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Wang D, Ji XL, Li Z, Zhang MY, Liu MP, Song XS. A Cerasus humilis transcription factor, ChDREB2C, enhances salt tolerance in transgenic Arabidopsis. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:82-92. [PMID: 38014504 DOI: 10.1111/plb.13599] [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: 12/01/2022] [Accepted: 10/22/2023] [Indexed: 11/29/2023]
Abstract
DREB transcription factors play important roles in plant responses to various abiotic and biotic stresses. We conducted bioinformatics analysis of ChDREB2C, explored subcellular localization, transcription activation activity, and heterologous expression in Arabidopsis, and measured expression of related physiological indicators and genes under salt stress. A transcription factor of the DREB family was cloned and named ChDREB2C. ChDREB2C protein was localized in the nucleus, and its C-terminal domain exhibited transcriptional activation activity. ChDREB2C formed a homologous dimer in yeast. Arabidopsis plants overexpressing ChDREB2C were more tolerant to salt stress than WT plants, through increased scavenging capacity of ROS and accumulation of proline. Overexpression of ChDREB2C resulted in increased expression of AtSOS1, AtNHX1, AtRD29A, AtRD29B, AtKIN1, AtABA4, and AtABF2 genes. The interaction between ChABF2 (ABA response element binding factor 2) and ChDREB2C was verified using yeast two-hybrid and firefly luciferase assays. The results suggest that ChDREB2C could have a positive role in mediating the abiotic response.
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Affiliation(s)
- D Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - X L Ji
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Z Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - M Y Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - M P Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - X S Song
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
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Yang Z, Mei W, Wang H, Zeng J, Dai H, Ding X. Comprehensive Analysis of NAC Transcription Factors Reveals Their Evolution in Malvales and Functional Characterization of AsNAC019 and AsNAC098 in Aquilaria sinensis. Int J Mol Sci 2023; 24:17384. [PMID: 38139213 PMCID: PMC10744133 DOI: 10.3390/ijms242417384] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
NAC is a class of plant-specific transcription factors that are widely involved in the growth, development and (a)biotic stress response of plants. However, their molecular evolution has not been extensively studied in Malvales, especially in Aquilaria sinensis, a commercial and horticultural crop that produces an aromatic resin named agarwood. In this study, 1502 members of the NAC gene family were identified from the genomes of nine species from Malvales and three model plants. The macroevolutionary analysis revealed that whole genome duplication (WGD) and dispersed duplication (DSD) have shaped the current architectural structure of NAC gene families in Malvales plants. Then, 111 NAC genes were systemically characterized in A. sinensis. The phylogenetic analysis suggests that NAC genes in A. sinensis can be classified into 16 known clusters and four new subfamilies, with each subfamily presenting similar gene structures and conserved motifs. RNA-seq analysis showed that AsNACs presents a broad transcriptional response to the agarwood inducer. The expression patterns of 15 AsNACs in A. sinensis after injury treatment indicated that AsNAC019 and AsNAC098 were positively correlated with the expression patterns of four polyketide synthase (PKS) genes. Additionally, AsNAC019 and AsNAC098 were also found to bind with the AsPKS07 promoter and activate its transcription. This comprehensive analysis provides valuable insights into the molecular evolution of the NAC gene family in Malvales plants and highlights the potential mechanisms of AsNACs for regulating secondary metabolite biosynthesis in A. sinensis, especially for the biosynthesis of 2-(2-phenyl) chromones in agarwood.
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Affiliation(s)
- Zhuo Yang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.Y.); (W.M.); (H.W.); (J.Z.)
| | - Wenli Mei
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.Y.); (W.M.); (H.W.); (J.Z.)
- International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Hao Wang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.Y.); (W.M.); (H.W.); (J.Z.)
- International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jun Zeng
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.Y.); (W.M.); (H.W.); (J.Z.)
- International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haofu Dai
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.Y.); (W.M.); (H.W.); (J.Z.)
- International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xupo Ding
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.Y.); (W.M.); (H.W.); (J.Z.)
