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Zuo WT, Meng JH, Liu HC, Zhu HY, Lu MZ, Wang LQ. PagWOX11/12a from hybrid poplar enhances drought tolerance by modulating reactive oxygen species. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108662. [PMID: 38691876 DOI: 10.1016/j.plaphy.2024.108662] [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: 02/20/2024] [Revised: 03/30/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
WOX11/12 is a homeobox gene of WOX11 and WOX12 in Arabidopsis that plays important roles in crown root development and growth. It has been reported that WOX11/12 participates in adventitious root (AR) formation and different abiotic stress responses, but the downstream regulatory network of WOX11/12 in poplar remains to be further investigated. In this study, we found that PagWOX11/12a is strongly induced by PEG-simulated drought stress. PagWOX11/12a-overexpressing poplar plantlets showed lower oxidative damage levels, greater antioxidant enzyme activities and reactive oxygen species (ROS) scavenging capacity than non-transgenic poplar plants, whereas PagWOX11/12a dominant repression weakened root biomass accumulation and drought tolerance in poplar. RNA-seq analysis revealed that several differentially expressed genes (DEGs) regulated by PagWOX11/12a are involved in redox metabolism and drought stress response. We used RT-qPCR and yeast one-hybrid (Y1H) assays to validate the downstream target genes of PagWOX11/12a. These results provide new insights into the biological function and molecular regulatory mechanism of WOX11/12 in the abiotic resistance processes of poplar.
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Affiliation(s)
- Wen-Teng Zuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jia-Hui Meng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Hong-Chao Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Hang-Yong Zhu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, 510520, China
| | - Meng-Zhu Lu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Liu-Qiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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2
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Monterisi S, Zhang L, Garcia-Perez P, Alzate Zuluaga MY, Ciriello M, El-Nakhel C, Buffagni V, Cardarelli M, Colla G, Rouphael Y, Cesco S, Lucini L, Pii Y. Integrated multi-omic approach reveals the effect of a Graminaceae-derived biostimulant and its lighter fraction on salt-stressed lettuce plants. Sci Rep 2024; 14:10710. [PMID: 38729985 PMCID: PMC11087557 DOI: 10.1038/s41598-024-61576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/07/2024] [Indexed: 05/12/2024] Open
Abstract
Plant biostimulants are widely applied in agriculture for their ability to improve plant fitness. In the present work, the impact of Graminaceae-derived protein hydrolysate (P) and its lighter molecular fraction F3 (< 1 kDa) on lettuce plants, subjected to either no salt or high salt conditions, was investigated through the combination of metabolomics and transcriptomics. The results showed that both treatments significantly modulated the transcriptome and metabolome of plants under salinity stress, highlighting an induction of the hormonal response. Nevertheless, P and F3 also displayed several peculiarities. F3 specifically modulated the response to ethylene and MAPK signaling pathway, whereas P treatment induced a down-accumulation of secondary metabolites, albeit genes controlling the biosynthesis of osmoprotectants and antioxidants were up-regulated. Moreover, according with the auxin response modulation, P promoted cell wall biogenesis and plasticity in salt-stressed plants. Notably, our data also outlined an epigenetic control of gene expression induced by P treatment. Contrarily, experimental data are just partially in agreement when not stressed plants, treated with P or F3, were considered. Indeed, the reduced accumulation of secondary metabolites and the analyses of hormone pathways modulation would suggest a preferential allocation of resources towards growth, that is not coherent with the down-regulation of the photosynthetic machinery, the CO2 assimilation rate and leaves biomass. In conclusion, our data demonstrate that, although they might activate different mechanisms, both the P and F3 can result in similar benefits, as far as the accumulation of protective osmolytes and the enhanced tolerance to oxidative stress are concerned. Notably, the F3 fraction exhibits slightly greater growth promotion effects under high salt conditions. Most importantly, this research further corroborates that biostimulants' mode of action is dependent on plants' physiological status and their composition, underscoring the importance of investigating the bioactivity of the different molecular components to design tailored applications for the agricultural practice.
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Affiliation(s)
- Sonia Monterisi
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen/Bolzano, 39100, Bolzano, Italy
| | - Leilei Zhang
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Pascual Garcia-Perez
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | - Michele Ciriello
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Christophe El-Nakhel
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Valentina Buffagni
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100, Viterbo, Italy
| | - Mariateresa Cardarelli
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100, Viterbo, Italy
| | - Giuseppe Colla
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100, Viterbo, Italy
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Stefano Cesco
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen/Bolzano, 39100, Bolzano, Italy
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Youry Pii
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen/Bolzano, 39100, Bolzano, Italy.
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Muthan B, Wang J, Welti R, Kosma DK, Yu L, Deo B, Khatiwada S, Vulavala VKR, Childs KL, Xu C, Durrett TP, Sanjaya SA. Mechanisms of Spirodela polyrhiza tolerance to FGD wastewater-induced heavy-metal stress: Lipidomics, transcriptomics, and functional validation. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133951. [PMID: 38492385 DOI: 10.1016/j.jhazmat.2024.133951] [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: 12/11/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
Unlike terrestrial angiosperm plants, the freshwater aquatic angiosperm duckweed (Spirodela polyrhiza) grows directly in water and has distinct responses to heavy-metal stress. Plantlets accumulate metabolites, including lipids and carbohydrates, under heavy-metal stress, but how they balance metabolite levels is unclear, and the gene networks that mediate heavy-metal stress responses remain unknown. Here, we show that heavy-metal stress induced by flue gas desulfurization (FGD) wastewater reduces chlorophyll contents, inhibits growth, reduces membrane lipid biosynthesis, and stimulates membrane lipid degradation in S. polyrhiza, leading to triacylglycerol and carbohydrate accumulation. In FGD wastewater-treated plantlets, the degraded products of monogalactosyldiacylglycerol, primarily polyunsaturated fatty acids (18:3), were incorporated into triacylglycerols. Genes involved in early fatty acid biosynthesis, β-oxidation, and lipid degradation were upregulated while genes involved in cuticular wax biosynthesis were downregulated by treatment. The transcription factor gene WRINKLED3 (SpWRI3) was upregulated in FGD wastewater-treated plantlets, and its ectopic expression increased tolerance to FGD wastewater in transgenic Arabidopsis (Arabidopsis thaliana). Transgenic Arabidopsis plants showed enhanced glutathione and lower malondialdehyde contents under stress, suggesting that SpWRI3 functions in S. polyrhiza tolerance of FGD wastewater-induced heavy-metal stress. These results provide a basis for improving heavy metal-stress tolerance in plants for industrial applications.
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Affiliation(s)
- Bagyalakshmi Muthan
- Agricultural and Environmental Research Station and Energy and Environmental Science Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Jie Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Ruth Welti
- Division of Biology, Kansas State University, Manhattan, KS 66506-4901, USA
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Linhui Yu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bikash Deo
- Department of Biology, Agricultural and Environmental Research Station and Energy and Environmental Science Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Subhiksha Khatiwada
- Department of Biology, Agricultural and Environmental Research Station and Energy and Environmental Science Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Vijaya K R Vulavala
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Changcheng Xu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Timothy P Durrett
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Sanju A Sanjaya
- Department of Biology, Agricultural and Environmental Research Station and Energy and Environmental Science Institute, West Virginia State University, Institute, WV 25112-1000, USA.
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Zinta R, Tiwari JK, Buckseth T, Goutam U, Singh RK, Kumar V, Thakur AK. Transcriptome profiling and characterization of genes associated with tuberization under high temperature in aeroponics in potato cv. Kufri Anand. Genes Genomics 2024; 46:409-421. [PMID: 38381322 DOI: 10.1007/s13258-024-01503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND High temperature stress is an important abiotic factor, which affects tuberization and ultimately causes heavy yield reduction in potato. OBJECTIVES Identification and characterization of genes associated with tuberization under high temperature stress is essential for future management through biotechnology. METHODOLOGY Two contrasting potato varieties Kufri Anand (profuse tuber-bearing) versus Kufri Frysona (very less/scanty tuber-bearing, control) were cultivated in aeroponics under high temperature stress, and transcriptomes were analyzed. RESULTS Potato cv. Kufri Anand was found superior over control (Kufri Frysona) for tuber yield and its component traits along with root morphology under aeroponics. Transcriptomes of tuber and leaf tissues were analyzed. Statistically significant (p < 0.05) differentially expressed genes (DEGs) were categorised into up-regulated (> 2 log2 fold change, FC) and down-regulated (< -2 log2 FC) genes. DEGs were annotated by gene ontology and KEGG pathways. A few selected up-regulated genes of both tissues were identified, and phylogeny tree and motif analysis were analysed based on 36 peptide sequences representing 15 selected DEGs in this study. Further, gene expression markers were developed and validated by real time qPCR analysis for the identification of high temperature tolerant genotypes. CONCLUSION A few key genes associated in tuberization under high temperature conditions were heat shock proteins (e.g. 18.5 kDa class I heat shock protein), sugar metabolism (e.g. glucosyltransferase), transcription factor (e.g. WRKY), and phytohormones (e.g. auxin-induced beta-glucosidase). Our study provides an overview of key genes involved in tuberization under high temperature stress in potato cv. Kufri Anand under aeroponics.
