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Li M, Zou J, Cheng Q, Fu R, Zhang D, Lai Y, Chen Y, Yang C, Hu W, Ding S. Genome-Wide Identification and Expression of the ERF Gene Family in Populus trichocarpa and Their Responses to Nitrogen and Abiotic Stresses. Life (Basel) 2025; 15:550. [PMID: 40283105 PMCID: PMC12029025 DOI: 10.3390/life15040550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 03/25/2025] [Accepted: 03/26/2025] [Indexed: 04/29/2025] Open
Abstract
The ethylene response factor (ERF) family is a prominent plant-specific transcription factor family, which plays a crucial role in modulating plant growth and stress tolerance. In this study, a total of 210 ERFs were identified in Populus trichocarpa, comprising 29 AP2 (APETALA2) subfamily members, 176 ERF subfamily members, and 5 RAV (related to ABI3/VP1) subfamily members. The duplication events of the PtERF family members exclusively occurred within the subfamilies. A total of 168 duplication pairs were found among 161 PtERF genes, and all of them were fragment duplications. Gene structure analysis revealed that most ERF subfamily members only had one exon without introns, the AP2 subfamily members had six or more introns and exons, and RAV subfamily members lacked introns except for PtERF102. Considerable cis-acting elements associated with plant growth and development, stress response, hormone response, and light response were detected in the promoters of PtERF genes. The expression levels of PtERFs were highest in roots across tissues and in winter among seasons. Furthermore, the nitrate and urea stimulated the expression of PtERF genes. The co-expression network analysis based on PtERFs indicated their potential roles in hormone signaling, acyltransferase activity, and response to chemicals. This study provides novel insights into investigating the role of PtERFs in environmental stress in poplar species.
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Affiliation(s)
- Mingwan Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (M.L.); (J.Z.); (R.F.); (D.Z.); (Y.L.); (Y.C.); (C.Y.)
| | - Jun Zou
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (M.L.); (J.Z.); (R.F.); (D.Z.); (Y.L.); (Y.C.); (C.Y.)
| | - Qian Cheng
- College of Horticulture and Forestry Science, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China;
| | - Ran Fu
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (M.L.); (J.Z.); (R.F.); (D.Z.); (Y.L.); (Y.C.); (C.Y.)
| | - Dangquan Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (M.L.); (J.Z.); (R.F.); (D.Z.); (Y.L.); (Y.C.); (C.Y.)
| | - Yong Lai
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (M.L.); (J.Z.); (R.F.); (D.Z.); (Y.L.); (Y.C.); (C.Y.)
| | - Yuanyuan Chen
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (M.L.); (J.Z.); (R.F.); (D.Z.); (Y.L.); (Y.C.); (C.Y.)
| | - Chaochen Yang
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (M.L.); (J.Z.); (R.F.); (D.Z.); (Y.L.); (Y.C.); (C.Y.)
| | - Wentao Hu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China;
| | - Shen Ding
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (M.L.); (J.Z.); (R.F.); (D.Z.); (Y.L.); (Y.C.); (C.Y.)
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Tang L, Zheng Y, Lu H, Qiu Y, Wang H, Liao H, Xie W. Tissue-specific transcriptomic analysis reveals the molecular mechanisms responsive to cold stress in Poa crymophila, and development of EST-SSR markers linked to cold tolerance candidate genes. BMC PLANT BIOLOGY 2025; 25:360. [PMID: 40102740 PMCID: PMC11921722 DOI: 10.1186/s12870-025-06383-3] [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: 06/18/2024] [Accepted: 03/11/2025] [Indexed: 03/20/2025]
Abstract
BACKGROUND Poa crymophila is a perennial, cold-tolerant, native grass species, widely distributed in the Qinghai-Tibet Plateau. However, the tissue-specific regulatory mechanisms and key regulatory genes underlying its cold tolerance remain poorly characterized. Therefore, in this study, based on the screening and evaluation of cold tolerance of four Poa species, the cold tolerance mechanism of P. crymophila's roots, stems, and leaves and its cold tolerance candidate genes were investigated through physiological and transcriptomic analyses. RESULTS Results of the present study suggested that the cold tolerance of the four Poa species was in the following order: P. crymophila > P. botryoides > P. pratensis var. anceps > P. pratensis. Cold stress significantly changed the physiological characteristics of roots, stems, and leaves of P. crymophila in this study. In addition, the transcriptome results showed that 4434, 8793, and 14,942 differentially expressed genes (DEGs) were identified in roots, stems, and leaves, respectively; however, 464 DEGs were commonly identified in these three tissues. KEGG enrichment analysis showed that these DEGs were mainly enriched in the phenylpropanoid biosynthesis pathway (roots), photosynthesis pathway (stems and leaves), circadian rhythm-plant pathway (stems and leaves), starch and sucrose metabolism pathway (roots, stems, and leaves), and galactose metabolism pathway (roots, stems, and leaves). A total of 392 candidate genes involved in Ca2+ signaling, ROS scavenging system, hormones, circadian clock, photosynthesis, and transcription factors (TFs) were identified in P. crymophila. Weighted gene co-expression network analysis (WGCNA) identified nine hub genes that may be involved in P. crymophila cold response. A total of 200 candidate gene-based EST-SSRs were developed and characterized. Twenty-nine polymorphic EST-SSRs primers were finally used to study genetic diversity of 40 individuals from four Poa species with different cold tolerance characteristics. UPGMA cluster and STRUCTURE analysis showed that the 40 Poa individuals were clustered into three major groups, individual plant with similar cold tolerance tended to group together. Notably, markers P37 (PcGA2ox3) and P148 (PcERF013) could distinguish P. crymophila from P. pratensis var. anceps, P. pratensis, and P. botryoides. CONCLUSIONS This study provides new insights into the molecular mechanisms underlying the cold tolerance of P. crymophila, and also lays a foundation for molecular marker-assisted selection for cold tolerance improvement in Poa species.
