as cold-responsive markers that can be harnessed in future studies and development of crop tolerant varieties.
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Affiliation(s)
- Khazar Edrisi Maryan
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
- Department of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran
| | - Naser Farrokhi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
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17
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Zhang WH, Zhang ZY, Liu Y, Tan ZY, Zhou Q, Lin YZ. High-throughput miRNA sequencing and identification of a novel ICE1-targeting miRNA in response to low temperature stress in Eucalyptus camaldulensis. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:541-550. [PMID: 36971569 DOI: 10.1111/plb.13520] [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] [Accepted: 03/14/2023] [Indexed: 05/17/2023]
Abstract
MicroRNAs (miRNAs) play a crucial role in the growth, development, morphogenesis, signal transduction, and stress response in plants. The ICE (Inducer of CBF expression)-CBF (C-repeat binding factor)-COR (Cold-regulated gene) regulatory cascade is an important signalling pathway in plant response to low temperature stress, and it remains unknown whether this pathway is regulated by miRNAs. In this study, high-throughput sequencing was employed for predicting and identifying the miRNAs that were likely to target the ICE-CBF-COR pathway in Eucalyptus camaldulensis. A novel ICE1-targeting miRNA, eca-novel-miR-259-5p (nov-miR259), was further analysed. A total of 392 conserved miRNAs and 97 novel miRNAs were predicted, including 80 differentially expressed miRNAs. Of these, 30 miRNAs were predicted to be associated with the ICE-CBF-COR pathway. The full-length of mature nov-miR259 was 22 bp and its precursor gene was 60 bp in length, with a typical hairpin structure. The RNA ligase-mediated 5' amplification of cDNA ends (5'-RLM-RACE) and Agrobacterium-mediated tobacco transient expression assays demonstrated that nov-miR259 could cleave EcaICE1 in vivo. Moreover, qRT-PCR and Pearson's correlation analysis further revealed that the expression levels of nov-miR259 were almost significantly negatively correlated with those of its target gene, EcaICE1, and the other genes in the ICE-CBF-COR pathway. We first identified the nov-miR259 as a novel ICE1-targeting miRNA, and the nov-miR259-ICE1 module may be involved in regulating the cold stress response in E. camaldulensis.
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Affiliation(s)
- W-H Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Academy of Forestry, Guangzhou, China
| | - Z-Y Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangzhou Huayin Medical Laboratory Center Limited, Guangzhou, China
| | - Y Liu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
| | - Z-Y Tan
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
| | - Q Zhou
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
| | - Y-Z Lin
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
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18
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Wang C, Feng G, Xu X, Huang L, Nie G, Li D, Zhang X. Genome-Wide Identification, Characterization, and Expression of TCP Genes Family in Orchardgrass. Genes (Basel) 2023; 14:genes14040925. [PMID: 37107682 PMCID: PMC10138293 DOI: 10.3390/genes14040925] [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: 03/29/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Plant-specific TCP transcription factors regulate several plant growth and development processes. Nevertheless, little information is available about the TCP family in orchardgrass (Dactylis glomerata L.). This study identified 22 DgTCP transcription factors in orchardgrass and determined their structure, phylogeny, and expression in different tissues and developmental stages. The phylogenetic tree classified the DgTCP gene family into two main subfamilies, including class I and II supported by the exon-intron structure and conserved motifs. The DgTCP promoter regions contained various cis-elements associated with hormones, growth and development, and stress responses, including MBS (drought inducibility), circadian (circadian rhythms), and TCA-element (salicylic acid responsiveness). Moreover, DgTCP9 possibly regulates tillering and flowering time. Additionally, several stress treatments upregulated DgTCP1, DgTCP2, DgTCP6, DgTCP12, and DgTCP17, indicting their potential effects regarding regulating responses to the respective stress. This research offers a valuable basis for further studies of the TCP gene family in other Gramineae and reveals new ideas for increasing gene utilization.
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Affiliation(s)
- Cheng Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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19
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Liu X, Pei L, Zhang L, Zhang X, Jiang J. Regulation of miR319b-Targeted SlTCP10 during the Tomato Response to Low-Potassium Stress. Int J Mol Sci 2023; 24:ijms24087058. [PMID: 37108222 PMCID: PMC10138608 DOI: 10.3390/ijms24087058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Potassium deficiency confines root growth and decreases root-to-shoot ratio, thereby limiting root K+ acquisition. This study aimed to identify the regulation network of microRNA319 involved in low-K+ stress tolerance in tomato (Solanum lycopersicum). SlmiR319b-OE roots demonstrated a smaller root system, a lower number of root hairs and lower K+ content under low-K+ stress. We identified SlTCP10 as the target of miR319b using a modified RLM-RACE procedure from some SlTCPs' predictive complementarity to miR319b. Then, SlTCP10-regulated SlJA2 (an NAC transcription factor) influenced the response to low-K+ stress. CR-SlJA2 (CRISPR-Cas9-SlJA2) lines showed the same root phenotype to SlmiR319-OE compared with WT lines. OE-SlJA2(Overexpression-SlJA2) lines showed higher root biomass, root hair number and K+ concentration in the roots under low-K+ conditions. Furthermore, SlJA2 has been reported to promote abscisic acid (ABA) biosynthesis. Therefore, SlJA2 increases low-K+ tolerance via ABA. In conclusion, enlarging root growth and K+ absorption by the expression of SlmiR319b-regulated SlTCP10, mediating SlJA2 in roots, could provide a new regulation mechanism for increasing K+ acquisition efficiency under low-K+ stress.
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Affiliation(s)
- Xin Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry, Shenyang 110866, China
| | - Lingling Pei
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Lingling Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xueying Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Jing Jiang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry, Shenyang 110866, China
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Shen X, Ping Y, Bao C, Liu C, Tahir MM, Li X, Song Y, Xu W, Ma F, Guan Q. Mdm-miR160-MdARF17-MdWRKY33 module mediates freezing tolerance in apple. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:262-278. [PMID: 36738108 DOI: 10.1111/tpj.16132] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 05/10/2023]
Abstract
Apple (Malus domestica) trees are vulnerable to freezing temperatures. Cold resistance in woody perennial plants can be improved through biotechnological approaches. However, genetic engineering requires a thorough understanding of the molecular mechanisms of the tree's response to cold. In this study, we demonstrated that the Mdm-miR160-MdARF17-MdWRKY33 module is crucial for apple freezing tolerance. Mdm-miR160 plays a negative role in apple freezing tolerance, whereas MdARF17, one of the targets of Mdm-miR160, is a positive regulator of apple freezing tolerance. RNA sequencing analysis revealed that in apple, MdARF17 mediates the cold response by influencing the expression of cold-responsive genes. EMSA and ChIP-qPCR assays demonstrated that MdARF17 can bind to the promoter of MdWRKY33 and promotes its expression. Overexpression of MdWRKY33 enhanced the cold tolerance of the apple calli. In addition, we found that the Mdm-miR160-MdARF17-MdWRKY33 module regulates cold tolerance in apple by regulating reactive oxygen species (ROS) scavenging, as revealed by (i) increased H2 O2 levels and decreased peroxidase (POD) and catalase (CAT) activities in Mdm-miR160e OE plants and MdARF17 RNAi plants and (ii) decreased H2 O2 levels and increased POD and CAT activities in MdmARF17 OE plants and MdWRKY33 OE calli. Taken together, our study uncovered the molecular roles of the Mdm-miR160-MdARF17-MdWRKY33 module in freezing tolerance in apple, thus providing support for breeding of cold-tolerant apple cultivars.