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Affiliation(s)
- Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
- ICAR-Indian Institute of Vegetable Research Institute, Varanasi, Uttar Pradesh, India.
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Umesh Goutam
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay Kumar Thakur
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Guo F, Meng X, Hong H, Liu S, Yu J, Huang C, Dong T, Geng H, Li Z, Zhu M. Systematic identification and expression analysis of bHLH gene family reveal their relevance to abiotic stress response and anthocyanin biosynthesis in sweetpotato. BMC PLANT BIOLOGY 2024; 24:156. [PMID: 38424529 PMCID: PMC10905920 DOI: 10.1186/s12870-024-04788-0] [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: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND bHLH transcription factors play significant roles in regulating plant growth and development, stress response, and anthocyanin biosynthesis. Sweetpotato is a pivotal food and industry crop, but little information is available on sweetpotato bHLH genes. RESULTS Herein, 227 putative IbbHLH genes were defined on sweetpotato chromosomes, and fragment duplications were identified as the dominant driving force for IbbHLH expansion. These IbbHLHs were divided into 26 subfamilies through phylogenetic analysis, as supported by further analysis of exon-intron structure and conserved motif composition. The syntenic analysis between IbbHLHs and their orthologs from other plants depicted evolutionary relationships of IbbHLHs. Based on the transcriptome data under salt stress, the expression of 12 IbbHLHs was screened for validation by qRT-PCR, and differential and significant transcriptions under abiotic stress were detected. Moreover, IbbHLH123 and IbbHLH215, which were remarkably upregulated by stress treatments, had obvious transactivation activity in yeasts. Protein interaction detections and yeast two-hybrid assays suggested an intricate interaction correlation between IbbHLHs. Besides, transcriptome screening revealed that multiple IbbHLHs may be closely related to anthocyanin biosynthesis based on the phenotype (purple vs. white tissues), which was confirmed by subsequent qRT-PCR analysis. CONCLUSIONS These results shed light on the promising functions of sweetpotato IbbHLHs in abiotic stress response and anthocyanin biosynthesis.
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Affiliation(s)
- Fen Guo
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Xiaoqing Meng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Haiting Hong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Siyuan Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Jing Yu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Can Huang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Huixue Geng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China.
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Zhang Y, Guo Z, Chen X, Li X, Shi Y, Xu L, Yu C, Jing B, Li W, Xu A, Shi X, Li K, Huang Z. Identification candidate genes for salt resistance through quantitative trait loci-sequencing in Brassica napus L. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154187. [PMID: 38422630 DOI: 10.1016/j.jplph.2024.154187] [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: 08/24/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops worldwide. However, its yield is greatly limited by salt stress, one of the primary abiotic stresses. Identification of salt-tolerance genes and breeding salt-tolerant varieties is an effective approach to address this issue. Unfortunately, little is known about the salt-tolerance quantitative trait locus (QTL) and the identification of salt tolerance genes in rapeseed. In this study, high-throughput quantitative trait locus sequencing (QTL-seq) was applied to identifying salt-tolerant major QTLs based on two DNA pools from an F2:3 population of a cross between rapeseed line 2205 (salt tolerant) and 1423 (salt sensitive). A total of twelve major QTLs related to the salt tolerance rating (STR) were detected on chromosomes A03, A08, C02, C03, C04, C06, C07 and C09. To further enhance our understanding, we integrated QTL-seq data with transcriptome analysis of the two parental rapeseed plants subjected to salt stress, through which ten candidate genes for salt tolerance were identified within the major QTLs by gene differential expression, variation and annotated functions analysis. The marker SNP820 linked to salt tolerance was successfully validated and would be useful as a diagnostic marker in marker-assisted breeding. These findings provide valuable insights for future breeding programs aimed at developing rapeseed cultivars resistant to salt stresses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhiting Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoqin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinru Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yiji Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Liang Xu
- Academy of Agricultural and Forestry Sciences of Qinghai University, Key Laboratory of Spring Rape Genetic Improvement of Qinghai Province, Rapeseed Research and Development Center of Qinghai Province, Xining, 810016, Qinghai, China
| | - Chengyu Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bing Jing
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weiwei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Keqi Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Zhai X, Wang X, Yang X, Huang Q, Wu D, Wang Y, Kang H, Sha L, Fan X, Zhou Y, Zhang H. Genome-wide identification of bHLH transcription factors and expression analysis under drought stress in Pseudoroegneria libanotica at germination. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:467-481. [PMID: 38633269 PMCID: PMC11018577 DOI: 10.1007/s12298-024-01433-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/24/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
The basic helix-loop-helix (bHLH) transcription factor family is the second largest in plants. bHLH transcription factor is not only universally involved in plant growth and metabolism, including photomorphogenesis, light signal transduction, and secondary metabolism, but also plays an important role in plant response to stress. However, the function of bHLH TFs in Pseudoroegneria species has not been studied yet. Pseudoroegneria (Nevski) Á. Löve is a perennial genus of the Triticeae. Pseudoroegneria species are mostly distributed in arid/semi-arid areas and they show good drought tolerance. In this study, we identified 152 PlbHLH TFs in Pseudoroegneria libanotica, which could be classified into 15 groups. Collinearity analysis indicates that 122 PlbHLH genes share homology with wbHLH genes in wheat, and it has lower homology with AtbHLH genes in Arabidopsis. Based on transcriptome profiling under an experiment with three PEG concentrations (0%, 10%, and 20%), 10 up-regulated genes and 11 down-regulated PlbHLH genes were screened. Among them, PlbHLH6, PlbHLH55 and PlbHLH64 as candidate genes may be the key genes related to drought tolerance response at germination, and they have been demonstrated to respond to drought, salt, oxidative, heat, and heavy metal stress in yeast. This study lays the foundation for an in-depth study of the biological roles of PlbHLHs in Pse. libanotica, and discovered new drought-tolerance candidate genes to enhance the genetic background of Triticeae crops. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01433-w.
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Affiliation(s)
- Xingguan Zhai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xia Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xunzhe Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Qingxiang Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
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8
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Sonsungsan P, Suratanee A, Buaboocha T, Chadchawan S, Plaimas K. Identification of Salt-Sensitive and Salt-Tolerant Genes through Weighted Gene Co-Expression Networks across Multiple Datasets: A Centralization and Differential Correlation Analysis. Genes (Basel) 2024; 15:316. [PMID: 38540375 PMCID: PMC10970189 DOI: 10.3390/genes15030316] [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: 01/11/2024] [Revised: 02/18/2024] [Accepted: 02/24/2024] [Indexed: 06/14/2024] Open
Abstract
Salt stress is a significant challenge that severely hampers rice growth, resulting in decreased yield and productivity. Over the years, researchers have identified biomarkers associated with salt stress to enhance rice tolerance. However, the understanding of the mechanism underlying salt tolerance in rice remains incomplete due to the involvement of multiple genes. Given the vast amount of genomics and transcriptomics data available today, it is crucial to integrate diverse datasets to identify key genes that play essential roles during salt stress in rice. In this study, we propose an integration of multiple datasets to identify potential key transcription factors. This involves utilizing network analysis based on weighted co-expression networks, focusing on gene-centric measurement and differential co-expression relationships among genes. Consequently, our analysis reveals 86 genes located in markers from previous meta-QTL analysis. Moreover, six transcription factors, namely LOC_Os03g45410 (OsTBP2), LOC_Os07g42400 (OsGATA23), LOC_Os01g13030 (OsIAA3), LOC_Os05g34050 (OsbZIP39), LOC_Os09g29930 (OsBIM1), and LOC_Os10g10990 (transcription initiation factor IIF), exhibited significantly altered co-expression relationships between salt-sensitive and salt-tolerant rice networks. These identified genes hold potential as crucial references for further investigation into the functions of salt stress response in rice plants and could be utilized in the development of salt-resistant rice cultivars. Overall, our findings shed light on the complex genetic regulation underlying salt tolerance in rice and contribute to the broader understanding of rice's response to salt stress.