- International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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Xu Y, Li P, Ma F, Huang D, Xing W, Wu B, Sun P, Xu B, Song S. Characterization of the NAC Transcription Factor in Passion Fruit ( Passiflora edulis) and Functional Identification of PeNAC-19 in Cold Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:1393. [PMID: 36987081 PMCID: PMC10051797 DOI: 10.3390/plants12061393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The NAC (NAM, ATAF and CUC) gene family plays an important role in plant development and abiotic stress response. However, up to now, the identification and research of the NAC (PeNAC) family members of passion fruit are still lacking. In this study, 25 PeNACs were identified from the passion fruit genome, and their functions under abiotic stress and at different fruit-ripening stages were analyzed. Furthermore, we analyzed the transcriptome sequencing results of PeNACs under four various abiotic stresses (drought, salt, cold and high temperature) and three different fruit-ripening stages, and verified the expression results of some genes by qRT-PCR. Additionally, tissue-specific analysis showed that most PeNACs were mainly expressed in flowers. In particular, PeNAC-19 was induced by four various abiotic stresses. At present, low temperatures have seriously endangered the development of passion fruit cultivation. Therefore, PeNAC-19 was transformed into tobacco, yeast and Arabidopsis to study their function of resisting low temperature. The results show that PeNAC-19 responded to cold stress significantly in tobacco and Arabidopsis, and could improve the low temperature tolerance of yeast. This study not only improved the understanding of the PeNAC gene family characteristics and evolution, but also provided new insights into the regulation of the PeNAC gene at different stages of fruit maturation and abiotic stresses.
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Affiliation(s)
- Yi Xu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
| | - Pengfei Li
- College of Tropical Crops, Yunnan Agricultural University, Kunming 650201, China
| | - Funing Ma
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
| | - Dongmei Huang
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Wenting Xing
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Bin Wu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Peiguang Sun
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Binqiang Xu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Shun Song
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
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Shen Q, Qian Z, Wang T, Zhao X, Gu S, Rao X, Lyu S, Zhang R, He L, Li F. Genome-wide identification and expression analysis of the NAC transcription factor family in Saccharum spontaneum under different stresses. PLANT SIGNALING & BEHAVIOR 2022; 17:2088665. [PMID: 35730557 PMCID: PMC9225438 DOI: 10.1080/15592324.2022.2088665] [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] [Indexed: 05/15/2023]
Abstract
The NAC (NAM, ATAF1/2, and CUC2) transcription factor family is one of the largest families unique to plants and is involved in plant growth and development, organs, morphogenesis, and stress responses. The NAC family has been identified in many plants. As the main source of resistance genes for sugarcane breeding, the NAC gene family in the wild species Saccharum spontaneum has not been systematically studied. In this study, 115 SsNAC genes were identified in the S. spontaneum genome, and these genes were heterogeneously distributed on 25 chromosomes. Phylogenetic analysis divided the SsNAC family members into 18 subgroups, and the gene structure and conserved motif analysis further supported the phylogenetic classification. Four groups of tandemly duplicated genes and nine pairs of segmentally duplicated genes were detected. The SsNAC gene has different expression patterns at different developmental stages of stems and leaves. Further qRT-PCR analysis showed that drought, low-temperature, salinity, pathogenic fungi, and other stresses as well as abscisic acid (ABA) and methyl jasmonate (MeJA) treatments significantly induced the expression of 12 SsNAC genes, indicating that these genes may play a key role in the resistance of S. spontaneum to biotic and abiotic stresses. In summary, the results from this study provide comprehensive information on the NAC transcription factor family, providing a reference for further functional studies of the SsNAC gene.