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Affiliation(s)
- Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yikun Ping
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chana Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chen Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Muhammad Mobeen Tahir
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yi Song
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weirong Xu
- Ningxia Engineering and Technology Research Center of Grape and Wine, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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21
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Chen G, Wang Y, Liu X, Duan S, Jiang S, Zhu J, Zhang Y, Hou H. The MdmiR156n Regulates Drought Tolerance and Flavonoid Synthesis in Apple Calli and Arabidopsis. Int J Mol Sci 2023; 24:ijms24076049. [PMID: 37047020 PMCID: PMC10094179 DOI: 10.3390/ijms24076049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/09/2023] [Accepted: 03/19/2023] [Indexed: 04/14/2023] Open
Abstract
Drought is the major abiotic stress that limits apple productivity and quality. To date, many important and divergent regulatory functions of miR156/SBP genes in plant growth and development have been well understood. However, little is known about the role of apple miR156 in response to abiotic stress. To better understand the functions of MdmiR156 in abiotic stress tolerance, we constructed the overexpression (OE) and short tandem target mimic (STTM) vector of MdmiR156n and performed its functional analysis through the characterization of transgenic apple calli and Arabidopsis thaliana plants. In this study, MdmiR156n overexpression significantly increased the length of primary roots and the number of lateral roots in transgenic Arabidopsis plants under drought stress. In addition, MdmiR156n transgenic Arabidopsis and apple calli had a lower electrolyte leakage rate and less cell membrane damage than WT and STTM156 after drought stress. Further studies showed that MdmiR156n overexpression promoted the accumulation of flavonoids and scavenging of reactive oxygen species (ROS) under drought conditions in transgenic apple calli and A. thaliana plants. Taken together, overexpression MdmiR156n enhances drought tolerance by regulating flavonoid synthesis and ROS signaling cascades in apple calli and A. thaliana.
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Affiliation(s)
- Guo Chen
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Yaping Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Xueli Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Siyue Duan
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Shenghui Jiang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Jun Zhu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Yugang Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Hongmin Hou
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
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22
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Huang L, Yu J, Liu Q, Yu K, Zhang Q, Fan M, Jiang F, Han J, Wei H, Jian W, Zhao Z. Study on tillering stage cold tolerant response in overwintering cultivated rice via comparative transcriptomic. Food Energy Secur 2023. [DOI: 10.1002/fes3.450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023] Open
Affiliation(s)
- Lunxiao Huang
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Jie Yu
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Qian Liu
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Kunchi Yu
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Qiuyu Zhang
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Mao Fan
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Fei Jiang
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Jiajia Han
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Hongyu Wei
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Wei Jian
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Zhengwu Zhao
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
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23
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Vera Hernández PF, Mendoza Onofre LE, Rosas Cárdenas FDF. Responses of sorghum to cold stress: A review focused on molecular breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1124335. [PMID: 36909409 PMCID: PMC9996117 DOI: 10.3389/fpls.2023.1124335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.
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Affiliation(s)
- Pedro Fernando Vera Hernández
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
| | | | - Flor de Fátima Rosas Cárdenas
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
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24
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Hussain MA, Li S, Gao H, Feng C, Sun P, Sui X, Jing Y, Xu K, Zhou Y, Zhang W, Li H. Comparative analysis of physiological variations and genetic architecture for cold stress response in soybean germplasm. FRONTIERS IN PLANT SCIENCE 2023; 13:1095335. [PMID: 36684715 PMCID: PMC9852849 DOI: 10.3389/fpls.2022.1095335] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Soybean (Glycine max L.) is susceptible to low temperatures. Increasing lines of evidence indicate that abiotic stress-responsive genes are involved in plant low-temperature stress response. However, the involvement of photosynthesis, antioxidants and metabolites genes in low temperature response is largely unexplored in Soybean. In the current study, a genetic panel of diverse soybean varieties was analyzed for photosynthesis, chlorophyll fluorescence and leaf injury parameters under cold stress and control conditions. This helps us to identify cold tolerant (V100) and cold sensitive (V45) varieties. The V100 variety outperformed for antioxidant enzymes activities and relative expression of photosynthesis (Glyma.08G204800.1, Glyma.12G232000.1), GmSOD (GmSOD01, GmSOD08), GmPOD (GmPOD29, GmPOD47), trehalose (GmTPS01, GmTPS13) and cold marker genes (DREB1E, DREB1D, SCOF1) than V45 under cold stress. Upon cold stress, the V100 variety showed reduced accumulation of H2O2 and MDA levels and subsequently showed lower leaf injury compared to V45. Together, our results uncovered new avenues for identifying cold tolerant soybean varieties from a large panel. Additionally, we identified the role of antioxidants, osmo-protectants and their posttranscriptional regulators miRNAs such as miR319, miR394, miR397, and miR398 in Soybean cold stress tolerance.
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Affiliation(s)
- Muhammad Azhar Hussain
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Senquan Li
- College of Tropical Crops, Hainan University, Haikou, China
| | - Hongtao Gao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Chen Feng
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Pengyu Sun
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xiangpeng Sui
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yan Jing
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Keheng Xu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yonggang Zhou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Wenping Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Haiyan Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
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25
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Zhang C, Shen J, Wang C, Wang Z, Guo L, Hou X. Characterization of PsmiR319 during flower development in early- and late-flowering tree peonies cultivars. PLANT SIGNALING & BEHAVIOR 2022; 17:2120303. [PMID: 36200538 PMCID: PMC9542857 DOI: 10.1080/15592324.2022.2120303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
The flowering period is the most important ornamental trait of tree peony, while industrial development of tree peony has been limited by short flowering period. miR319 plays an important regulatory role in plant flowering. In the current study, the expression characteristics and evolution of PsmiR319 in tree peony flowering was explored using 'Feng Dan' and 'Lian He', which are early-flowering and late-flowering varieties of tree peony, respectively. The structure, evolution, and target(s) of PsmiR319 were analyzed by bioinformatics. Evolution analysis showed that pre-PsmiR319 was distributed in 41 plant species, among which the length of the precursor sequence exhibited marked differences (between 52 and 308 bp). Pre-PsmiR319 of tree peony was located close to the corresponding sequences of Linum usitatissimum and Picea abies in the phylogenetic tree, and in addition, could form a typical hairpin structure including a mature body with a length of 20 bp located on the 3p arm and part of the loop sequence. The mature sequence of miR319 was highly conserved among different species. Target genes of PsmiR319 include MYB-related transcription factor in tree peony. Expression of PsmiR319, assayed by qRT-PCR, differed between 'Feng Dan' and 'Lian He' during different flower development periods. PsmiR319 and its target gene showed a negative expression regulation relationship during the periods of CE (color exposure), BS (blooming stage), IF (initial flowering), and HO (half opening) in the early-flowering 'Feng Dan', and the same in FB (Full blooming) periods of late-flowering 'Lian He'. Findings from this study provide a reference for further investigation into the mechanism of miR319 in the development of different varieties of tree peony.
