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Li Z, Lu S, Yi S, Mo S, Yu X, Yin J, Zhang C. Physiological and transcriptomic comparisons shed light on the cold stress response mechanisms of Dendrobium spp. BMC PLANT BIOLOGY 2024; 24:230. [PMID: 38561687 PMCID: PMC10985946 DOI: 10.1186/s12870-024-04903-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Dendrobium spp. comprise a group of tropical orchids with ornamental and medicinal value. Dendrobium spp. are sensitive to low temperature, and the underlying cold response regulatory mechanisms in this group are unclear. To understand how these plants respond to cold stress, we compared the transcriptomic responses of the cold-tolerant cultivar 'Hongxing' (HX) and the cold-sensitive cultivar 'Sonia Hiasakul' (SH) to cold stress. RESULTS Chemometric results showed that the physiological response of SH in the later stages of cold stress is similar to that of HX throughout the cold treatment. Orthogonal partial least squares discriminant analysis (OPLS-DA) revealed that soluble protein content and peroxidase activity are key physiological parameters for assessing the cold tolerance of these two Dendrobium spp. cultivars. Additionally, weighted gene co-expression network analysis (WGCNA) results showed that many cold response genes and metabolic pathways significantly associated with the physiological indices were enriched in the 12 detected modules. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analyses of the 105 hub genes showed that Dendrobium spp. adapt to cold stress by regulating signal transduction, phytohormones, transcription factors, protein translation and modification, functional proteins, biosynthesis and metabolism, cell structure, light, and the circadian clock. Hub genes of the cold stress response network included the remorin gene pp34, the abscisic acid signaling pathway-related genes PROTEIN PHOSPATASE 2 C (PP2C), SNF1-RELATED PROTEIN KINASE 2 (SnRK2), ABRE-BINDING FACTOR 1 (ABF1) and SKI-INTERACTING PROTEIN 17 (SKIP17), the Ca2+ signaling-related GTP diphosphokinase gene CRSH1, the carbohydrate-related gene STARCH SYNTHASE 2 (SS2), the cell wall biosynthesis gene CINNAMYL ALCOHOL DEHYDROGENASE (CAD7), and the endocytosis-related gene VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 52 A (VPS52A). CONCLUSIONS The cold-responsive genes and metabolic pathways of Dendrobium spp. revealed in this study provide important insight to enable the genetic enhancement of cold tolerance in Dendrobium spp., and to facilitate cold tolerance breeding in related plants.
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Affiliation(s)
- Zhiyuan Li
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Shunjiao Lu
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China
| | - Shuangshuang Yi
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China
| | - Shunjin Mo
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China
| | - Xiaoyun Yu
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China
| | - Junmei Yin
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China.
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China.
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571101, Sanya, China.
| | - Changqing Zhang
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China.
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, 100193, Beijing, China.
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Dorjee T, Cui Y, Zhang Y, Liu Q, Li X, Sumbur B, Yan H, Bing J, Geng Y, Zhou Y, Gao F. Characterization of NAC Gene Family in Ammopiptanthus mongolicus and Functional Analysis of AmNAC24, an Osmotic and Cold-Stress-Induced NAC Gene. Biomolecules 2024; 14:182. [PMID: 38397419 PMCID: PMC10886826 DOI: 10.3390/biom14020182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The NAC family of transcription factors (TFs) is recognized as a significant group within the plant kingdom, contributing crucially to managing growth and development processes in plants, as well as to their response and adaptation to various environmental stressors. Ammopiptanthus mongolicus, a temperate evergreen shrub renowned for its remarkable resilience to low temperatures and drought stress, presents an ideal subject for investigating the potential involvement of NAC TFs in stress response mechanisms. Here, the structure, evolution, and expression profiles of NAC family TFs were analyzed systematically, and a cold and osmotic stress-induced member, AmNAC24, was selected and functionally characterized. A total of 86 NAC genes were identified in A. mongolicus, and these were divided into 15 groups. Up to 48 and 8 NAC genes were generated by segmental duplication and tandem duplication, respectively, indicating that segmental duplication is a predominant mechanism in the expansion of the NAC gene family in A. mongolicus. A considerable amount of NAC genes, including AmNAC24, exhibited upregulation in response to cold and osmotic stress. This observation is in line with the detection of numerous cis-acting elements linked to abiotic stress response in the promoters of A. mongolicus NAC genes. Subcellular localization revealed the nuclear residence of the AmNAC24 protein, coupled with demonstrable transcriptional activation activity. AmNAC24 overexpression enhanced the tolerance of cold and osmotic stresses in Arabidopsis thaliana, possibly by maintaining ROS homeostasis. The present study provided essential data for understanding the biological functions of NAC TFs in plants.
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Affiliation(s)
- Tashi Dorjee
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yican Cui
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yuxin Zhang
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Qi Liu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xuting Li
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Batu Sumbur
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Hongxi Yan
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Jie Bing
- College of Life Sciences, Beijing Normal University, Beijing 100080, China;
| | - Yuke Geng
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yijun Zhou
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Fei Gao
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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Cao F, Guo C, Wang X, Wang X, Yu L, Zhang H, Zhang J. Genome-wide identification, evolution, and expression analysis of the NAC gene family in chestnut ( Castanea mollissima). Front Genet 2024; 15:1337578. [PMID: 38333622 PMCID: PMC10850246 DOI: 10.3389/fgene.2024.1337578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
The NAC gene family is one of the most important transcription factor families specific to plants, responsible for regulating many biological processes, including development, stress response, and signal transduction. However, it has not yet been characterized in chestnut, an important nut tree species. Here, we identified 115 CmNAC genes in the chestnut genome, which were divided into 16 subgroups based on the phylogenetic analysis. Numerous cis-acting elements related to auxin, gibberellin, and abscisic acid were identified in the promoter region of CmNACs, suggesting that they play an important role in the growth and development of chestnut. The results of the collinear analysis indicated that dispersed duplication and whole-genome-duplication were the main drivers of CmNAC gene expansion. RNA-seq data of developmental stages of chestnut nut, bud, and ovule revealed the expression patterns of CmNAC genes. Additionally, qRT-PCR experiments were used to verify the expression levels of some CmNAC genes. The comprehensive analysis of the above results revealed that some CmNAC members may be related to chestnut bud and nut development, as well as ovule fertility. The systematic analysis of this study will help to increase understanding of the potential functions of the CmNAC genes in chestnut growth and development.
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Affiliation(s)
- Fei Cao
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Chunlei Guo
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xiangyu Wang
- The Office of Scientific Research, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xuan Wang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Liyang Yu
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Haie Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Jingzheng Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Hebei Collaborative Innovation Center of Chestnut Industry, Qinhuangdao, Hebei, China
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