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Affiliation(s)
- Qingqing Shen
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zhenfeng Qian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Tianju Wang
- Institute for Bio-resources Research and Development of Central Yunnan Plateau, Chuxiong Normal University, Chuxiong, China
| | - Xueting Zhao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shujie Gu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xibing Rao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shaozhi Lyu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Rongqiong Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lilian He
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
- CONTACT Lilian He Sugarcane Research Institute, Yunnan Agricultural University, Kunming, China
| | - Fusheng Li
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, China
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Rai N, Rai KK, Singh MK, Singh J, Kaushik P. Investigating NAC Transcription Factor Role in Redox Homeostasis in Solanum lycopersicum L.: Bioinformatics, Physiological and Expression Analysis under Drought Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:2930. [PMID: 36365384 PMCID: PMC9654907 DOI: 10.3390/plants11212930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
NAC transcription factors regulate stress-defence pathways and developmental processes in crop plants. However, their detailed functional characterization in tomatoes needs to be investigated comprehensively. In the present study, tomato hybrids subjected to 60 and 80 days of drought stress conditions showed a significant increase in membrane damage and reduced relative water, chlorophyll and proline content. However, hybrids viz., VRTH-16-3 and VRTH-17-68 showed superior growth under drought stress, as they were marked with low electrolytic leakage, enhanced relative water content, proline content and an enhanced activity of enzymatic antioxidants, along with the upregulation of NAC and other stress-defence pathway genes. Candidate gene(s) exhibiting maximum expression in all the hybrids under drought stress were subjected to detailed in silico characterization to provide significant insight into its structural and functional classification. The homology modelling and superimposition analysis of predicted tomato NAC protein showed that similar amino acid residues were involved in forming the conserved WKAT domain. DNA docking discovered that the SlNAC1 protein becomes activated and exerts a stress-defence response after the possible interaction of conserved DNA elements using Pro72, Asn73, Trp81, Lys82, Ala83, Thr84, Gly85, Thr86 and Asp87 residues. A protein-protein interaction analysis identified ten functional partners involved in the induction of stress-defence tolerance.
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Affiliation(s)
- Nagendra Rai
- Indian Institute of Vegetable Research (IIVR), Varanasi 221305, UP, India
| | - Krishna Kumar Rai
- Indian Institute of Vegetable Research (IIVR), Varanasi 221305, UP, India
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, UP, India
| | - Manish Kumar Singh
- Indian Institute of Vegetable Research (IIVR), Varanasi 221305, UP, India
| | - Jagdish Singh
- Indian Institute of Vegetable Research (IIVR), Varanasi 221305, UP, India
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
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Wei N, Zhai Q, Li H, Zheng S, Zhang J, Liu W. Genome-Wide Identification of ERF Transcription Factor Family and Functional Analysis of the Drought Stress-Responsive Genes in Melilotus albus. Int J Mol Sci 2022; 23:ijms231912023. [PMID: 36233332 PMCID: PMC9570465 DOI: 10.3390/ijms231912023] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
As an important forage legume with high values in feed and medicine, Melilotus albus has been widely cultivated. The AP2/ERF transcription factor has been shown to play an important regulatory role in plant drought resistance, but it has not been reported in the legume forage crop M. albus. To digger the genes of M. albus in response to drought stress, we identified and analyzed the ERF gene family of M. albus at the genome-wide level. A total of 100 MaERF genes containing a single AP2 domain sequence were identified in this study, named MaERF001 to MaERF100, and bioinformatics analysis was performed. Collinearity analysis indicated that segmental duplication may play a key role in the expansion of the M. albus ERF gene family. Cis-acting element predictions suggest that MaERF genes are involved in various hormonal responses and abiotic stresses. The expression patterns indicated that MaERFs responded to drought stress to varying degrees. Furthermore, four up-regulated ERFs (MaERF008, MaERF037, MaERF054 and MaERF058) under drought stress were overexpressed in yeast and indicated their biological functions to confer the tolerance to drought. This work will advance the understanding of the molecular mechanisms underlying the drought response in M. albus. Further study of the promising potential candidate genes identified in this study will provide a valuable resource as the next step in functional genomics studies and improve the possibility of improving drought tolerance in M. albus by transgenic approaches.
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Figueroa N, Gómez R. Bolstered plant tolerance to low temperatures by overexpressing NAC transcription factors: identification of critical variables by meta-analysis. PLANTA 2022; 256:92. [PMID: 36181642 DOI: 10.1007/s00425-022-04007-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The potential biotechnological application of NAC overexpression has been challenged by meta-analysis, establishing a correlation between the magnitudes of several physiological and biochemical parameters and the enhanced tolerance to cold. Overexpression of various NAC (NAM/ATAF/CUC) transcription factors in different plant systems was shown to confer enhanced tolerance to low temperatures by inducing both common and distinctive stress response pathways. However, lack of consensus on the type of parameters evaluated, their magnitudes, and direction of the responses complicates drawing general conclusions on the effects of NAC expression in plant physiology. We report herein a meta-analysis summarizing the most critical response variables used to study the effect of overexpressing NAC regulators on cold stress tolerance. We found that NAC overexpression affected all of the outcome parameters in stressed plants, and one response in control conditions. Transformed plants displayed an increase of at least 40% in positive responses, while negative outcomes were reduced by at least 30%. The most reported parameters included survival, electrolyte leakage, and malondialdehyde contents, whereas the most sensitive to the treatments were the Fv/Fm parameter, survival, and the activity of catalases. We also explored how different experimental arrangements affected the magnitudes of the responses. NAC-mediated improvements were best observed after severe stress episodes and during brief treatments (ranging from 5 to 24 h), especially in terms of antioxidant activities, accumulation of free proline, and parameters related to membrane integrity. Use of heterologous expression also favored several indicators of plant fitness. Our findings should help both basic and applied research on the influence of NAC expression on enhanced tolerance to cold.