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Affiliation(s)
- Chenjie Zhang
- College of Agriculture/Tree Peony, Henan University of Science and Technology, LuoyangChina
| | - Jiajia Shen
- College of Agriculture/Tree Peony, Henan University of Science and Technology, LuoyangChina
| | - Can Wang
- College of Agriculture/Tree Peony, Henan University of Science and Technology, LuoyangChina
| | - Zhanying Wang
- Peony Research Institute, Luoyang Academy of Agricultural and Forestry Sciences, LuoyangChina
| | - Lili Guo
- College of Agriculture/Tree Peony, Henan University of Science and Technology, LuoyangChina
| | - Xiaogai Hou
- College of Agriculture/Tree Peony, Henan University of Science and Technology, LuoyangChina
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26
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Huo C, Zhang B, Wang R. Research progress on plant noncoding RNAs in response to low-temperature stress. PLANT SIGNALING & BEHAVIOR 2022; 17:2004035. [PMID: 34927551 PMCID: PMC8932918 DOI: 10.1080/15592324.2021.2004035] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Low temperature (LT) is an important factor limiting plant growth and distribution. Plants have evolved sophisticated adaptive mechanisms to cope with hypothermia. RNA silencing is the orchestrator of these cellular responses. RNA silencing, which modifies gene expression through noncoding RNAs (ncRNAs), is a strategy used by plants to combat environmental stress. ncRNAs, which have very little protein-coding capacity, work by binding reverse complementary endogenous transcripts. In plants, ncRNAs include small non-coding RNAs (sncRNAs), medium-sized non-coding RNAs (mncRNAs), and long non-coding RNAs (lncRNAs). Apart from describing the biogenesis of different ncRNAs (miRNAs, siRNAs, and lncRNAs), we thoroughly discuss the functions of these ncRNAs during cold acclimation. Two major classes of sncRNAs, microRNAs and siRNAs, play essential regulatory roles in cold response processes through the posttranscriptional gene silencing (PTGS) pathway or transcriptional gene silencing (TGS) pathway. Microarray or transcriptome sequencing analysis can reveal a large number of cold-responsive miRNAs in plants. In this review, the cold-response patterns of miRNAs verified by Northern blotting or quantitative PCR in Arabidopsis thaliana, rice, and many other important crops are discussed. The detailed molecular mechanisms of several miRNAs in Arabidopsis (miR397, miR408, miR402, and miR394) and rice (Osa-miR156, Osa-miR319, and Osa-miR528) that regulate plant cold resistance are elucidated. In addition, the regulatory mechanism of the lncRNA SVALKA in the cold signaling pathway is explained in detail. Finally, we present the challenges for understanding the roles of small ncRNAs in cold signal transduction.
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Affiliation(s)
- Chenmin Huo
- College of Biology Science & Engineering, Hebei University of Economics & Business, Shijiazhuang, China
| | - Baowen Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ruiju Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- CONTACT Ruiju Wang College of Biology Science & Engineering, Hebei University of Economics & Business, Shijiazhuang, China
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Chen L, Xu Z, Fan X, Zhou Q, Yu Q, Liu X, Liao S, Jiang C, Lin D, Ma F, Feng B, Wang T. Genetic dissection of quantitative trait loci for flag leaf size in bread wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1047899. [PMID: 36600920 PMCID: PMC9807109 DOI: 10.3389/fpls.2022.1047899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Flag leaf size is a crucial trait influencing plant architecture and yield potential in wheat. A recombinant inbred line (RIL) population derived from the cross of W7268 and Chuanyu 12 was employed to identify quantitative trait loci (QTL) controlling flag leaf length (FLL), flag leaf width (FLW), and flag leaf area (FLA) in six environments and the best linear unbiased estimator (BLUE) datasets. Using a 55 K SNP-based genetic map, six major and stable QTL were detected with 6.33-53.12% of explained phenotypic variation. Except for QFlw.cib-4B.3, the other five major QTL were co-located within two intervals on chromosomes 2B and 2D, namely QFll/Fla.cib-2B and QFll/Flw/Fla.cib-2D, respectively. Their interactions and effects on the corresponding traits and yield-related traits were also assessed based on flanking markers. QFll/Fla.cib-2B showed pleiotropic effects on spikelet number per spike (SNS). QFlw.cib-4B.3 and QFll/Flw/Fla.cib-2D had effects on grain number per spike (GNS) and thousand-grain weight (TGW). Comparison analysis suggested that QFll/Fla.cib-2B was likely a new locus. Two candidate genes, TraesCS2B03G0222800 and TraesCS2B03G0230000, associated with leaf development within the interval of QFll/Fla.cib-2B were identified based on expression-pattern analysis, gene annotation, ortholog analysis, and sequence variation. The major QTL and markers reported here provide valuable information for understanding the genetic mechanism underlying flag leaf size as well as breeding utilization in wheat.
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Affiliation(s)
- Liangen Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qin Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dian Lin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fang Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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28
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Zhang L, Song J, Lin R, Tang M, Shao S, Yu J, Zhou Y. Tomato SlMYB15 transcription factor targeted by sly-miR156e-3p positively regulates ABA-mediated cold tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7538-7551. [PMID: 36103722 DOI: 10.1093/jxb/erac370] [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: 05/05/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
Cold is a common abiotic stress that seriously affects plant growth and development. MYB transcription factors are regulatory molecules that play important roles in various biological processes. We have previously demonstrated that SlMYB15 positively regulates cold tolerance in tomato. However, the underlying mechanism of SlMYB15-induced cold tolerance remains largely unexplored. Here, cold-induced SlMYB15 was found to be targeted by Solanum lycopersicum (sly)-miR156e-3p, which was decreased by cold stimulus in tomato. Tomato plants overexpressing sly-MIR156e-3p displayed significant enhancement in susceptibility to cold stress, while silencing of sly-miR156e-3p by an artificial microRNA interference strategy caused tomato plants to be more tolerant to cold. Moreover, both overexpression of SlMYB15 and silencing of sly-miR156e-3p increased the accumulation of ABA. SlMYB15 directly binds to the promoter regions of ABA biosynthesis and signalling genes, SlNCED1 and SlABF4, resulting in enhanced cold tolerance. Further experiments showed that SlMYB15 and sly-miR156e-3p also coordinated the cold tolerance of tomato via the reactive oxygen species (ROS) signalling pathway, as reflected by the increased expression of SlRBOH1, enhanced H2O2 and O2•-accumulation, and amplified activity of antioxidant enzymes in SlMYB15-overexpressing and sly-miR156e-3p-silenced plants. Taken together, our results demonstrate that SlMYB15 targeted by sly-miR156e-3p confers higher survivability to cold stress via ABA and ROS signals. This study provides valuable information for breeding improved crop cultivars better equipped with cold tolerance.