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Affiliation(s)
- Pajaree Sonsungsan
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand;
| | - Teerapong Buaboocha
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology (CEEPP), Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kitiporn Plaimas
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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9
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Gambhir P, Raghuvanshi U, Kumar R, Sharma AK. Transcriptional regulation of tomato fruit ripening. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:289-303. [PMID: 38623160 PMCID: PMC11016043 DOI: 10.1007/s12298-024-01424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/15/2024] [Accepted: 02/27/2024] [Indexed: 04/17/2024]
Abstract
An intrinsic and genetically determined ripening program of tomato fruits often depends upon the appropriate activation of tissue- and stage-specific transcription factors in space and time. The past two decades have yielded considerable progress in detailing these complex transcriptional as well as hormonal regulatory circuits paramount to fleshy fruit ripening. This non-linear ripening process is strongly controlled by the MADS-box and NOR family of proteins, triggering a transcriptional response associated with the progression of fruit ripening. Deepening insights into the connection between MADS-RIN and plant hormones related transcription factors, such as ERFs and ARFs, further conjugates the idea that several signaling units work in parallel to define an output fruit ripening transcriptome. Besides these TFs, the role of other families of transcription factors such as MYB, GLK, WRKY, GRAS and bHLH have also emerged as important ripening regulators. Other regulators such as EIN and EIL proteins also determine the transcriptional landscape of ripening fruits. Despite the abundant knowledge of the complex spectrum of ripening networks in the scientific domain, identifying more ripening effectors would pave the way for a better understanding of fleshy fruit ripening at the molecular level. This review provides an update on the transcriptional regulators of tomato fruit ripening.
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Affiliation(s)
- Priya Gambhir
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
| | - Rahul Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046 India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
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10
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Guo Z, Liu H, Zheng S, Qi K, Xie Z, Wang X, Hong Y, Cui Y, Liu X, Gu C, Zhang SL. The transcription factor PbbHLH164 is destabilized by PbRAD23C/D.1 and mediates ethylene biosynthesis during pear fruit ripening. J Adv Res 2024:S2090-1232(24)00004-3. [PMID: 38190939 DOI: 10.1016/j.jare.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/17/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
The phytohormone ethylene plays an important role in climacteric fruit ripening. However, the knowledge on molecular regulation of ethylene biosynthesis remains limited in pear fruit. Herein, a new basic helix-loop-helix transcription factor, PbbHLH164, was identified based on the transcriptome analysis of different developing and ripening fruits of two pear cultivars 'Sucui No. 1' and 'Cuiguan'. PbbHLH164 was more highly expressed in ripening fruit than in developing fruit and positively correlated with ethylene production in both cultivars. PbbHLH164 could directly bind to the promoter of 1-aminocyclopropane-1-carboxylate synthase, PbACS1b, to enhance the expression, leading to the increase of ethylene production and the acceleration of fruit ripening. Interestingly, PbbHLH164 physically interacted with an ubiquitin-like/ubiquitin-associated protein PbRAD23C/D.1, and the interaction of PbbHLH164 with PbRAD23C/D.1 attenuated the function of PbbHLH164 in enhancing the activity of the PbACS1b promoter. Notably, PbRAD23C/D.1 was involved in the degradation of PbbHLH164, and this degradation was inhibited by an ubiquitin proteasome inhibitor MG132. Different from PbbHLH164, PbRAD23C/D.1 was more highly expressed in developing fruit than in ripening fruit of both cultivars. These results suggest that the increase of ethylene production during pear fruit ripening results from the up-regulated expression of PbbHLH164 and the down-regulated expression of PbRAD23C/D.1. This information provided new insights into the molecular regulation of ethylene biosynthesis during fruit ripening.
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Affiliation(s)
- ZhiHua Guo
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Liu
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - SiQi Zheng
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - KaiJie Qi
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - ZhiHua Xie
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - XuePing Wang
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - YeMei Hong
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - YanBo Cui
- Nanjing Ningcui Biological Seed Company Limited, Nanjing, Jiangsu, China
| | - Xiaoxiang Liu
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Gu
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shao-Ling Zhang
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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11
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Zhao X, Wang Q, Yan C, Sun Q, Wang J, Li C, Yuan C, Mou Y, Shan S. The bHLH transcription factor AhbHLH121 improves salt tolerance in peanut. Int J Biol Macromol 2024; 256:128492. [PMID: 38035960 DOI: 10.1016/j.ijbiomac.2023.128492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
Plants have developed a number of protective mechanisms to respond to salt and other stresses. Previous studies have shown that the basic helix-loop-helix (bHLH) transcription factor AhbHLH121 plays a crucial role in the response to abiotic stresses in peanut, but the mechanisms and functions related to AhbHLH121 remain unclear. In the current research, AhbHLH121 was induced by salt treatment. Overexpression of AhbHLH121 improved salt resistance, whereas silencing AhbHLH121 resulted in the inverse correlation. Our results also demonstrated that overexpression of AhbHLH121 results in greater activity of antioxidant enzymes under stress condition by promoting the expression of the genes for peroxidase, catalase and superoxide dismutase (AhPOD, AhCAT and AhSOD), indicating enhanced scavenging of reactive oxygen species. Further analysis including Yeast one-hybrid (Y1H) assays and electrophoretic mobility shift assays (EMSAs), suggested that AhbHLH121 can bind directly to the G/E-box regions of the AhPOD, AhCAT and AhSOD promoters, thereby promoting their expression and leading to improved antioxidant enzyme activity. Our research improves the understanding of the mechanisms that allow this peanut bHLH transcription factor to improve abiotic tolerance, and provides valuable gene resources for breeding programs to promote salt stress resistance.
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Affiliation(s)
- Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao 266100, China.
| | - Qi Wang
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Yifei Mou
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao 266100, China.
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12
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Zahra N, Uzair M, Zaid IU, Attia KA, Inam S, Fiaz S, Abdallah RM, Naeem MK, Farooq U, Rehman N, Ali GM, Xu J, Li Z, Khan MR. The comparative transcriptome analysis of two green super rice genotypes with varying tolerance to salt stress. Mol Biol Rep 2023; 51:22. [PMID: 38110786 DOI: 10.1007/s11033-023-08998-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Salinity is one of the main abiotic factors that restrict plant growth, physiology, and crop productivity is salt stress. About 33% of the total irrigated land suffers from severe salinity because of intensive underground water extraction and irrigation with brackish water. Thus, it is important to understand the genetic mechanism and identify the novel genes involved in salt tolerance for the development of climate-resilient rice cultivars. METHODS AND RESULTS In this study, two rice genotypes with varying tolerance to salt stress were used to investigate the differential expressed genes and molecular pathways to adapt under saline soil by comparative RNA sequencing at 42 days of the seedling stage. Salt-susceptible (S3) and -tolerant (S13) genotypes revealed 3982 and 3463 differentially expressed genes in S3 and S13 genotypes. The up-regulated genes in both genotypes were substantially enriched in different metabolic processes and binding activities. Biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and plant signal transduction mechanisms were highly enriched. Salt-susceptible and -tolerant genotypes shared the same salt adaptability mechanism with no significant quantitative differences at the transcriptome level. Moreover, bHLH, ERF, NAC, WRKY, and MYB transcription factors were substantially up-regulated under salt stress. 391 out of 1806 identified novel genes involved in signal transduction mechanisms. Expression profiling of six novel genes further validated the findings from RNA-seq data. CONCLUSION These findings suggest that the differentially expressed genes and molecular mechanisms involved in salt stress adaptation are conserved in both salt-susceptible and salt-tolerant rice genotypes. Further molecular characterization of novel genes will help to understand the genetic mechanism underlying salt tolerance in rice.
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Affiliation(s)
- Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Imdad Ullah Zaid
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan.
| | - Rizk M Abdallah
- Department of Rice, Field Crops Research Institute, ARC, Sakha, Kafrelshiekh, 33717, Egypt
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | | | - Jianlong Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan.
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13
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Du T, Zhou Y, Qin Z, Li A, Wang Q, Li Z, Hou F, Zhang L. Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato. FRONTIERS IN PLANT SCIENCE 2023; 14:1301848. [PMID: 38152142 PMCID: PMC10752007 DOI: 10.3389/fpls.2023.1301848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023]
Abstract
Introduction The higher plant transcription factor C2H2 zinc finger protein (C2H2-ZFP) is essential for plant growth, development, and stress response. There are limited studies on C2H2-ZFP genes in sweetpotato, despite a substantial number of C2H2-ZFP genes having been systematically found in plants. Methods In this work, 178 C2H2-ZFP genes were found in sweetpotato, distributed randomly on 15 chromosomes, and given new names according to where they were located. These members of the zinc finger gene family are separated into six branches, as shown by the phylogenetic tree. 24 tandem repeats of IbZFP genes and 46 fragment repeats were identified, and a homology study revealed that IbZFP genes linked more regions with wild relative species of sweetpotato as well as rhizome plants like potato and cassava. And we analyzed the expression patterns of IbZFP genes during the early development of sweetpotato storage roots (SRs) and salt stress using transcriptome data, and identified 44 IbZFP genes that exhibited differences in expression levels during the early expansion of sweetpotato SRs in different varieties, and 92 IbZFP genes that exhibited differences in expression levels under salt stress in salt tolerant and salt sensitive sweetpotato varieties. Additionally, we cloned six IbZFP genes in sweetpotato and analyzed their expression patterns in different tissues, their expression patterns under abiotic stress and hormone treatment, and subcellular localization. Results and discussion The results showed that the IbZFP genes had tissue specificity in sweetpotato and were induced to varying degrees by drought and salt stress. ABA and GA3 treatments also affected the expression of the IbZFP genes. We selected IbZFP105, which showed significant differences in expression levels under salt stress and ABA treatment, to be heterologously expressed in Arabidopsis thaliana. We found that IbZFP105 OE lines exhibited higher tolerance to salt stress and ABA stress. This indicates that IbZFP105 can enhance the salt tolerance of plants. These results systematically identified the evolution and expression patterns of members of the C2H2-ZFP gene family in sweetpotato, providing a theoretical basis for studying the role of IbZFP genes in the development of sweetpotato SRs and in resistance to stress.