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Affiliation(s)
- Nicolás Figueroa
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina.
| | - Rodrigo Gómez
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario (UNR), 2123, Zavalla, Santa Fe, Argentina
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Min X, Wang Q, Wei Z, Liu Z, Liu W. Full-length transcriptional analysis reveals the complex relationship of leaves and roots in responses to cold-drought combined stress in common vetch. FRONTIERS IN PLANT SCIENCE 2022; 13:976094. [PMID: 36212304 PMCID: PMC9538161 DOI: 10.3389/fpls.2022.976094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/25/2022] [Indexed: 05/27/2023]
Abstract
Plant responses to single or combined abiotic stresses between aboveground and underground parts are complex and require crosstalk signaling pathways. In this study, we explored the transcriptome data of common vetch (Vicia sativa L.) subjected to cold and drought stress between leaves and roots via meta-analysis to identify the hub abiotic stress-responsive genes. A total of 4,836 and 3,103 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Transcriptome analysis results showed that the set of stress-responsive DEGs to concurrent stress is distinct from single stress, indicating a specialized and unique response to combined stresses in common vetch. Gene Ontology (GO) enrichment analyses identified that "Photosystem II," "Defence response," and "Sucrose synthase/metabolic activity" were the most significantly enriched categories in leaves, roots, and both tissues, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results indicated that "ABC transporters" are the most enriched pathway and that all of the genes were upregulated in roots. Furthermore, 29 co-induced DEGs were identified as hub genes based on the consensus expression profile module of single and co-occurrence stress analysis. In transgenic yeast, the overexpression of three cross-stress tolerance candidate genes increased yeast tolerance to cold-drought combined stress. The elucidation of the combined stress-responsive network in common vetch to better parse the complex regulation of abiotic responses in plants facilitates more adequate legume forage breeding for combined stress tolerance.
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Affiliation(s)
- Xueyang Min
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Engineering Research Centre of Grassland Industry, Ministry of Education, Western China Technology Innovation Centre for Grassland Industry, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qiuxia Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Engineering Research Centre of Grassland Industry, Ministry of Education, Western China Technology Innovation Centre for Grassland Industry, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhipeng Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Engineering Research Centre of Grassland Industry, Ministry of Education, Western China Technology Innovation Centre for Grassland Industry, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Engineering Research Centre of Grassland Industry, Ministry of Education, Western China Technology Innovation Centre for Grassland Industry, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
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Yang Q, Li B, Rizwan HM, Sun K, Zeng J, Shi M, Guo T, Chen F. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis. FRONTIERS IN PLANT SCIENCE 2022; 13:972734. [PMID: 36092439 PMCID: PMC9453495 DOI: 10.3389/fpls.2022.972734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/27/2022] [Indexed: 05/07/2023]
Abstract
The NAC gene family is one of the largest plant transcription factors (TFs) families and plays important roles in plant growth, development, metabolism, and biotic and abiotic stresses. However, NAC gene family has not been reported in passion fruit (Passiflora edulis). In this study, a total of 105 NAC genes were identified in the passion fruit genome and were unevenly distributed across all nine-passion fruit chromomere, with a maximum of 48 PeNAC genes on chromosome one. The physicochemical features of all 105 PeNAC genes varied including 120 to 3,052 amino acids, 3 to 8 conserved motifs, and 1 to 3 introns. The PeNAC genes were named (PeNAC001-PeNAC105) according to their chromosomal locations and phylogenetically grouped into 15 clades (NAC-a to NAC-o). Most PeNAC proteins were predicted to be localized in the nucleus. The cis-element analysis indicated the possible roles of PeNAC genes in plant growth, development, light, hormones, and stress