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Affiliation(s)
- Luyue Zhang
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou 45001, China
| | - Jianing Song
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Rui Lin
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Mingjia Tang
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Shujun Shao
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Jingquan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
- Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Yuhangtang Road 866, Hangzhou, 310058, P.R. China
| | - Yanhong Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
- Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Yuhangtang Road 866, Hangzhou, 310058, P.R. China
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Jiang L, Fu Y, Sun P, Tian X, Wang G. Identification of microRNA158 from Anthurium andraeanum and Its Function in Cold Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2022; 11:3371. [PMID: 36501408 PMCID: PMC9735552 DOI: 10.3390/plants11233371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Anthurium andraeanum is a tropical flower with high ornamental and economic value. Cold stress is one of the major abiotic stresses affecting the quality and value of A. andraeanum; thus, improving the cold tolerance of this species is an important breeding objective. MicroRNAs (miRNAs) have a critical role in plant abiotic stress responses, but their specific molecular regulatory mechanisms are largely unknown, including those related to the cold stress response in A. andraeanum. Here, we identified and cloned the precursor of miR158 from A. andraeanum (Aa-miR158). Both Aa-miR158 and its target gene (c48247) had higher expression levels in strong leaves than in other tissues or organs. Further study revealed that the transcript level of Aa-miR158 was increased by cold stress. Heterologous overexpression of Aa-miR158 improved cold stress tolerance in Arabidopsis, which was associated with decreases in the malondialdehyde (MDA) concentration and relative electrical conductivity (REC) as well as increases in peroxidase (POD) and catalase (CAT) activity. Moreover, overexpressing Aa-miR158 significantly increased the expression of endogenous genes related to cold stress tolerance and reactive oxygen species (ROS) levels in transgenic Arabidopsis under cold stress. Overall, our results demonstrate that Aa-miR158 is significantly involved in the cold stress response and provide a new strategy for cold tolerance breeding of A. andraeanum.
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Li J, Li Y, Wang R, Fu J, Zhou X, Fang Y, Wang Y, Liu Y. Multiple Functions of MiRNAs in Brassica napus L. Life (Basel) 2022; 12:1811. [PMID: 36362967 PMCID: PMC9694376 DOI: 10.3390/life12111811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 09/05/2023] Open
Abstract
The worldwide climate changes every year due to global warming, waterlogging, drought, salinity, pests, and pathogens, impeding crop productivity. Brassica napus is one of the most important oil crops in the world, and rapeseed oil is considered one of the most health-beneficial edible vegetable oils. Recently, miRNAs have been found and confirmed to control the expression of targets under disruptive environmental conditions. The mechanism is through the formation of the silencing complex that mediates post-transcriptional gene silencing, which pairs the target mRNA and target cleavage and/or translation inhibition. However, the functional role of miRNAs and targets in B. napus is still not clarified. This review focuses on the current knowledge of miRNAs concerning development regulation and biotic and abiotic stress responses in B. napus. Moreover, more strategies for miRNA manipulation in plants are discussed, along with future perspectives, and the enormous amount of transcriptome data available provides cues for miRNA functions in B. napus. Finally, the construction of the miRNA regulatory network can lead to the significant development of climate change-tolerant B. napus through miRNA manipulation.
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Affiliation(s)
- Jian Li
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Yangyang Li
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Rongyuan Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Jiangyan Fu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Xinxing Zhou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Yaju Liu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
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Ullah I, Kamel EAR, Shah ST, Basit A, Mohamed HI, Sajid M. Application of RNAi technology: a novel approach to navigate abiotic stresses. Mol Biol Rep 2022; 49:10975-10993. [PMID: 36057876 DOI: 10.1007/s11033-022-07871-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Due to the rising population globally, and the demand for food, it is critical to significantly increase crop production by 2050. However, climate change estimates show that droughts and heatwaves will become more prevalent in many parts of the world, posing a severe danger to food output. METHODS Selective breeding based on genetic diversity is falling short of meeting the expanding need for food and feed. However, the advent of modern plant genetic engineering, genome editing, and synthetic biology provides precise techniques for producing crops capable of sustaining yield under stress situations. RESULTS As a result, crop varieties with built-in genetic tolerance to environmental challenges are desperately needed. In the recent years, small RNA (sRNA) data has progressed to become one of the most effective approaches for the improvement of crops. So many sRNAs (18-30nt) have been found with the use of hi-tech bioinformatics and sequencing techniques which are involved in the regulation of sequence specific gene noncoding RNAs (short ncRNAs) i.e., microRNA (miRNA) and small interfering RNA (siRNA). Such research outcomes may advance our understanding of the genetic basis of adaptability of plants to various environmental challenges and the genetic variation of plant's tolerance to a number of abiotic stresses. CONCLUSION The review article highlights current trends and advances in sRNAs' critical role in responses of plants to drought, heat, cold, and salinity, and also the potential technology that identifies the abiotic stress-regulated sRNAs, and techniques for analyzing and validating the target genes.
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Affiliation(s)
- Izhar Ullah
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Ehab A R Kamel
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt
| | - Syed Tanveer Shah
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Abdul Basit
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Heba I Mohamed
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt.
| | - Muhammad Sajid
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
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Li X, Yang Q, Liao X, Tian Y, Zhang F, Zhang L, Liu Q. A natural antisense RNA improves chrysanthemum cold tolerance by regulating the transcription factor DgTCP1. PLANT PHYSIOLOGY 2022; 190:605-620. [PMID: 35728057 PMCID: PMC9434197 DOI: 10.1093/plphys/kiac267] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/10/2022] [Indexed: 05/20/2023]
Abstract
Long noncoding RNAs (lncRNAs) are widely involved in the regulation of plant growth and development, but their mechanism of action in response to cold stress in plants remains unclear. Here, we found an lncRNA transcribed from the antisense strand of DgTCP1 (class I Teosinte branched1/Cycloidea/Proliferating [TCP] transcription factor) of chrysanthemum (Chrysanthemum morifolium Ramat.), named DglncTCP1. During the response of chrysanthemum to cold stress, overexpression of DgTCP1 improved the cold tolerance of chrysanthemum, while the DgTCP1 editing line (dgtcp1) showed decreased tolerance to cold stress. Overexpression of DglncTCP1 also increased the cold tolerance of chrysanthemum, while the DglncTCP1 amiRNA lines (DglncTCP1 amiR-18/38) also showed decreased tolerance to cold stress. Additionally, the overexpression of DglncTCP1 upregulated the expression of DgTCP1. This indicated that DglncTCP1 may play a cis-regulatory role in the regulatory process of DgTCP1 in cold tolerance. DglncTCP1 acts as a scaffold to recruit the histone modification protein DgATX (ARABIDOPSIS TRITHORAX from chrysanthemum) to DgTCP1 to enhance H3K4me3 levels, thereby activating DgTCP1 expression. Moreover, DgTCP1 can directly target DgPOD (peroxidase gene from chrysanthemum) to promote its expression and reduce reactive oxygen species accumulation, thereby improving the cold tolerance of chrysanthemum. In conclusion, these results suggest that natural antisense lncRNA plays a key role in improving the cold tolerance of chrysanthemum.
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Affiliation(s)
- Xin Li
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, People’s Republic of China
| | - Qing Yang
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, People’s Republic of China
| | - Xiaoqin Liao
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, People’s Republic of China
| | - Yuchen Tian
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, People’s Republic of China
| | - Fan Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, People’s Republic of China
| | - Lei Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, People’s Republic of China
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Zhang F, Yang J, Zhang N, Wu J, Si H. Roles of microRNAs in abiotic stress response and characteristics regulation of plant. FRONTIERS IN PLANT SCIENCE 2022; 13:919243. [PMID: 36092392 PMCID: PMC9459240 DOI: 10.3389/fpls.2022.919243] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.