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Affiliation(s)
- Taifeng Du
- Key Laboratory of Phylogeny and Comparative Genomics of the Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yuanyuan Zhou
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Zhen Qin
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Aixian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Qingmei Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Zongyun Li
- Key Laboratory of Phylogeny and Comparative Genomics of the Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Fuyun Hou
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Liming Zhang
- Key Laboratory of Phylogeny and Comparative Genomics of the Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, China
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14
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Chen S, Liu H, Yangzong Z, Gardea-Torresdey JL, White JC, Zhao L. Seed Priming with Reactive Oxygen Species-Generating Nanoparticles Enhanced Maize Tolerance to Multiple Abiotic Stresses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19932-19941. [PMID: 37975618 DOI: 10.1021/acs.est.3c07339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Climate change-induced extreme weather events (heat, cold, drought, and flooding) will severely affect crop production. Increasing the resilience of crops to fluctuating environmental conditions is critically important. Here, we report that nanomaterials (NMs) with reactive oxygen species (ROS)-generating properties can be used as seed priming agents to simultaneously enhance the tolerance of maize seeds and seedlings to diverse and even multiple stresses. Maize seeds primed with 40 mg/L silver nanoparticles (AgNPs) exhibited accelerated seed germination and an increased germination rate, greater seedling vigor, and better seedling growth under drought (10% and 20% PEG), saline (50 and 100 mM NaCl), and cold (15 °C) stress conditions, indicating enhanced resilience to diverse stresses. Importantly, maize resistance to simultaneous multiple stresses (drought and cold, drought and salt, and salt and cold) was markedly enhanced. Under drought conditions, seed priming significantly boosted root hair density and length (17.3-82.7%), which enabled greater tolerance to water deficiency. RNA-seq analysis reveals that AgNPs seed priming induced a transcriptomic shift in maize seeds. Plant hormone signal transduction and MAPK signaling pathways were activated upon seed priming. Importantly, low-cost and environmentally friendly ROS-generating Fe-based NMs (Fe2O3 and Fe3O4 NPs) were also demonstrated to enhance the resistance of seeds and seedlings to drought, salt, and cold stresses. These findings demonstrate that a simple seed priming strategy can be used to significantly enhance the climate resilience of crops through modulated ROS homeostasis and that this approach could be a powerful nanoenabled tool for addressing worsening food insecurity.
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Affiliation(s)
- Si Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haolin Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Zhaxi Yangzong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Jorge L Gardea-Torresdey
- Chemistry and Biochemistry Department, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Jason C White
- The Connecticut Agricultural Experiment Station (CAES), New Haven, Connecticut 06511, United States
| | - Lijuan Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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15
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Huang X, Zhang W, Liao Y, Ye J, Xu F. Contemporary understanding of transcription factor regulation of terpenoid biosynthesis in plants. PLANTA 2023; 259:2. [PMID: 37971670 DOI: 10.1007/s00425-023-04268-z] [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: 06/20/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
KEY MESSAGE This review summarized how TFs function independently or in response to environmental factors to regulate terpenoid biosynthesis via fine-tuning the expression of rate-limiting enzymes. Terpenoids are derived from various species and sources. They are essential for interacting with the environment and defense mechanisms, such as antimicrobial, antifungal, antiviral, and antiparasitic properties. Almost all terpenoids have high medicinal value and economic performance. Recently, the control of enzyme genes on terpenoid biosynthesis has received a great deal of attention, but transcriptional factors regulatory network on terpenoid biosynthesis and accumulation has yet to get a thorough review. Transcription factors function as activators or suppressors independently or in response to environmental stimuli, fine-tuning terpenoid accumulation through regulating rate-limiting enzyme expression. This study investigates the advancements in transcription factors related to terpenoid biosynthesis and systematically summarizes previous works on the specific mechanisms of transcription factors that regulate terpenoid biosynthesis via hormone signal-transcription regulatory networks in plants. This will help us to better comprehend the regulatory network of terpenoid biosynthesis and build the groundwork for terpenoid development and effective utilization.
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Affiliation(s)
- Xinru Huang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
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16
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Tan Z, Lu D, Yu Y, Li L, Dong W, Xu L, Yang Q, Wan X, Liang H. Genome-Wide Identification and Characterization of the bHLH Gene Family and Its Response to Abiotic Stresses in Carthamus tinctorius. PLANTS (BASEL, SWITZERLAND) 2023; 12:3764. [PMID: 37960120 PMCID: PMC10648185 DOI: 10.3390/plants12213764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/16/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
The basic helix-loop-helix (bHLH) transcription factors possess DNA-binding and dimerization domains and are involved in various biological and physiological processes, such as growth and development, the regulation of secondary metabolites, and stress response. However, the bHLH gene family in C. tinctorius has not been investigated. In this study, we performed a genome-wide identification and analysis of bHLH transcription factors in C. tinctorius. A total of 120 CtbHLH genes were identified, distributed across all 12 chromosomes, and classified into 24 subfamilies based on their phylogenetic relationships. Moreover, the 120 CtbHLH genes were subjected to comprehensive analyses, including protein sequence alignment, evolutionary assessment, motif prediction, and the analysis of promoter cis-acting elements. The promoter region analysis revealed that CtbHLH genes encompass cis-acting elements and were associated with various aspects of plant growth and development, responses to phytohormones, as well as responses to both abiotic and biotic stresses. Expression profiles, sourced from transcriptome databases, indicated distinct expression patterns among these CtbHLH genes, which appeared to be either tissue-specific or specific to certain cultivars. To further explore their functionality, we determined the expression levels of fifteen CtbHLH genes known to harbor motifs related to abiotic and hormone responses. This investigation encompassed treatments with ABA, salt, drought, and MeJA. The results demonstrated substantial variations in the expression patterns of CtbHLH genes in response to these abiotic and hormonal treatments. In summary, our study establishes a solid foundation for future inquiries into the roles and regulatory mechanisms of the CtbHLH gene family.
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Affiliation(s)
- Zhengwei Tan
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Dandan Lu
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yongliang Yu
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Li
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wei Dong
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lanjie Xu
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qing Yang
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiufu Wan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijng 100700, China;
| | - Huizhen Liang
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
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17
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Liu Y, Li T, Zhu H, Zhou Y, Shen Q, Liu D. Cysteine facilitates the lignocellulolytic response of Trichoderma guizhouense NJAU4742 by indirectly up-regulating membrane sugar transporters. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:159. [PMID: 37891614 PMCID: PMC10612256 DOI: 10.1186/s13068-023-02418-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Filamentous fungi possess a rich CAZymes system, which is widely studied and applied in the bio-conversion of plant biomass to alcohol chemicals. Carbon source acquisition is the fundamental driver for CAZymes-producing sustainability and secondary metabolism, therefore, a deeper insight into the regulatory network of sugar transport in filamentous fungi has become urgent. RESULTS This study reports an important linkage of sulfur assimilation to lignocellulose response of filamentous fungus. Inorganic sulfur addition facilitated biodegradation of rice straw by Trichoderma guizhouense NJAU4742. Cysteine and glutathione were revealed as major intracellular metabolites responsive to sulfur addition by metabolomics, cysteine content was increased in this process and glutathione increased correspondingly. Two membrane sugar transporter genes, Tgmst1 and Tgmst2, were identified as the critical response genes significantly up-regulated when intracellular cysteine increased. Tgmst1 and Tgmst2 were both positively regulated by the glucose regulation-related protein (GRP), up-regulation of both Tgmst1 and Tggrp can cause a significant increase in intracellular glucose. The transcriptional regulatory function of GRP mainly relied on GSH-induced glutathionylation, and the transcription activating efficiency was positively related to the glutathionylation level, furthermore, DTT-induced deglutathionylation resulted in the down-regulation of downstream genes. CONCLUSIONS Inorganic sulfur addition induces a rise in intracellular Cys content, and the conversion of cysteine to glutathione caused the increase of glutathionylation level of GRP, which in turn up-regulated Tgmst1 and Tgmst2. Subsequently, the sugar transport efficiency of single cells was improved, which facilitated the maintenance of vigorous CAZymes metabolism and the straw-to-biomass conversion.
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Affiliation(s)
- Yang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Tuo Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Han Zhu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yihao Zhou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing, People's Republic of China.