responsiveness. Moreover, the PeNAC gene duplications including tandem (11 gene pairs) and segmental (12 gene pairs) were identified and subjected to purifying selection. All PeNAC proteins exhibited similar 3D structures, and a protein-protein interaction network analysis with known Arabidopsis proteins was predicted. Furthermore, 17 putative ped-miRNAs were identified to target 25 PeNAC genes. Potential TFs including ERF, BBR-BPC, Dof, and bZIP were identified in promoter region of all 105 PeNAC genes and visualized in a TF regulatory network. GO and KEGG annotation analysis exposed that PeNAC genes were related to different biological, molecular, and cellular terms. The qRT-PCR expression analysis discovered that most of the PeNAC genes including PeNAC001, PeNAC003, PeNAC008, PeNAC028, PeNAC033, PeNAC058, PeNAC063, and PeNAC077 were significantly upregulated under Fusarium kyushuense and drought stress conditions compared to controls. In conclusion, these findings lay the foundation for further functional studies of PeNAC genes to facilitate the genetic improvement of plants to stress resistance.
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Affiliation(s)
| | | | | | | | | | | | | | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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Molecular Characterization of the miR156/MsSPL Model in Regulating the Compound Leaf Development and Abiotic Stress Response in Alfalfa. Genes (Basel) 2022; 13:genes13020331. [PMID: 35205375 PMCID: PMC8871590 DOI: 10.3390/genes13020331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022] Open
Abstract
Plant leaf patterns and shapes are spectacularly diverse. Changing the complexity of leaflet numbers is a valuable approach to increase its nutrition and photosynthesis. Alfalfa (Medicago sativa) is the most important forage legume species and has diversified compound leaf patterns, which makes it a model species for studying compound leaf development. However, transcriptomic information from alfalfa remains limited. In this study, RNA-Seq technology was used to identify 3746 differentially expressed genes (DEGs) between multifoliate and trifoliate alfalfa. Through an analysis of annotation information and expression data, SPL, one of the key regulators in modifiable plant development and abiotic stress response, was further analyzed. Here, thirty MsSPL genes were obtained from the alfalfa genome, of which 16 had the putative miR156 binding site. A tissue expression pattern analysis showed that the miR156-targeted MsSPLs were divided into two classes, namely, either tissue-specific or widely expressed in all tissues. All miR156-targeted SPLs strongly showed diversification and positive roles under drought and salt conditions. Importantly, miR156/MsSPL08 was significantly suppressed in multifoliate alfalfa. Furthermore, in the paralogous mutant of MsSPL08 isolated from Medicago truncatula, the phenotypes of mutant plants reveal that miR156/MsSPL08 is involved not only involved the branches but also especially regulates the number of leaflets. The legume is a typical compound leaf plant; the ratio of the leaflet often affects the quality of the forage. This study sheds light on new functions of SPL genes that regulate leaflet number development.
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Jozefkowicz C, Gómez C, Odorizzi A, Iantcheva A, Ratet P, Ayub N, Soto G. Expanding the Benefits of Tnt1 for the Identification of Dominant Mutations in Polyploid Crops: A Single Allelic Mutation in the MsNAC39 Gene Produces Multifoliated Alfalfa. FRONTIERS IN PLANT SCIENCE 2021; 12:805032. [PMID: 35046986 PMCID: PMC8763170 DOI: 10.3389/fpls.2021.805032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Most major crops are polyploid species and the production of genetically engineered cultivars normally requires the introgression of transgenic or gene-edited traits into elite germplasm. Thus, a main goal of plant research is the search of systems to identify dominant mutations. In this article, we show that the Tnt1 element can be used to identify dominant mutations in allogamous tetraploid cultivated alfalfa. Specifically, we show that a single allelic mutation in the MsNAC39 gene produces multifoliate leaves (mfl) alfalfa plants, a pivot trait of breeding programs of this forage species. Finally, we discuss the potential application of a combination of preliminary screening of beneficial dominant mutants using Tnt1 mutant libraries and genome editing via the CRISPR/Cas9 system to identify target genes and to rapidly improve both autogamous and allogamous polyploid crops.