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Affiliation(s)
- Liuban Tang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yuying Zheng
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Huanhuan Lu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yongsen Qiu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Huizhi Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Haoqin Liao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Wengang Xie
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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Zhang D, Zeng B, He Y, Li J, Yu Z. Genome-wide identification and comparative analysis of the AP2/ERF gene family in Prunus dulcis and Prunus tenella: expression of PdAP2/ERF genes under freezing stress during dormancy. BMC Genomics 2025; 26:95. [PMID: 39891077 PMCID: PMC11783870 DOI: 10.1186/s12864-025-11275-9] [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: 11/04/2024] [Accepted: 01/22/2025] [Indexed: 02/03/2025] Open
Abstract
The AP2/ERF (APETALA2/ethylene responsive factor) transcription factor family, one of the largest in plants, plays a crucial role in regulating various biological processes, including plant growth and development, hormone signaling, and stress response. This study identified 114 and 116 AP2/ERF genes in the genomes of 'Wanfeng' almond (Prunus dulcis) and 'Yumin' wild dwarf almond (Prunus tenella), respectively. These genes were categorized into five subfamilies: AP2, DREB, ERF, RAV, and Soloist. The PdAP2/ERF and PtAP2/ERF members both demonstrated high conservation in protein motifs and gene structures. Members of both families were unevenly distributed across eight chromosomes, with 30 and 27 pairs of segmental duplications and 15 and 18 pairs of tandem repeated genes, respectively. The promoter regions of PdAP2/ERF and PtAP2/ERF family members contained numerous important cis-elements related to growth and development, hormone regulation, and stress response. Expression pattern analysis revealed that PdAP2/ERF family members exhibited responsive characteristics under freezing stress at different temperatures in perennial dormant branches. Quantitative fluorescence analysis indicated that PdAP2/ERF genes might be more intensely expressed in the phloem of perennial dormant branches of almond, with the opposite trend observed in the xylem. This study compared the characteristics of PdAP2/ERF and PtAP2/ERF gene family members and initially explored the expression patterns of PdAP2/ERF genes in the phloem and xylem of perennial dormant branches. The findings provide a theoretical foundation for future research on almond improvement and breeding, as well as the molecular mechanisms underlying resistance to freezing stress.
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Grants
- 2024B02018 The key research and development project of Xinjiang Uyghur Autonomous Region, "Research and Demonstration of Key Technologies for Selection and Breeding of Elite Varieties, Efficient Production, Storage, and Processing of Almonds,"
- 2024B02018 The key research and development project of Xinjiang Uyghur Autonomous Region, "Research and Demonstration of Key Technologies for Selection and Breeding of Elite Varieties, Efficient Production, Storage, and Processing of Almonds,"
- 2023B02026 The key research and development project of Xinjiang Uyghur Autonomous Region, "Research on Key Technologies for Cold Resistance in Major Fruit Trees as Apricot plum and Apricot in Xinjiang
- 2024D01B35 Xinjiang Uygur Autonomous Region Youth Fund Project
- The key research and development project of Xinjiang Uyghur Autonomous Region, “Research on Key Technologies for Cold Resistance in Major Fruit Trees as Apricot plum and Apricot in Xinjiang
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Affiliation(s)
- Dongdong Zhang
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Bin Zeng
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Yawen He
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Jiangui Li
- Forestry and Landscape Architecture College, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zhenfan Yu
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830052, China.