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Affiliation(s)
- Feiyan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Meng J, Yin J, Wang H, Li H. A TCP Transcription Factor in Malus halliana, MhTCP4, Positively Regulates Anthocyanins Biosynthesis. Int J Mol Sci 2022; 23:ijms23169051. [PMID: 36012317 PMCID: PMC9409405 DOI: 10.3390/ijms23169051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 02/08/2023] Open
Abstract
Anthocyanins belong to a group of flavonoids, which are the most important flower pigments. Clarifying the potential anthocyanins biosynthesis molecular mechanisms could facilitate artificial manipulation of flower pigmentation in plants. In this paper, we screened a differentially expressed gene, MhTCP4, from the transcriptome data of Malus halliana petals at different development stages and explored its role in anthocyanins biosynthesis. The transcriptome data and qRT-PCR analysis showed that the expression level of MhTCP4 gradually decreased from the flower color fades. Tissue specific expression analysis showed MhTCP4 was expressed in the petal, leaf, and fruit of M. halliana, and was highly expressed in the scarlet petal. Overexpression of MhTCP4 promoted anthocyanins accumulation and increased pigments in infected parts of M. 'Snowdrift' and M. 'Fuji' fruit peels. In contrast, when endogenous MhTCP4 was silenced, the anthocyanins accumulation was inhibited and pigments decreased in the infected peels. The qRT-PCR analysis revealed that overexpression or silence of MhTCP4 caused expression changes of a series of structural genes included in anthocyanins biosynthesis pathway. The yeast two-hybrid assays indicated that MhTCP4 did not interact with MhMYB10. Furthermore, the yeast one-hybrid assays indicated that MhTCP4 did not directly bind to the promoter of MhMYB10, but that of the anthocyanins biosynthesis genes, MhCHI and MhF3'H. Dual luciferase assays further confirmed that MhTCP4 can strongly activate the promoters of MhCHI and MhF3'H in tobacco. Overall, the results suggest that MhTCP4 positively regulates anthocyanins biosynthesis by directly activated MhCHI and MhF3'H in M. halliana flowers.
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Affiliation(s)
| | | | | | - Houhua Li
- Correspondence: ; Tel.: +86-151-1480-0050
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Sun M, Shen Y, Chen Y, Wang Y, Cai X, Yang J, Jia B, Dong W, Chen X, Sun X. Osa-miR1320 targets the ERF transcription factor OsERF096 to regulate cold tolerance via JA-mediated signaling. PLANT PHYSIOLOGY 2022; 189:2500-2516. [PMID: 35522026 PMCID: PMC9342977 DOI: 10.1093/plphys/kiac208] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/09/2022] [Indexed: 05/08/2023]
Abstract
MicroRNAs play key roles in abiotic stress response. Rice (Oryza sativa L.) miR1320 is a species-specific miRNA that contributes to miR168-regulated immunity. However, it is still unknown whether miR1320 is involved in rice response to abiotic stress. In this study, we illustrated that the miR1320 precursor generated two mature miR1320s, miR1320-3p, and miR1320-5p, and they both displayed decreased expression under cold stress. Genetic evidence showed that miR1320 overexpression resulted in increased cold tolerance, while miR1320 knock down (KD) reduced cold tolerance. Furthermore, an APETALA2/ethylene-responsive factor (ERF) transcription factor OsERF096 was identified as a target of miR1320 via 5'-RACE and dual luciferase assays. OsERF096 expression was altered by miR1320 overexpression and KD and exhibited an opposite pattern to that of miR1320 in different tissues and under cold stress. Consistently, OsERF096 negatively regulated cold stress tolerance. Furthermore, we suggested that OsERF096 could bind to the GCC and DRE cis-elements and act as a transcriptional activator in the nucleus. Based on RNA-sequencing and targeted metabolomics assays, we found that OsERF096 modified hormone content and signaling pathways. Finally, phenotypic and reverse transcription-quantitative PCR assays showed that jasmonic acid (JA) methyl ester application recovered the cold-sensitive phenotype and JA-activated expression of three Dehydration Responsive Element Binding genes in the OsERF096-OE line. Taken together, our results strongly suggest that the miR1320-OsERF096 module regulates cold tolerance by repressing the JA-mediated cold signaling pathway.
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Affiliation(s)
| | | | | | - Yan Wang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaoxi Cai
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Junkai Yang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Bowei Jia
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Weifeng Dong
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xi Chen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaoli Sun
- Authors for correspondence: (X.S.), (M.S.)
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Kumar K, Mandal SN, Neelam K, de los Reyes BG. MicroRNA-mediated host defense mechanisms against pathogens and herbivores in rice: balancing gains from genetic resistance with trade-offs to productivity potential. BMC PLANT BIOLOGY 2022; 22:351. [PMID: 35850632 PMCID: PMC9290239 DOI: 10.1186/s12870-022-03723-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 06/29/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is the major source of daily caloric intake for more than 30% of the human population. However, the sustained productivity of this staple food crop is continuously threatened by various pathogens and herbivores. Breeding has been successful in utilizing various mechanisms of defense by gene pyramiding in elite cultivars, but the continuous resurgence of highly resistant races of pathogens and herbivores often overcomes the inherent capacity of host plant immunity. MicroRNAs (miRNAs) are endogenous, short, single-stranded, non-coding RNA molecules that regulate gene expression by sequence-specific cleavage of target mRNA or suppressing target mRNA translation. While miRNAs function as upstream regulators of plant growth, development, and host immunity, their direct effects on growth and development in the context of balancing defenses with agronomic potential have not been extensively discussed and explored as a more viable strategy in breeding for disease and pest resistant cultivars of rice with optimal agronomic potentials. RESULTS Using the available knowledge in rice and other model plants, this review examines the important roles of miRNAs in regulating host responses to various fungal, bacterial, and viral pathogens, and insect pests, in the context of gains and trade-offs to crop yield. Gains from R-gene-mediated resistance deployed in modern rice cultivars are often undermined by the rapid breakdown of resistance, negative pleiotropic effects, and linkage drags with undesirable traits. In stark contrast, several classes of miRNAs are known to efficiently balance the positive gains from host immunity without significant costs in terms of losses in agronomic potentials (i.e., yield penalty) in rice. Defense-related miRNAs such as Osa-miR156, Osa-miR159, Osa-miR162, Osa-miR396, Osa-530, Osa-miR1432, Osa-miR1871, and Osa-miR1873 are critical in fine-tuning and integrating immune responses with physiological processes that are necessary to the maintenance of grain yield. Recent research has shown that many defense-related miRNAs regulate complex and agronomically important traits. CONCLUSIONS Identification of novel immune-responsive miRNAs that orchestrate physiological processes critical to the full expression of agronomic potential will facilitate the stacking of optimal combinations of miRNA-encoding genes to develop high-yielding cultivars with durable resistance to disease and insect pests with minimal penalties to yield.