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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Zhang Q, Teng R, Yuan Z, Sheng S, Xiao Y, Deng H, Tang W, Wang F. Integrative transcriptomic analysis deciphering the role of rice bHLH transcription factor Os04g0301500 in mediating responses to biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1266242. [PMID: 37828923 PMCID: PMC10565216 DOI: 10.3389/fpls.2023.1266242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
Understanding the signaling pathways activated in response to these combined stresses and their crosstalk is crucial to breeding crop varieties with dual or multiple tolerances. However, most studies to date have predominantly focused on individual stress factors, leaving a significant gap in understanding plant responses to combined biotic and abiotic stresses. The bHLH family plays a multifaceted regulatory role in plant response to both abiotic and biotic stresses. In order to comprehensively identify and analyze the bHLH gene family in rice, we identified putative OsbHLHs by multi-step homolog search, and phylogenic analysis, molecular weights, isoelectric points, conserved domain screening were processed using MEGAX version 10.2.6. Following, integrative transcriptome analysis using 6 RNA-seq data including Xoo infection, heat, and cold stress was processed. The results showed that 106 OsbHLHs were identified and clustered into 17 clades. Os04g0301500 and Os04g0489600 are potential negative regulators of Xoo resistance in rice. In addition, Os04g0301500 was involved in non-freezing temperatures (around 4°C) but not to 10°C cold stresses, suggesting a complex interplay with temperature signaling pathways. The study concludes that Os04g0301500 may play a crucial role in integrating biotic and abiotic stress responses in rice, potentially serving as a key regulator of plant resilience under changing environmental conditions, which could be important for further multiple stresses enhancement and molecular breeding through genetic engineering in rice.
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Affiliation(s)
- Qiuping Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Yuelushan Laboratory, Changsha, China
| | - Rong Teng
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Yuelushan Laboratory, Changsha, China
| | - Ziyi Yuan
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Yuelushan Laboratory, Changsha, China
| | - Song Sheng
- Yuelushan Laboratory, Changsha, China
- College of Forest, Central South University of Forestry and Technology, Changsha, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Yuelushan Laboratory, Changsha, China
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Hybrid Rice Centre, Hunan Academy of Agricultural Science, Changsha, China
| | - Wenbang Tang
- Yuelushan Laboratory, Changsha, China
- Hunan Hybrid Rice Centre, Hunan Academy of Agricultural Science, Changsha, China
| | - Feng Wang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Yuelushan Laboratory, Changsha, China
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19
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Niu X, Lai Z, Wang L, Ma R, Ren Y, Wang X, Cheng C, Wang T, Chen F, Xu Y. Co-Expression of JcNAC1- and JcZFP8-Improved Agronomic Traits of Tobacco and Enhanced Drought Resistance through NbbHLH1 and NbbHLH2. PLANTS (BASEL, SWITZERLAND) 2023; 12:3029. [PMID: 37687275 PMCID: PMC10490288 DOI: 10.3390/plants12173029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Previous studies have identified numerous transcription factors involved in drought response, each of which play different roles in plants. The objective of the present study was to evaluate the effectiveness of two transcription factors on drought response in Jatropha curcas L., JcNAC1 and JcZFP8. The overexpression of these transcription factors in tobacco (Nicotiana benthamiana L.) improved drought resistance, but JcZFP8 delayed germination and JcNAC1 reduced biomass and yield. By constitutively co-expressing these two genes in tobacco, drought resistance was improved, and the negative effects of each of them were overcome. The transgenic plants with double-gene co-expression showed stronger drought tolerance with 1.76-fold greater accumulation of proline and lower H2O2 and malondialdehyde (MDA) content to 43 and 65% of wildtype (WT) levels, respectively. The expression levels of NbbHLH1 and NbbHLH2 genes upregulated linearly with the increased drought tolerance of double genes co-expression plants. In drought conditions, the leaf water contents of bhlh1, bhlh2, and bhlh1bhlh2 deletion mutants obtained by CRISPR-CAS9 knockout technique were maintained at 99%, 97%, and 97% of WT. The bhlh1bhlh2 was found with lower germination rate but with higher reactive oxygen levels (1.64-fold H2O2 and 1.41-fold MDA levels). Thus, the co-expression of two transcription factors with different functions overcame the adverse traits brought by a single gene and enhanced the shared drought-tolerant traits, which can provide guidance on theory and selection of gene combinations for the application of multi-gene co-expression in agriculture in the future.
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Affiliation(s)
- Xianfei Niu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhiping Lai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Linghui Wang
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China
| | - Rui Ma
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yingying Ren
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xueying Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Cheng Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ting Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Fang Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ying Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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20
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Tang Y, Li J, Song Q, Cheng Q, Tan Q, Zhou Q, Nong Z, Lv P. Transcriptome and WGCNA reveal hub genes in sugarcane tiller seedlings in response to drought stress. Sci Rep 2023; 13:12823. [PMID: 37550374 PMCID: PMC10406934 DOI: 10.1038/s41598-023-40006-x] [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: 05/08/2023] [Accepted: 08/03/2023] [Indexed: 08/09/2023] Open
Abstract
Drought stress can severely affect sugarcane growth and yield. The objective of this research was to identify candidate genes in sugarcane tillering seedlings in response to drought stress. We performed a comparative phenotypic, physiological and transcriptomic analysis of tiller seedlings of drought-stressed and well-watered "Guire 2" sugarcane, in a time-course experiment (5 days, 9 days and 15 days). Physiological examination reviewed that SOD, proline, soluble sugars, and soluble proteins accumulated in large amounts in tiller seedlings under different intensities of drought stress, while MDA levels remained at a stable level, indicating that the accumulation of osmoregulatory substances and the enhancement of antioxidant enzyme activities helped to limit further damage caused by drought stress. RNA-seq and weighted gene co-expression network analysis (WGCNA) were performed to identify genes and modules associated with sugarcane tillering seedlings in response to drought stress. Drought stress induced huge down-regulated in gene expression profiles, most of down-regulated genes were mainly associated with photosynthesis, sugar metabolism and fatty acid synthesis. We obtained four gene co-expression modules significantly associated with the physiological changes under drought stress (three modules positively correlated, one module negatively correlated), and found that LSG1-2, ERF1-2, SHKA, TIL, HSP18.1, HSP24.1, HSP16.1 and HSFA6A may play essential regulatory roles as hub genes in increasing SOD, Pro, soluble sugar or soluble protein contents. In addition, one module was found mostly involved in tiller stem diameter, among which members of the BHLH148 were important nodes. These results provide new insights into the mechanisms by which sugarcane tillering seedlings respond to drought stress.
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Affiliation(s)
- Yuwei Tang
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Jiahui Li
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China.
| | - Qiqi Song
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Qin Cheng
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Qinliang Tan
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Quanguang Zhou
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Zemei Nong
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Ping Lv
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
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21
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Dwivedi AK, Singh V, Anwar K, Pareek A, Jain M. Integrated transcriptome, proteome and metabolome analyses revealed secondary metabolites and auxiliary carbohydrate metabolism augmenting drought tolerance in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107849. [PMID: 37393858 DOI: 10.1016/j.plaphy.2023.107849] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/01/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023]
Abstract
Drought is one of the major consequences of climate change and a serious threat to rice production. Drought stress activates interactions among genes, proteins and metabolites at the molecular level. A comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars can decipher the molecular mechanisms involved in drought tolerance/response. Here, we characterized the global-level transcriptome, proteome, and metabolome profiles, and performed integrated analyses thereof in a drought-sensitive (IR64) and a drought-tolerant (Nagina 22) rice cultivar under control and drought-stress conditions. The transcriptional dynamics and its integration with proteome analysis revealed the role of transporters in regulation of drought stress. The proteome response illustrated the contribution of translational machinery to drought tolerance in N22. The metabolite profiling revealed that aromatic amino acids and soluble sugars contribute majorly to drought tolerance in rice. The integrated transcriptome, proteome and metabolome analysis performed using statistical and knowledge-based methods revealed the preference for auxiliary carbohydrate metabolism through glycolysis and pentose phosphate pathway contributed to drought tolerance in N22. In addition, L-phenylalanine and the genes/proteins responsible for its biosynthesis were also found to contribute to drought tolerance in N22. In conclusion, our study provided mechanistic insights into the drought response/adaptation mechanism and is expected to facilitate engineering of drought tolerance in rice.