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Yu Y, Liu D, Wang F, Kong L, Lin Y, Chen L, Jiang W, Hou X, Xiao Y, Fu G, Liu W, Huo X. Comparative Transcriptomic Analysis and Candidate Gene Identification for Wild Rice (GZW) and Cultivated Rice (R998) Under Low-Temperature Stress. Int J Mol Sci 2024; 25:13380. [PMID: 39769145 PMCID: PMC11676510 DOI: 10.3390/ijms252413380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 11/17/2024] [Accepted: 11/19/2024] [Indexed: 01/11/2025] Open
Abstract
Rice is a short-day thermophilic crop that originated from the low latitudes of the tropics and subtropics; it requires high temperatures for growth but is sensitive to low temperatures. Therefore, it is highly important to explore and analyze the molecular mechanism of cold tolerance in rice to expand rice planting areas. Here, we report a phenotypic evaluation based on low-temperature stress in indica rice (R998) and wild rice (GZW) and a comparative transcriptomic study conducted at six time points. After 7 days of low-temperature treatment at 10 °C, R998 exhibited obvious yellowing and greening of the leaves, while GZW exhibited high low-temperature resistance, and the leaves maintained their normal morphology and exhibited no yellowing; GZW has a higher survival rate. Principal component analysis (PCA) and cluster analysis of the RNA-seq data revealed that the difference in low-temperature resistance between the two cultivars was caused mainly by the difference in low-temperature treatment after 6 h. Differential expression analysis revealed 2615 unique differentially expressed genes (DEGs) in the R998 material, 1578 unique DEGs in the GZW material, 1874 unique DEGs between R998 and GZW, and 2699 DEGs that were differentially expressed not only between cultivars but also at different time points in the same material under low-temperature treatment. A total of 15,712 DEGs were detected and were significantly enriched in the phenylalanine metabolism, photosynthesis, plant hormone signal transduction, and starch and sucrose metabolism pathways. These 15,712 DEGs included 1937 genes encoding transcription factors (TFs), of which 10 have been identified with functional validation in previous studies. In addition, a gene regulatory network was constructed via weighted gene correlation network analysis (WGCNA), and 12 key genes related to low-temperature tolerance in rice were identified, including five genes encoding TFs, one of which was identified and verified in previous studies. These results provide a theoretical basis for an in-depth understanding of the molecular mechanism of low-temperature tolerance in rice and provide new genetic resources for the study of low-temperature tolerance in rice.
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Affiliation(s)
- Yongmei Yu
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (Y.Y.); (W.J.); (Y.X.); (G.F.)
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Feng Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Le Kong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Yanhui Lin
- Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou 571100, China;
| | - Leiqing Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Wenjing Jiang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (Y.Y.); (W.J.); (Y.X.); (G.F.)
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Xueru Hou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Yanxia Xiao
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (Y.Y.); (W.J.); (Y.X.); (G.F.)
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Gongzhen Fu
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (Y.Y.); (W.J.); (Y.X.); (G.F.)
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Wuge Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
| | - Xing Huo
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China; (D.L.); (F.W.); (L.K.); (L.C.); (X.H.)
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Zhang H, Wang S, Zhao X, Dong S, Chen J, Sun Y, Sun Q, Liu Q. Genome-wide identification and comprehensive analysis of the AP2/ERF gene family in Prunus sibirica under low-temperature stress. BMC PLANT BIOLOGY 2024; 24:883. [PMID: 39342089 PMCID: PMC11438396 DOI: 10.1186/s12870-024-05601-8] [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: 05/21/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024]
Abstract
BACKGROUND AP2/ERF transcription factors are involved in the regulation of growth, development, and stress response in plants. Although the gene family has been characterized in various species, such as Oryza sativa, Arabidopsis thaliana, and Populus trichocarpa, studies on the Prunus sibirica AP2/ERF (PsAP2/ERF) gene family are lacking. In this study, PsAP2/ERFs in P. sibirica were characterized by genomic and transcriptomic analyses. RESULTS In the study, 112 PsAP2/ERFs were identified and categorized into 16 subfamilies. Within each subfamily, PsAP2/ERFs exhibited similar exon-intron structures and motif compositions. Additionally, 50 pairs of segmentally duplicated genes were identified within the PsAP2/ERF gene family. Our experimental results showed that 20 PsAP2/ERFs are highly expressed in leaves, roots, and pistils under low-temperature stress conditions. Among them, the expression of PsAP2/ERF21, PsAP2/ERF56 and PsAP2/ERF88 was significantly up-regulated during the treatment period, and it was hypothesised that members of the PsAP2/ERF family play an important role inlow temperature stress tolerance. CONCLUSIONS This study improves our understanding of the molecular basis of development and low-temperature stress response in P. sibirica and provides a solid scientific foundation for further functional assays and evolutionary analyses of PsAP2/ERFs.