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Affiliation(s)
- Cintia Jozefkowicz
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - Cristina Gómez
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - Ariel Odorizzi
- Estación Experimental Agropecuaria Manfredi, Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | | | - Pascal Ratet
- Université Paris-Saclay, INRAE, CNRS, Université d’Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Nicolás Ayub
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
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12
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Li X, Cai K, Pei X, Li Y, Hu Y, Meng F, Song X, Tigabu M, Ding C, Zhao X. Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening. Int J Mol Sci 2021; 22:ijms222212414. [PMID: 34830294 PMCID: PMC8625062 DOI: 10.3390/ijms222212414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 12/17/2022] Open
Abstract
The NAC (NAM, ATAF and CUC) gene family plays a crucial role in the transcriptional regulation of various biological processes and has been identified and characterized in multiple plant species. However, genome-wide identification of this gene family has not been implemented in Juglans mandshurica, and specific functions of these genes in the development of fruits remain unknown. In this study, we performed genome-wide identification and functional analysis of the NAC gene family during fruit development and identified a total of 114 JmNAC genes in the J. mandshurica genome. Chromosomal location analysis revealed that JmNAC genes were unevenly distributed in 16 chromosomes; the highest numbers were found in chromosomes 2 and 4. Furthermore, according to the homologues of JmNAC genes in Arabidopsis thaliana, a phylogenetic tree was constructed, and the results demonstrated 114 JmNAC genes, which were divided into eight subgroups. Four JmNAC gene pairs were identified as the result of tandem duplicates. Tissue-specific analysis of JmNAC genes during different developmental stages revealed that 39 and 25 JmNAC genes exhibited upregulation during the mature stage in walnut exocarp and embryos, indicating that they may serve key functions in fruit development. Furthermore, 12 upregulated JmNAC genes were common in fruit ripening stage in walnut exocarp and embryos, which demonstrated that these genes were positively correlated with fruit development in J. mandshurica. This study provides new insights into the regulatory functions of JmNAC genes during fruit development in J. mandshurica, thereby improving the understanding of characteristics and evolution of the JmNAC gene family.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Kewei Cai
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Xiaona Pei
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China;
| | - Yan Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Yanbo Hu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Fanjuan Meng
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Xingshun Song
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Mulualem Tigabu
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden;
| | - Changjun Ding
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Correspondence: (C.D.); (X.Z.); Tel.: +86-15246668860 (X.Z.)
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China;
- Correspondence: (C.D.); (X.Z.); Tel.: +86-15246668860 (X.Z.)
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Ma B, Liu X, Guo S, Xie X, Zhang J, Wang J, Zheng L, Wang Y. RtNAC100 involved in the regulation of ROS, Na + accumulation and induced salt-related PCD through MeJA signal pathways in recretohalophyte Reaumuria trigyna. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110976. [PMID: 34315592 DOI: 10.1016/j.plantsci.2021.110976] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
NAM, ATAF1/2, and CUC2 (NAC) proteins regulate plant responses to salt stress. However, the molecular mechanisms by which NAC proteins regulate salt-induced programmed cell death (PCD) are unclear. We identified 56 NAC genes, 35 of which had complete open reading frames with complete NAM domain, in the R. trigyna transcriptome. Salt stress and methyl jasmonate (MeJA) mediated PCD-induced leaf senescence in R. trigyna seedlings. Salt stress accelerated endogenous JA biosynthesis, upregulating RtNAC100 expression. This promoted salt-induced leaf senescence in R. trigyna by regulating RtRbohE and RtSAG12/20 and enhancing ROS accumulation. Transgenic assays showed that RtNAC100 overexpression aggravated salt-induced PCD in transgenic lines by promoting ROS and Na+ accumulation, ROS-Ca2+ hub activation, and PCD-related gene expression. Therefore, RtNAC100 induces PCD via the MeJA signaling pathway in R. trigyna under salt stress.