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Affiliation(s)
- Anuj Kumar Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Vikram Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Khalid Anwar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ashwani Pareek
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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22
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Smet D, Opdebeeck H, Vandepoele K. Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1212073. [PMID: 37528982 PMCID: PMC10390317 DOI: 10.3389/fpls.2023.1212073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/16/2023] [Indexed: 08/03/2023]
Abstract
Plants have evolved various mechanisms to adapt to adverse environmental stresses, such as the modulation of gene expression. Expression of stress-responsive genes is controlled by specific regulators, including transcription factors (TFs), that bind to sequence-specific binding sites, representing key components of cis-regulatory elements and regulatory networks. Our understanding of the underlying regulatory code remains, however, incomplete. Recent studies have shown that, by training machine learning (ML) algorithms on genomic sequence features, it is possible to predict which genes will transcriptionally respond to a specific stress. By identifying the most important features for gene expression prediction, these trained ML models allow, in theory, to further elucidate the regulatory code underlying the transcriptional response to abiotic stress. Here, we trained random forest ML models to predict gene expression in rice (Oryza sativa) in response to heat or drought stress. Apart from thoroughly assessing model performance and robustness across various input training data, the importance of promoter and gene body sequence features to train ML models was evaluated. The use of enriched promoter oligomers, complementing known TF binding sites, allowed us to gain novel insights in DNA motifs contributing to the stress regulatory code. By comparing genomic feature importance scores for drought and heat stress over time, general and stress-specific genomic features contributing to the performance of the learned models and their temporal variation were identified. This study provides a solid foundation to build and interpret ML models accurately predicting transcriptional responses and enables novel insights in biological sequence features that are important for abiotic stress responses.
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Affiliation(s)
- Dajo Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Helder Opdebeeck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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23
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Adak S, Agarwal T, Das P, Ray S, Lahiri Majumder A. Characterization of myo-inositol oxygenase from rice ( OsMIOX): influence of salinity stress in different indica rice cultivars. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:927-945. [PMID: 37649879 PMCID: PMC10462604 DOI: 10.1007/s12298-023-01340-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023]
Abstract
Myo-inositol oxygenase (MIOX), the only catabolic enzyme of the inositol pathway, catalyzes conversion of myo-inositol to D-GlcA (glucuronic acid). The present study encompasses bioinformatic analysis of MIOX gene across phylogenetically related plant lineages and representative animal groups. Comparative motif analysis of the MIOX gene(s) across various plant groups suggested existence of abiotic- stress related cis-acting elements such as, DRE, MYB, MYC, STRE, MeJa among others. A detailed analysis revealed a single isoform of MIOX gene, located in chromosome 6 of indica rice (Oryza sativa) with an open reading frame of 938 bp coding for 308 amino acids producing a protein of ~ 35 kD. Secondary structure prediction of the protein gave the predicted number of 144 alpha helices and 154 random coils. The three-dimensional structure suggested it to be a monomeric protein with a single domain. Bacterial overexpression of the protein, purification and enzyme assay showed optimal catalytic activity at pH 7.5-8 at an optimal temperature of 37 °C with Michaelis constant of 40.92 mM. The range of Km was determined as 22.74-28.7 mM and the range of Vmax was calculated as 3.51-3.6 µM/min, respectively. Four salt-tolerant and salt-sensitive rice cultivars displayed differential gene expression of OsMIOX at different time points in different tissues under salinity and drought stress as observed from qRT-PCR data, microarray results and protein expression profile in immunoblot analysis. Gel volumetric analysis confirmed a very high expression of MIOX in roots and leaves on 7th day following germination. Microarray data showed high expression of MIOX at all developmental stages including seedling growth and reproduction. These data suggest that OsMIOX might have a role to play in rice abiotic stress responses mediated through the myo-inositol oxidation pathway. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01340-6.
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Affiliation(s)
- Sanghamitra Adak
- Division of Plant Biology, Bose Institute, Kolkata, 700054 India
| | - Tanushree Agarwal
- Centre of Advanced Study, Department of Botany, Ballygunge Science College, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Priyanka Das
- Division of Plant Biology, Bose Institute, Kolkata, 700054 India
| | - Sudipta Ray
- Centre of Advanced Study, Department of Botany, Ballygunge Science College, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Arun Lahiri Majumder
- Division of Plant Biology, Bose Institute, Kolkata, 700054 India
- Present Address: Department of Microbiology and Biotechnology, Sister Nivedita University, DG 1/2, Action Area I, New Town, Kolkata, 700156 India
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24
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Zhang XM, Duan SG, Xia Y, Li JT, Liu LX, Tang M, Tang J, Sun W, Yi Y. Transcriptomic, Physiological, and Metabolomic Response of an Alpine Plant, Rhododendron delavayi, to Waterlogging Stress and Post-Waterlogging Recovery. Int J Mol Sci 2023; 24:10509. [PMID: 37445685 DOI: 10.3390/ijms241310509] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Climate change has resulted in frequent heavy and prolonged rainfall events that exacerbate waterlogging stress, leading to the death of certain alpine Rhododendron trees. To shed light on the physiological and molecular mechanisms behind waterlogging stress in woody Rhododendron trees, we conducted a study of Rhododendron delavayi, a well-known alpine flower species. Specifically, we investigated the physiological and molecular changes that occurred in leaves of R. delavayi subjected to 30 days of waterlogging stress (WS30d), as well as subsequent post-waterlogging recovery period of 10 days (WS30d-R10d). Our findings reveal that waterlogging stress causes a significant reduction in CO2 assimilation rate, stomatal conductance, transpiration rate, and maximum photochemical efficiency of PSII (Fv/Fm) in the WS30d leaves, by 91.2%, 95.3%, 93.3%, and 8.4%, respectively, when compared to the control leaves. Furthermore, the chlorophyll a and total chlorophyll content in the WS30d leaves decreased by 13.5% and 16.6%, respectively. Both WS30d and WS30d-R10d leaves exhibited excessive H2O2 accumulation, with a corresponding decrease in lignin content in the WS30d-R10d leaves. At the molecular level, purine metabolism, glutathione metabolism, photosynthesis, and photosynthesis-antenna protein pathways were found to be primarily involved in WS30d leaves, whereas phenylpropanoid biosynthesis, fatty acid metabolism, fatty acid biosynthesis, fatty acid elongation, and cutin, suberin, and wax biosynthesis pathways were significantly enriched in WS30d-R10d leaves. Additionally, both WS30d and WS30d-R10d leaves displayed a build-up of sugars. Overall, our integrated transcriptomic, physiological, and metabolomic analysis demonstrated that R. delavayi is susceptible to waterlogging stress, which causes irreversible detrimental effects on both its physiological and molecular aspects, hence compromising the tree's ability to fully recover, even under normal growth conditions.
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Affiliation(s)
- Xi-Min Zhang
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang 550025, China
- Key Laboratory of Environment Friendly Management on Alpine Rhododendron Diseases and Pests of Institutions of Higher Learning in Guizhou Province, Guizhou Normal University, Guiyang 550025, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Sheng-Guang Duan
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Ying Xia
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang 550025, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Jie-Ting Li
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Area of Southwest, Guizhou Normal University, Guiyang 550025, China
| | - Lun-Xian Liu
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang 550025, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Ming Tang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Area of Southwest, Guizhou Normal University, Guiyang 550025, China
| | - Jing Tang
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang 550025, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Wei Sun
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang 550025, China
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Yin Yi
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang 550025, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Area of Southwest, Guizhou Normal University, Guiyang 550025, China
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25
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Paul M, Tanskanen J, Jääskeläinen M, Chang W, Dalal A, Moshelion M, Schulman AH. Drought and recovery in barley: key gene networks and retrotransposon response. FRONTIERS IN PLANT SCIENCE 2023; 14:1193284. [PMID: 37377802 PMCID: PMC10291200 DOI: 10.3389/fpls.2023.1193284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/09/2023] [Indexed: 06/29/2023]
Abstract
Introduction During drought, plants close their stomata at a critical soil water content (SWC), together with making diverse physiological, developmental, and biochemical responses. Methods Using precision-phenotyping lysimeters, we imposed pre-flowering drought on four barley varieties (Arvo, Golden Promise, Hankkija 673, and Morex) and followed their physiological responses. For Golden Promise, we carried out RNA-seq on leaf transcripts before and during drought and during recovery, also examining retrotransposon BARE1expression. Transcriptional data were subjected to network analysis. Results The varieties differed by their critical SWC (ϴcrit), Hankkija 673 responding at the highest and Golden Promise at the lowest. Pathways connected to drought and salinity response were strongly upregulated during drought; pathways connected to growth and development were strongly downregulated. During recovery, growth and development pathways were upregulated; altogether, 117 networked genes involved in ubiquitin-mediated autophagy were downregulated. Discussion The differential response to SWC suggests adaptation to distinct rainfall patterns. We identified several strongly differentially expressed genes not earlier associated with drought response in barley. BARE1 transcription is strongly transcriptionally upregulated by drought and downregulated during recovery unequally between the investigated cultivars. The downregulation of networked autophagy genes suggests a role for autophagy in drought response; its importance to resilience should be further investigated.