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Affiliation(s)
- Kishor Kumar
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, Kolkata, 700103 India
| | - Swarupa Nanda Mandal
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX-79415 USA
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Extended Campus, Burdwan, West Bengal 713101 India
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004 India
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Liu DH, Luo Y, Han H, Liu YZ, Alam SM, Zhao HX, Li YT. Genome-wide analysis of citrus TCP transcription factors and their responses to abiotic stresses. BMC PLANT BIOLOGY 2022; 22:325. [PMID: 35790897 PMCID: PMC9258177 DOI: 10.1186/s12870-022-03709-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Citrus is one of the most important fruit crops in the world, and it is worthy to conduct more research on artificially controlling citrus plant growth and development to adapt to different cultivation patterns and environmental conditions. The plant-specific TEOSINTE BRANCHED1, CYCOLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors are crucial regulators controlling plant growth and development, as well as responding to abiotic stresses. However, the information about citrus TCP transcription factors remains unclear. RESULTS In this study, twenty putative TCP genes (CsTCPs) with the TCP domain were explored from Citrus sinensis genome, of which eleven (CsTCP3, - 4, - 5, - 6, - 10, - 11, - 15, - 16, - 18, - 19, - 20), five (CsTCP1, - 2, - 7, - 9, - 13), and four genes (CsTCP8, - 12, - 14, - 17) were unevenly distributed on chromosomes and divided into three subclades. Cis-acting element analysis indicated that most CsTCPs contained many phytohormone- and environment-responsive elements in promoter regions. All of CsTCPs were predominantly expressed in vegetative tissues or organs (stem, leaf, thorn, and bud) instead of reproductive tissues or organs (flower, fruit, and seed). Combined with collinearity analysis, CsTCP3, CsTCP9, and CsTCP13 may take part in leaf development; CsTCP12 and CsTCP14 may function in shoot branching, leaf development, or thorn development; CsTCP15 may participate in the development of stem, leaf, or thorn. In mature leaf, transcript levels of two CsTCPs (CsTCP19, - 20) were significantly increased while transcript levels of eight CsTCPs (CsTCP2, - 5, - 6, - 7, - 8, - 9, - 10, - 13) were significantly decreased by shading; except for two CsTCPs (CsTCP11, - 19), CsTCPs' transcript levels were significantly influenced by low temperature; moreover, transcript levels of two CsTCPs (CsTCP11, - 12) were significantly increased while five CsTCPs' (CsTCP14, - 16, - 18, - 19, - 20) transcript levels were significantly reduced by drought. CONCLUSIONS This study provides significant clues for research on roles of CsTCPs in regulating citrus plant growth and development, as well as responding to abiotic stresses.
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Affiliation(s)
- Dong-Hai Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Yin Luo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Han Han
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Yong-Zhong Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Shariq Mahmood Alam
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Hui-Xing Zhao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Yan-Ting Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
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Shang X, Han Z, Zhang D, Wang Y, Qin H, Zou Z, Zhou L, Zhu X, Fang W, Ma Y. Genome-Wide Analysis of the TCP Gene Family and Their Expression Pattern Analysis in Tea Plant ( Camellia sinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:840350. [PMID: 35845692 PMCID: PMC9284231 DOI: 10.3389/fpls.2022.840350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors TEOSINTE BRANCHED1/CYCLOIDEA/PCF have been suggested to control the cell growth and proliferation in meristems and lateral organs. A total of 37 CsTCP genes were identified and divided into two classes, class I (PCF, group 1) and class II (CIN CYC/TB1, groups 2, and 3). The residues of TEOSINTE BRANCHED1/CYCLOIDEA/PCF of Camellia sinensis (Tea plant) (CsTCP) proteins between class I and class II were definitely different in the loop, helix I, and helix II regions; however, eighteen conserved tandem was found in bHLH. There are a large number of CsTCP homologous gene pairs in three groups. Additionally, most CsTCP proteins have obvious differences in motif composition. The results illuminated that CsTCP proteins in different groups are supposed to have complementary functions, whereas those in the same class seem to display function redundancies. There is no relationship between the number of CsTCP gene members and genome size, and the CsTCP gene family has only expanded since the divergence of monocots and eudicots. WGD/segmental duplication played a vital role in the expansion of the CsTCP gene family in tea plant, and the CsTCP gene family has expanded a lot. Most CsTCP genes of group 1 are more widely and non-specifically expressed, and the CsTCP genes of group 2 are mainly expressed in buds, flowers, and leaves. Most genes of group 1 and some genes of group 2 were up-/downregulated in varying degrees under different stress, CsTCP genes of group 3 basically do not respond to stress. TCP genes involved in abiotic stress response mostly belong to PCF group. Some CsTCP genes may have the same function as the homologous genes in Arabidopsis, but there is functional differentiation.
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Affiliation(s)
- Xiaowen Shang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhaolan Han
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Dayan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ya Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hao Qin
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Agricultural and Forestry Service Center, Suzhou, China
| | - Zhongwei Zou
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Lin Zhou
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Xu Y, Wang L, Liu H, He W, Jiang N, Wu M, Xiang Y. Identification of TCP family in moso bamboo (Phyllostachys edulis) and salt tolerance analysis of PheTCP9 in transgenic Arabidopsis. PLANTA 2022; 256:5. [PMID: 35670871 DOI: 10.1007/s00425-022-03917-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Bioinformatic analysis of moso bamboo TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors reveals their conservation and variation as well as the probable biological functions in abiotic stress response. Overexpressing PheTCP9 in Arabidopsis thaliana illustrates it may exhibit a new vision in different aspects of response to salt stress. Plant specific TCPs play important roles in plant growth, development and stress response, but studies of TCP in moso bamboo are limited. Therefore, in this study, a total of 40 TCP genes (PheTCP1 ~ 40) were identified and characterized from moso bamboo genome and divided into three different subfamilies, namely, 7 in TEOSINTE BRANCHED 1 / CYCLOIDEA (TB1/CYC), 14 in CINCINNATA (CIN) and 19 in PROLIFERATING CELL FACTOR (PCF). Subsequently, we analyzed the gene structures and conserved domain of these genes and found that the members from the same subfamilies exhibited similar exon/intron distribution patterns. Selection pressure and gene duplication analysis results indicated that PheTCP genes underwent strong purification selection during evolution. There were many cis-elements related to phytohermone and stress responsive existing in the upstream promoter regions of PheTCP genes, such as ABRE, CGTCA-motif and ARE. Subcellular localization experiments showed that PheTCP9 was a nuclear localized protein. As shown by β-glucuronidase (GUS) activity, the promoter of PheTCP9 was significantly indicated by salt stress. PheTCP9 was significantly induced in the roots, stems and leaves of moso bamboo. It was also significantly induced by NaCl solution. Overexpressing PheTCP9 increased the salt tolerance of transgenic Arabidopsis. Meanwhile, H2O2 and malondialdehyde (MDA) contents were significantly lower in PheTCP9 over expression (OE) transgenic Arabidopsis than WT. Catalase (CAT) activity, K+/Na+ ratio as well as CAT2 expression level was also much improved in transgenic Arabidopsis than WT under salt conditions. In addition, PheTCP9 OE transgenic Arabidopsis held higher survival rates of seedlings than WT under NaCl conditions. These results showed the positive regulation functions of PheTCP9 in plants under salt conditions.