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Affiliation(s)
- Binjie Ma
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, PR China; Key Laboratory of Herbage and Endemic Crop Biotechnology, and College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Xiaofei Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, PR China; Key Laboratory of Herbage and Endemic Crop Biotechnology, and College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Shuyu Guo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, PR China; Key Laboratory of Herbage and Endemic Crop Biotechnology, and College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Xinlei Xie
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, PR China; Key Laboratory of Herbage and Endemic Crop Biotechnology, and College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Jie Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, PR China; Key Laboratory of Herbage and Endemic Crop Biotechnology, and College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Jianye Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, PR China; Key Laboratory of Herbage and Endemic Crop Biotechnology, and College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Linlin Zheng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, PR China; Key Laboratory of Herbage and Endemic Crop Biotechnology, and College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Yingchun Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, PR China; Key Laboratory of Herbage and Endemic Crop Biotechnology, and College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Liang J, Zheng J, Wu Z, Wang H. Strawberry FaNAC2 Enhances Tolerance to Abiotic Stress by Regulating Proline Metabolism. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9111417. [PMID: 33114021 PMCID: PMC7690739 DOI: 10.3390/plants9111417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/17/2020] [Accepted: 10/21/2020] [Indexed: 05/28/2023]
Abstract
The quality and yields of strawberry plants are seriously affected by abiotic stress every year. NAC (NAM, ATAF, CUC) transcription factors are plant-specific, having various functions in plant development and response to stress. In our study, FaNAC2 from strawberry (Fragaria × ananassa, cultivar "Benihoppe") was isolated and found to be a member of the ATAF sub-family, belonging to the NAC family of transcription factors. FaNAC2 was strongly expressed in the shoot apical meristem and older leaves of strawberries, and was induced by cold, high salinity, and drought stress. To investigate how FaNAC2 functions in plant responses to abiotic stress, transgenic Nicotiana benthamiana plants ectopically overexpressing FaNAC2 were generated. The transgenic plants grew better under salt and cold stress, and, during simulated drought treatment, these transgenic lines not only grew better, but also showed higher seed germination rates than wild-type plants. Gene expression analysis revealed that key genes in proline biosynthesis pathways were up-regulated in FaNAC2 overexpression lines, while its catabolic pathway genes were down-regulated and proline was accumulated more with the overexpression of FaNAC2 after stress treatments. Furthermore, the gene expression of abscisic acid biosynthesis was also promoted. Our results demonstrate that FaNAC2 plays an important positive role in response to different abiotic stresses and may be further utilized to improve the stress tolerance of strawberry plants.
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Affiliation(s)
- Jiahui Liang
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (J.L.); (J.Z.)
| | - Jing Zheng
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (J.L.); (J.Z.)
| | - Ze Wu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Hongqing Wang
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (J.L.); (J.Z.)
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Genome-Wide Analysis of the Role of NAC Family in Flower Development and Abiotic Stress Responses in Cleistogenes songorica. Genes (Basel) 2020; 11:genes11080927. [PMID: 32806602 PMCID: PMC7464430 DOI: 10.3390/genes11080927] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 11/19/2022] Open
Abstract
Plant-specific NAC (NAM, ATAF, CUC) transcription factor (TF) family plays important roles in biological processes such as plant growth and response to stress. Nevertheless, no information is known about NAC TFs in Cleistogenes songorica, a prominent xerophyte desert grass in northwestern China. In this study, 162 NAC genes were found from the Cleistogenes songorica genome, among which 156 C. songoricaNAC (CsNAC) genes (96.3%) were mapped onto 20 chromosomes. The phylogenetic tree constructed by CsNAC and rice NAC TFs can be separated into 14 subfamilies. Syntenic and Ka/Ks analyses showed that CsNACs were primarily expanded by genomewide replication events, and purifying selection was the primary force driving the evolution of CsNAC family genes. The CsNAC gene expression profiles showed that 36 CsNAC genes showed differential expression between cleistogamous (CL) and chasmogamous (CH) flowers. One hundred and two CsNAC genes showed differential expression under heat, cold, drought, salt and ABA treatment. Twenty-three CsNAC genes were commonly differentially expressed both under stress responses and during dimorphic floret development. Gene Ontology (GO) annotation, coexpression network and qRT-PCR tests revealed that these CsNAC genes may simultaneously regulate dimorphic floret development and the response to stress. Our results may help to characterize the NAC transcription factors in C. songorica and provide new insights into the functional research and application of the NAC family in crop improvement, especially in dimorphic floret plants.
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