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Affiliation(s)
- Maitry Paul
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Jaakko Tanskanen
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
- Production Systems, Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Marko Jääskeläinen
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Wei Chang
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Ahan Dalal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alan H. Schulman
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
- Production Systems, Natural Resources Institute Finland (LUKE), Helsinki, Finland
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Quan X, Meng C, Zhang N, Liang X, Li J, Li H, He W. Genome-Wide Analysis of Barley bHLH Transcription Factors and the Functional Characterization of HvbHLH56 in Low Nitrogen Tolerance in Arabidopsis. Int J Mol Sci 2023; 24:ijms24119740. [PMID: 37298691 DOI: 10.3390/ijms24119740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Improvement of low nitrogen (LN) tolerance or nitrogen use efficiency (NUE) in crops is imperative for environment-friendly agriculture development. The basic helix-loop-helix (bHLH) transcription factors are involved in multiple abiotic stresses and are suitable as candidate genes for improving LN tolerance. Few studies were performed on the characterization of the HvbHLH gene family and their function in response to LN stress in barley. In this study, 103 HvbHLH genes were identified through genome-wide analysis. HvbHLH proteins were classified into 20 subfamilies based on phylogenetic analysis in barley, which was supported by conserved motifs and gene structure analysis. The stress-related cis-element analysis in the promoters showed that HvbHLHs are probably involved in multiple stress responses. By phylogenetic analysis of HvbHLHs and bHLHs in other plants, some HvbHLHs were predicted to play roles in response to nutrition deficiency stress. Furthermore, at least 16 HvbHLHs were differentially expressed in two barley genotypes differing in LN tolerance under LN stress. Finally, overexpression of HvbHLH56 enhanced LN stress tolerance in transgenic Arabidopsis, suggesting it is an important regulator in LN stress response. The differentially expressed HvbHLHs identified herein may be valuable for the breeding of barley cultivars with LN tolerance.
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Affiliation(s)
- Xiaoyan Quan
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Chen Meng
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Ning Zhang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xiaoli Liang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Hongmei Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
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Ma H, Zou F, Li D, Wan Y, Zhang Y, Zhao Z, Wang X, Gao H. Transcription Factor MdbHLH093 Enhances Powdery Mildew Resistance by Promoting Salicylic Acid Signaling and Hydrogen Peroxide Accumulation. Int J Mol Sci 2023; 24:ijms24119390. [PMID: 37298341 DOI: 10.3390/ijms24119390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/10/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Powdery mildew is an apple disease caused by the obligate trophic fungus Podosphaera leucotricha. Basic helix-loop-helix (bHLH) transcription factors play important roles in plant development and stress responses, and they have been widely studied in model plants such as Arabidopsis thaliana. However, their role in the stress response of perennial fruit trees remains unclear. Here, we investigated the role of MdbHLH093 in the powdery mildew of apples. The expression of MdbHLH093 was significantly induced during the infection of apples with powdery mildew, and the allogenic overexpression of MdbHLH093 in A. thaliana enhanced the resistance to powdery mildew by increasing the accumulation of hydrogen peroxide (H2O2) and activating the salicylic acid (SA) signaling pathway. The transient overexpression of MdbHLH093 in apple leaves increased the resistance to powdery mildew. Conversely, when MdbHLH093 expression was silenced, the sensitivity of apple leaves to powdery mildew was increased. The physical interaction between MdbHLH093 and MdMYB116 was demonstrated by yeast two-hybrid, bi-molecular fluorescence complementation, and split luciferase experiments. Collectively, these results indicate that MdbHLH093 interacts with MdMYB116 to improve apple resistance to powdery mildew by increasing the accumulation of H2O2 and activating the SA signaling pathway, as well as by providing a new candidate gene for resistance molecular breeding.
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Affiliation(s)
- Hai Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Fuyan Zou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Dongmei Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Ye Wan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Yiping Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Zhengyang Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Hua Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
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Wang N, Wang Y, Wang C, Leng Z, Qi F, Wang S, Zhou Y, Meng W, Liu K, Zhang C, Ma J. Evaluating the Differential Response of Transcription Factors in Diploid versus Autotetraploid Rice Leaves Subjected to Diverse Saline-Alkali Stresses. Genes (Basel) 2023; 14:1151. [PMID: 37372331 DOI: 10.3390/genes14061151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/26/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Saline-alkali stress is a significant abiotic stress factor that impacts plant growth, development, and crop yield. Consistent with the notion that genome-wide replication events can enhance plant stress resistance, autotetraploid rice exhibited a higher level of tolerance to saline-alkali stress than its donor counterparts, which is reflected by differential gene expression between autotetraploid and diploid rice in response to salt, alkali, and saline-alkali stress. In this study, we investigated the expression of the transcription factors (TFs) in the leaf tissues of autotetraploid and diploid rice under different types of saline-alkali stress. Transcriptome analysis identified a total of 1040 genes from 55 TF families that were altered in response to these stresses, with a significantly higher number in autotetraploid rice compared to diploid rice. Contrarily, under these stresses, the number of expressed TF genes in autotetraploid rice was greater than that in diploid rice for all three types of stress. In addition to the different numbers, the differentially expressed TF genes were found to be from significantly distinct TF families between autotetraploid and diploid rice genotypes. The GO enrichment analysis unraveled that all the DEGs were distributed with differentially biological functions in rice, in particular those that were enriched in the pathways of phytohormones and salt resistance, signal transduction, and physiological and biochemical metabolism in autotetraploid rice compared to its diploid counterpart. This may provide useful guidance for studying the biological roles of polyploidization in plant resilience in response to saline-alkali stress.
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Affiliation(s)
- Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yingkai Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Chenxi Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Zitian Leng
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Shiyan Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yiming Zhou
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Weilong Meng
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Keyan Liu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Chunying Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Jian Ma
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
- Key Laboratory of Crop Molecular Breeding, Universities of Jilin Province, Changchun 130117, China
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Shi F, Zhao Z, Jiang Y, Liu S, Tan C, Liu C, Ye X, Liu Z. Whole transcriptome analysis and construction of a ceRNA regulatory network related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). BMC Genomics 2023; 24:144. [PMID: 36964498 PMCID: PMC10039531 DOI: 10.1186/s12864-023-09239-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/09/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND The growth and development of leaves and petioles have a significant effect on photosynthesis. Understanding the molecular mechanisms underlying leaf and petiole development is necessary for improving photosynthetic efficiency, cultivating varieties with high photosynthetic efficiency, and improving the yield of crops of which the leaves are foodstuffs. This study aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). The data were used to construct a competitive endogenous RNA (ceRNA) network to obtain insights into the mechanisms underlying leaf and petiole development. RESULTS The leaves and petioles of the 'PHL' inbred line of Chinese cabbage were used as research materials for whole transcriptome sequencing. A total of 10,646 differentially expressed (DE) mRNAs, 303 DElncRNAs, 7 DEcircRNAs, and 195 DEmiRNAs were identified between leaves and petioles. Transcription factors and proteins that play important roles in leaf and petiole development were identified, including xyloglucan endotransglucosylase/hydrolase, expansion proteins and their precursors, transcription factors TCP15 and bHLH, lateral organ boundary domain protein, cellulose synthase, MOR1-like protein, and proteins related to plant hormone biosynthesis. A ceRNA regulatory network related to leaf and petiole development was constructed, and 85 pairs of ceRNA relationships were identified, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA, and 2 DEmiRNA-DEcircRNA pairs. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaves and petioles were screened from transcriptome data, and their functions were explored through subcellular localization analysis and transgenic overexpression verification. BrLSH1, BrLSH2 and BrLSH3 were nuclear proteins, and BrLSH2 inhibited the growth and development of Arabidopsis thaliana. CONCLUSIONS This study identifies mRNAs and non-coding RNAs that may be involved in the development of leaves and petioles in Chinese cabbage, and establishes a ceRNA regulatory network related to development of the leaves and petioles, providing valuable genomic resources for further research on the molecular mechanisms underlying leaf and petiole development in this crop species.
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Affiliation(s)
- Fengyan Shi
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
- Vegetable Research Institute of Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Zifan Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yang Jiang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Song Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Chong Tan
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Chuanhong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Xueling Ye
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
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Liu Z, Fu X, Xu H, Zhang Y, Shi Z, Zhou G, Bao W. Comprehensive Analysis of bHLH Transcription Factors in Ipomoea aquatica and Its Response to Anthocyanin Biosynthesis. Int J Mol Sci 2023; 24:ijms24065652. [PMID: 36982726 PMCID: PMC10057536 DOI: 10.3390/ijms24065652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
The basic helix-loop-helix (bHLH) proteins compose one of the largest transcription factor (TF) families in plants, which play a vital role in regulating plant biological processes including growth and development, stress response, and secondary metabolite biosynthesis. Ipomoea aquatica is one of the most important nutrient-rich vegetables. Compared to the common green-stemmed I. aquatica, purple-stemmed I. aquatica has extremely high contents of anthocyanins. However, the information on bHLH genes in I. aquatica and their role in regulating anthocyanin accumulation is still unclear. In this study, we confirmed a total of 157 bHLH genes in the I. aquatica genome, which were classified into 23 subgroups according to their phylogenetic relationship with the bHLH of Arabidopsis thaliana (AtbHLH). Of these, 129 IabHLH genes were unevenly distributed across 15 chromosomes, while 28 IabHLH genes were spread on the scaffolds. Subcellular localization prediction revealed that most IabHLH proteins were localized in the nucleus, while some were in the chloroplast, extracellular space, and endomembrane system. Sequence analysis revealed conserved motif distribution and similar patterns of gene structure within IabHLH genes of the same subfamily. Analysis of gene duplication events indicated that DSD and WGD played a vital role in the IabHLH gene family expansion. Transcriptome analysis showed that the expression levels of 13 IabHLH genes were significantly different between the two varieties. Of these, the IabHLH027 had the highest expression fold change, and its expression level was dramatically higher in purple-stemmed I. aquatica than that in green-stemmed I. aquatica. All upregulated DEGs in purple-stemmed I. aquatica exhibited the same expression trends in both qRT-PCR and RNA-seq. Three downregulated genes including IabHLH142, IabHLH057, and IabHLH043 determined by RNA-seq had opposite expression trends of those detected by qRT-PCR. Analysis of the cis-acting elements in the promoter region of 13 differentially expressed genes indicated that light-responsive elements were the most, followed by phytohormone-responsive elements and stress-responsive elements, while plant growth and development-responsive elements were the least. Taken together, this work provides valuable clues for further exploring IabHLH function and facilitating the breeding of anthocyanin-rich functional varieties of I. aquatica.