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Affiliation(s)
- Hongrui Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, China
| | - Shipeng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, China
| | - Xin Zhao
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, China
| | - Shengjun Dong
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, China
| | - Jianhua Chen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, China
| | - Yongqiang Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, China
| | - Qiaowei Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, China
| | - Quangang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China.
- Key Laboratory for Silviculture of Liaoning Province, Shenyang, China.
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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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Dai J, Wang M, Yin H, Han X, Fan Y, Wei Y, Lin J, Liu J. Integrating GC-MS and comparative transcriptome analysis reveals that TsERF66 promotes the biosynthesis of caryophyllene in Toona sinensis tender leaves. FRONTIERS IN PLANT SCIENCE 2024; 15:1378418. [PMID: 38872893 PMCID: PMC11171135 DOI: 10.3389/fpls.2024.1378418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/09/2024] [Indexed: 06/15/2024]
Abstract
Introduction The strong aromatic characteristics of the tender leaves of Toona sinensis determine their quality and economic value. Methods and results Here, GC-MS analysis revealed that caryophyllene is a key volatile compound in the tender leaves of two different T. sinensis varieties, however, the transcriptional mechanisms controlling its gene expression are unknown. Comparative transcriptome analysis revealed significant enrichment of terpenoid synthesis pathway genes, suggesting that the regulation of terpenoid synthesis-related gene expression is an important factor leading to differences in aroma between the two varieties. Further analysis of expression levels and genetic evolution revealed that TsTPS18 is a caryophyllene synthase, which was confirmed by transient overexpression in T. sinensis and Nicotiana benthamiana leaves. Furthermore, we screened an AP2/ERF transcriptional factor ERF-IX member, TsERF66, for the potential regulation of caryophyllene synthesis. The TsERF66 had a similar expression trend to that of TsTPS18 and was highly expressed in high-aroma varieties and tender leaves. Exogenous spraying of MeJA also induced the expression of TsERF66 and TsTPS18 and promoted the biosynthesis of caryophyllene. Transient overexpression of TsERF66 in T. sinensis significantly promoted TsTPS18 expression and caryophyllene biosynthesis. Discussion Our results showed that TsERF66 promoted the expression of TsTPS18 and the biosynthesis of caryophyllene in T. sinensis leaves, providing a strategy for improving the aroma of tender leaves.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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Ma Z, Hu L, Jiang W. Understanding AP2/ERF Transcription Factor Responses and Tolerance to Various Abiotic Stresses in Plants: A Comprehensive Review. Int J Mol Sci 2024; 25:893. [PMID: 38255967 PMCID: PMC10815832 DOI: 10.3390/ijms25020893] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Abiotic stress is an adverse environmental factor that severely affects plant growth and development, and plants have developed complex regulatory mechanisms to adapt to these unfavourable conditions through long-term evolution. In recent years, many transcription factor families of genes have been identified to regulate the ability of plants to respond to abiotic stresses. Among them, the AP2/ERF (APETALA2/ethylene responsive factor) family is a large class of plant-specific proteins that regulate plant response to abiotic stresses and can also play a role in regulating plant growth and development. This paper reviews the structural features and classification of AP2/ERF transcription factors that are involved in transcriptional regulation, reciprocal proteins, downstream genes, and hormone-dependent signalling and hormone-independent signalling pathways in response to abiotic stress. The AP2/ERF transcription factors can synergise with hormone signalling to form cross-regulatory networks in response to and tolerance of abiotic stresses. Many of the AP2/ERF transcription factors activate the expression of abiotic stress-responsive genes that are dependent or independent of abscisic acid and ethylene in response to abscisic acid and ethylene. In addition, the AP2/ERF transcription factors are involved in gibberellin, auxin, brassinosteroid, and cytokinin-mediated abiotic stress responses. The study of AP2/ERF transcription factors and interacting proteins, as well as the identification of their downstream target genes, can provide us with a more comprehensive understanding of the mechanism of plant action in response to abiotic stress, which can improve plants' ability to tolerate abiotic stress and provide a more theoretical basis for increasing plant yield under abiotic stress.
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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;
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Lanjuan Hu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China;
| | - Wenzhu Jiang
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China;
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