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Affiliation(s)
- Yuzeng Xu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Linna Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Hongxia Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Wei He
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Nianqin Jiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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Jin K, Wang Y, Zhuo R, Xu J, Lu Z, Fan H, Huang B, Qiao G. TCP Transcription Factors Involved in Shoot Development of Ma Bamboo ( Dendrocalamus latiflorus Munro). FRONTIERS IN PLANT SCIENCE 2022; 13:884443. [PMID: 35620688 PMCID: PMC9127963 DOI: 10.3389/fpls.2022.884443] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/08/2022] [Indexed: 05/10/2023]
Abstract
Ma bamboo (Dendrocalamus latiflorus Munro) is the most widely cultivated clumping bamboo in Southern China and is valuable for both consumption and wood production. The development of bamboo shoots involving the occurrence of lateral buds is unique, and it affects both shoot yield and the resulting timber. Plant-specific TCP transcription factors are involved in plant growth and development, particularly in lateral bud outgrowth and morphogenesis. However, the comprehensive information of the TCP genes in Ma bamboo remains poorly understood. In this study, 66 TCP transcription factors were identified in Ma bamboo at the genome-wide level. Members of the same subfamily had conservative gene structures and conserved motifs. The collinear analysis demonstrated that segmental duplication occurred widely in the TCP transcription factors of Ma bamboo, which mainly led to the expansion of a gene family. Cis-acting elements related to growth and development and stress response were found in the promoter regions of DlTCPs. Expression patterns revealed that DlTCPs have tissue expression specificity, which is usually highly expressed in shoots and leaves. Subcellular localization and transcriptional self-activation experiments demonstrated that the five candidate TCP proteins were typical self-activating nuclear-localized transcription factors. Additionally, the transcriptome analysis of the bamboo shoot buds at different developmental stages helped to clarify the underlying functions of the TCP members during the growth of bamboo shoots. DlTCP12-C, significantly downregulated as the bamboo shoots developed, was selected to further verify its molecular function in Arabidopsis. The DlTCP12-C overexpressing lines exhibited a marked reduction in the number of rosettes and branches compared with the wild type in Arabidopsis, suggesting that DlTCP12-C conservatively inhibits lateral bud outgrowth and branching in plants. This study provides useful insights into the evolutionary patterns and molecular functions of the TCP transcription factors in Ma bamboo and provides a valuable reference for further research on the regulatory mechanism of bamboo shoot development and lateral bud growth.
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Affiliation(s)
- Kangming Jin
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Forestry Faculty, Nanjing Forestry University, Nanjing, China
| | - Yujun Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Jing Xu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Zhuchou Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Huijin Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Biyun Huang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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Huang F, Shi C, Zhang Y, Hou X. Genome-Wide Identification and Characterization of TCP Family Genes in Pak-Choi [ Brassica campestris (syn. Brassica rapa) ssp. chinensis var. communis]. FRONTIERS IN PLANT SCIENCE 2022; 13:854171. [PMID: 35615139 PMCID: PMC9125175 DOI: 10.3389/fpls.2022.854171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/17/2022] [Indexed: 06/15/2023]
Abstract
The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) gene family, a kind of plant specific transcription factor, is essential for stress response, cell growth, and cell proliferation. However, the characterization of TCP family is still not clear in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis var. communis]. In this study, genome-wide analysis of TCP gene family was performed and 26 TCP genes were identified in Pak-choi. Phylogenetic analysis demonstrated that the 26 BcTCPs were divided into two classes: Class I and Class II. Class II was further classified into two subclasses, CIN and CYC/TB1. The qPCR results suggested that most BcTCPs respond to abiotic stresses. The expressions of BcTCP3, BcTCP12, BcTCP21, and BcTCP22 were significantly changed under ABA and cold treatment. BcTCP3 and BcTCP12 were also up-regulated under osmotic treatment. Subcellular localization showed that BcTCP3 and BcTCP21 were located in the nucleus. Our results will facilitate revealing the functions and regulatory mechanisms of BcTCPs.
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Begum Y. Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants. Gene 2022; 821:146283. [PMID: 35143944 DOI: 10.1016/j.gene.2022.146283] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/12/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, West Bengal, India; Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, JD-2, Sector III, Salt Lake, Kolkata 700106, West Bengal, India.
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Tang Y, Gao X, Cui Y, Xu H, Yu J. 植物TCP转录因子研究进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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The Genome-Wide Identification of Long Non-Coding RNAs Involved in Floral Thermogenesis in Nelumbo nucifera Gaertn. Int J Mol Sci 2022; 23:ijms23094901. [PMID: 35563291 PMCID: PMC9102460 DOI: 10.3390/ijms23094901] [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: 03/26/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
The sacred lotus (Nelumbo nucifera Gaertn.) can maintain a stable floral chamber temperature when blooming, despite ambient temperature fluctuations; however, the long non-coding RNAs (lncRNAs) involved in floral thermogenesis remain unclear. In the present study, we obtain comprehensive lncRNAs expression profiles from receptacles at five developmental stages by strand-specific RNA sequencing to reveal the lncRNAs regulatory mechanism of the floral thermogenesis of N. nucifera. A total of 22,693 transcripts were identified as lncRNAs, of which approximately 44.78% had stage-specific expression patterns. Subsequently, we identified 2579 differential expressed lncRNAs (DELs) regulating 2367 protein-coding genes mainly involved in receptacle development and reproductive process. Then, lncRNAs with floral thermogenesis identified by weighted gene co-expression network analysis (WGCNA) were mainly related to sulfur metabolism and mitochondrial electron transport chains. Meanwhile, 70 lncRNAs were predicted to act as endogenous target mimics (eTMs) for 29 miRNAs and participate in the regulation of 16 floral thermogenesis-related genes. Our dual luciferase reporter assays indicated that lncRNA LTCONS_00068702 acted as eTMs for miR164a_4 to regulate the expression of TrxL2 gene. These results deepen our understanding of the regulation mechanism of floral thermogenesis by lncRNAs and accumulate data for further research.
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Ma X, Zhao F, Zhou B. The Characters of Non-Coding RNAs and Their Biological Roles in Plant Development and Abiotic Stress Response. Int J Mol Sci 2022; 23:ijms23084124. [PMID: 35456943 PMCID: PMC9032736 DOI: 10.3390/ijms23084124] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding.
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Affiliation(s)
- Xu Ma
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China;
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fei Zhao
- Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
- Correspondence: (F.Z.); (B.Z.); Tel.: +86-0538-8243-965 (F.Z.); +86-0451-8219-1738 (B.Z.)
| | - Bo Zhou
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China;
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (F.Z.); (B.Z.); Tel.: +86-0538-8243-965 (F.Z.); +86-0451-8219-1738 (B.Z.)
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Tian C, Zhai L, Zhu W, Qi X, Yu Z, Wang H, Chen F, Wang L, Chen S. Characterization of the TCP Gene Family in Chrysanthemum nankingense and the Role of CnTCP4 in Cold Tolerance. PLANTS (BASEL, SWITZERLAND) 2022; 11:936. [PMID: 35406918 PMCID: PMC9002959 DOI: 10.3390/plants11070936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Plant-specific TCP transcription factors play a key role in plant development and stress responses. Chrysanthemum nankingense shows higher cold tolerance than its ornamental polyploid counterpart. However, whether the TCP gene family plays a role in conferring cold tolerance upon C. nankingense remains unknown. Here, we identified 23 CnTCP genes in C. nankingense, systematically analyzed their phylogenetic relationships and synteny with TCPs from other species, and evaluated their expression profiles at low temperature. Phylogenetic analysis of the protein sequences suggested that CnTCP proteins fall into two classes and three clades, with a typical bHLH domain. However, differences between C. nankingense and Arabidopsis in predicted protein structure and binding sites suggested a unique function of CnTCPs in C. nankingense. Furthermore, expression profiles showed that expression of most CnTCPs were downregulated under cold conditions, suggesting their importance in plant responses to cold stress. Notably, expression of miR319 and of its predicted target genes, CnTCP2/4/14, led to fast responses to cold. Overexpression of Arabidopsis CnTCP4 led to hypersensitivity to cold, suggesting that CnTCP4 might play a negative role in C. nankingense responses to cold stress. Our results provide a foundation for future functional genomic studies on this gene family in chrysanthemum.
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Affiliation(s)
- Chang Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lisheng Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Wenjing Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Xiangyu Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Zhongyu Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Likai Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
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Ren L, Zhang T, Wu H, Ge X, Wan H, Chen S, Li Z, Ma D, Wang A. Blocking IbmiR319a Impacts Plant Architecture and Reduces Drought Tolerance in Sweet Potato. Genes (Basel) 2022; 13:genes13030404. [PMID: 35327958 PMCID: PMC8953241 DOI: 10.3390/genes13030404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 01/15/2023] Open
Abstract
MicroRNA319 (miR319) plays a key role in plant growth, development, and multiple resistance by repressing the expression of targeted TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) genes. Two members, IbmiR319a and IbmiR319c, were discovered in the miR319 gene family in sweet potato (Ipomoea batatas [L.] Lam). Here, we focused on the biological function and potential molecular mechanism of the response of IbmiR319a to drought stress in sweet potato. Blocking IbmiR319a in transgenic sweet potato (MIM319) resulted in a slim and tender phenotype and greater sensitivity to drought stress. Microscopic observations revealed that blocking IbmiR319a decreased the cell width and increased the stomatal distribution in the adaxial leaf epidermis, and also increased the intercellular space in the leaf and petiole. We also found that the lignin content was reduced, which led to increased brittleness in MIM319. Quantitative real-time PCR showed that the expression levels of key genes in the lignin biosynthesis pathway were much lower in the MIM319 lines than in the wild type. Ectopic expression of IbmiR319a-targeted genes IbTCP11 and IbTCP17 in Arabidopsis resulted in similar phenotypes to MIM319. We also showed that the expression of IbTCP11 and IbTCP17 was largely induced by drought stress. Transcriptome analysis indicated that cell growth-related pathways, such as plant hormonal signaling, were significantly downregulated with the blocking of IbmiR319a. Taken together, our findings suggest that IbmiR319a affects plant architecture by targeting IbTCP11/17 to control the response to drought stress in sweet potato.
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Affiliation(s)
- Lei Ren
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Tingting Zhang
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Haixia Wu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Xinyu Ge
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Huihui Wan
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Shengyong Chen
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang 524094, China;
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Daifu Ma
- Key Laboratory for Biology and Genetic Breeding of Sweetpotato (Xuzhou), Ministry of Agriculture/Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou Institute of Agricultural Sciences, Xuzhou 221131, China
- Correspondence: (D.M.); (A.W.); Tel.: +86-516-82189200 (D.M.); +86-516-83400033 (A.W.)
| | - Aimin Wang
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
- Correspondence: (D.M.); (A.W.); Tel.: +86-516-82189200 (D.M.); +86-516-83400033 (A.W.)
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Meng X, Zhang Y, Wang N, He H, Tan Q, Wen B, Zhang R, Sun M, Zhao X, Fu X, Li D, Lu W, Chen X, Li L. Prunus persica Terpene Synthase PpTPS1 Interacts with PpABI5 to Enhance Salt Resistance in Transgenic Tomatoes. FRONTIERS IN PLANT SCIENCE 2022; 13:807342. [PMID: 35283925 PMCID: PMC8905318 DOI: 10.3389/fpls.2022.807342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Terpene synthase (TPS) is related to the production of aromatic substances, but there are few studies on the impact of abiotic stress on TPS and its molecular mechanism, especially in peaches. This study found that salt resistance and abscisic acid (ABA) sensitivity of transgenic tomatoes were enhanced by overexpression of PpTPS1. Moreover, it was found that PpTPS1 interacted with and antagonized the expression of the bZIP transcription factor ABA INSENSITIVE 5 (PpABI5), which is thought to play an important role in salt suitability. In addition, PpTCP1, PpTCP13, and PpTCP15 were found to activate the expression of PpTPS1 by yeast one-hybrid (Y1H) and dual-luciferase assays, and they could also be induced by ABA. In summary, PpTPS1 may be involved in the ABA signaling regulatory pathway and play an important role in salt acclimation, providing a new reference gene for the improvement of salt resistance in peaches.
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Affiliation(s)
- Xiangguang Meng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Yuzheng Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Ning Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Huajie He
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Qiuping Tan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Rui Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Mingyue Sun
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Xuehui Zhao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Wenli Lu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
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Li J, Zhang Z, Chong K, Xu Y. Chilling tolerance in rice: Past and present. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153576. [PMID: 34875419 DOI: 10.1016/j.jplph.2021.153576] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Rice is generally sensitive to chilling stress, which seriously affects growth and yield. Since early in the last century, considerable efforts have been made to understand the physiological and molecular mechanisms underlying the response to chilling stress and improve rice chilling tolerance. Here, we review the research trends and advances in this field. The phenotypic and biochemical changes caused by cold stress and the physiological explanations are briefly summarized. Using published data from the past 20 years, we reviewed the past progress and important techniques in the identification of quantitative trait loci (QTL), novel genes, and cellular pathways involved in rice chilling tolerance. The advent of novel technologies has significantly advanced studies of cold tolerance, and the characterization of QTLs, key genes, and molecular modules have sped up molecular design breeding for cold tolerance in rice varieties. In addition to gene function studies based on overexpression or artificially generated mutants, elucidating natural allelic variation in specific backgrounds is emerging as a novel approach for the study of cold tolerance in rice, and the superior alleles identified using this approach can directly facilitate breeding.
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Affiliation(s)
- Junhua Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Zeyong Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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Rath M, Challa KR, Sarvepalli K, Nath U. CINCINNATA-Like TCP Transcription Factors in Cell Growth - An Expanding Portfolio. FRONTIERS IN PLANT SCIENCE 2022; 13:825341. [PMID: 35273626 PMCID: PMC8902296 DOI: 10.3389/fpls.2022.825341] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/13/2022] [Indexed: 05/09/2023]
Abstract
Post-mitotic cell growth is a key process in plant growth and development. Cell expansion drives major growth during morphogenesis and is influenced by both endogenous factors and environmental stimuli. Though both isotropic and anisotropic cell growth can contribute to organ size and shape at different degrees, anisotropic cell growth is more likely to contribute to shape change. While much is known about the mechanisms that increase cellular turgor and cell-wall biomass during expansion, the genetic factors that regulate these processes are less studied. In the past quarter of a century, the role of the CINCINNATA-like TCP (CIN-TCP) transcription factors has been well documented in regulating diverse aspects of plant growth and development including flower asymmetry, plant architecture, leaf morphogenesis, and plant maturation. The molecular activity of the CIN-TCP proteins common to these biological processes has been identified as their ability to suppress cell proliferation. However, reports on their role regulating post-mitotic cell growth have been scanty, partly because of functional redundancy among them. In addition, it is difficult to tease out the effect of gene activity on cell division and expansion since these two processes are linked by compensation, a phenomenon where perturbation in proliferation is compensated by an opposite effect on cell growth to keep the final organ size relatively unaltered. Despite these technical limitations, recent genetic and growth kinematic studies have shown a distinct role of CIN-TCPs in promoting cellular growth in cotyledons and hypocotyls, the embryonic organs that grow solely by cell expansion. In this review, we highlight these recent advances in our understanding of how CIN-TCPs promote cell growth.
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Affiliation(s)
- Monalisha Rath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Krishna Reddy Challa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | | | - Utpal Nath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- *Correspondence: Utpal Nath,
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