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Affiliation(s)
- Zheng Liu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, China
| | - Xiaoai Fu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, China
| | - Hao Xu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, China
| | - Yuxin Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, China
| | - Zhidi Shi
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, China
| | - Guangzhen Zhou
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Wenlong Bao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Correspondence:
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Zhang P, Ni Y, Jiao Z, Li J, Wang T, Yao Z, Jiang Y, Yang X, Sun Y, Li H, He D, Niu J. The wheat leaf delayed virescence of mutant dv4 is associated with the abnormal photosynthetic and antioxidant systems. Gene X 2023; 856:147134. [PMID: 36586497 DOI: 10.1016/j.gene.2022.147134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
Chlorophyll (Chl) is a key pigment for wheat (Triticum aestivum L.) photosynthesis, consequently impacts grain yield. A wheat mutant named as delayed virescence 4 (dv4) was obtained from cultivar Guomai 301 (wild type, WT) treated with ethyl methane sulfonate (EMS). The seedling leaves of dv4 were shallow yellow, apparently were chlorophyll deficient. They started to turn green at the jointing stage and returned to almost ordinary green at the heading stage. Leaf transcriptome comparison of Guomai 301 and dv4 at the jointing stage showed that most differentially expressed genes (DEGs) of transcription and translation were highly expressed in dv4, one key gene nicotianamine aminotransferase A (NAAT-A) involved in the synthesis and metabolism pathways of tyrosine, methionine and phenylalanine was significantly lowly expressed. The expression levels of the most photosynthesis related genes, such as photosystem I (PS I), ATPase and light-harvesting chlorophyll protein complex-related homeotypic genes, and protochlorophyllide reductase A (PORA) were lower; but macromolecule degradation and hypersensitivity response (HR) related gene heat shock protein 82 (HSP82) was highly expressed. Compared to WT, the contents of macromolecules such as proteins and sugars were reduced; the contents of Chl a, Chl b, total Chl, and carotenoids in leaves of dv4 were significantly less at the jointing stage, while the ratio of Chl a / Chl b was the same as that of WT. The net photosynthetic rate, stomatal conductance and transpiration rate of dv4 were significantly lower. The H2O2 content were higher, while the contents of total phenol and malondialdehyde (MDA), antioxidant enzyme activities were lower in leaves of dv4. In conclusion, the reduced contents of macromolecules and photosynthetic pigments, the abnormal photosynthetic and antioxidant systems were closely related to the phenotype of dv4.
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Affiliation(s)
- Peipei Zhang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yongjing Ni
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu 476000, Henan, China
| | - Zhixin Jiao
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Junchang Li
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Ting Wang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Ziping Yao
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yumei Jiang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Xiwen Yang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yulong Sun
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Huijuan Li
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Dexian He
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Jishan Niu
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China.
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Chang Y, Peng L, Ji L, Wang S, Wang L, Wu J. Genome-wise association study identified genomic regions associated with drought tolerance in mungbean (Vigna radiata (L.) R. Wilczek). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:40. [PMID: 36897414 DOI: 10.1007/s00122-023-04303-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
A total of 282 mungbean accessions were resequenced to identify genome-wide variants and construct a highly precise variant map, and drought tolerance-related loci and superior alleles were identified by GWAS. Mungbean (Vigna radiata (L.) R. Wilczek) is an important food legume crop that is highly adapted to drought environments, but severe drought significantly curtails mungbean production. Here, we resequenced 282 mungbean accessions to identify genome-wide variants and constructed a highly precise map of mungbean variants. A genome-wide association study was performed to identify genomic regions for 14 drought tolerance-related traits in plants grown under stress and well-watered conditions over three years. One hundred forty-six SNPs associated with drought tolerance were detected, and 26 candidate loci associated with more than two traits were subsequently selected. Two hundred fifteen candidate genes were identified at these loci, including eleven transcription factor genes, seven protein kinase genes and other protein coding genes that may respond to drought stress. Furthermore, we identified superior alleles that were associated with drought tolerance and positively selected during the breeding process. These results provide valuable genomic resources for molecular breeding and will accelerate future efforts aimed at mungbean improvement.
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Affiliation(s)
- Yujie Chang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lin Peng
- Institute of Food Crop, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Liang Ji
- Institute of Food Crop, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Shumin Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lanfen Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jing Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Zhou W, Duan Y, Jiang X, Tan X, Li Q, Wang H, Zhang Y, Zhang M. Transcriptome and metabolome analyses reveal novel insights into the seed germination of Michelia chapensis, an endangered species in China. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 328:111568. [PMID: 36528126 DOI: 10.1016/j.plantsci.2022.111568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Michelia chapensis Dandy, a well-known medicinal woody plant endemic to China, is endangered and seriously constricted by seed dormancy-induced low-regeneration in natural conditions. Cold stratification can effectively reduce seed dormancy and promote the seed germination of M. chapensis. However, the molecular events and systematic changes that occurred during seed germination in M. chapensis remain largely unknown. In this study, we carried out transcriptomic and metabolomic analyses to elucidate the potential molecular mechanisms underlying seed germination in M. chapensis under cold stratification. The results showed that the embryo cells became bigger and looser with increasing stratification time. Moreover, the endosperm appeared reduced due to the consumption of nutrients. Seventeen phytohormones were examined by the metabolome targeted for hormones. Compared with the ES (no stratification), the levels of indole-3-acetic acid (IAA) and gibberellin A3 (GA3) were increased in the MS (stratification for 45 days), while the abscisic acid (ABA) was downregulated in both MS and LS (stratification for 90 days). The transcriptome profiling identified 24975 differentially expressed genes (DEGs) in the seeds during germination. The seed germination of M. chapensis was mainly regulated by the biological pathways of plant hormone signal transduction, energy supply, secondary metabolite biosynthesis, photosynthesis-related metabolism, and transcriptional regulation. This study reveals the biological evidence of seed germination at the transcriptional level and provides a foundation for unraveling molecular mechanisms regulating the seed germination of M. chapensis.
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Affiliation(s)
- Wuxian Zhou
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China; Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agricultural and Rural Affairs, Enshi, China
| | - Yuanyuan Duan
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China; Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agricultural and Rural Affairs, Enshi, China
| | - Xiaogang Jiang
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China; Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agricultural and Rural Affairs, Enshi, China
| | - Xuhui Tan
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China; Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agricultural and Rural Affairs, Enshi, China
| | - Qin Li
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China; Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agricultural and Rural Affairs, Enshi, China
| | - Hua Wang
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China; Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agricultural and Rural Affairs, Enshi, China
| | - Yajuan Zhang
- Agricultural and Rural Bureau of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Meide Zhang
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China; Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agricultural and Rural Affairs, Enshi, China.
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Huang X, Qiu X, Wang Y, Abubakar AS, Chen P, Chen J, Chen K, Yu C, Wang X, Gao G, Zhu A. Genome-Wide Investigation of the NAC Transcription Factor Family in Apocynum venetum Revealed Their Synergistic Roles in Abiotic Stress Response and Trehalose Metabolism. Int J Mol Sci 2023; 24:ijms24054578. [PMID: 36902009 PMCID: PMC10003206 DOI: 10.3390/ijms24054578] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are one of the most prominent plant-specific TF families and play essential roles in plant growth, development and adaptation to abiotic stress. Although the NAC gene family has been extensively characterized in many species, systematic analysis is still relatively lacking in Apocynum venetum (A. venetum). In this study, 74 AvNAC proteins were identified from the A. venetum genome and were classified into 16 subgroups. This classification was consistently supported by their gene structures, conserved motifs and subcellular localizations. Nucleotide substitution analysis (Ka/Ks) showed the AvNACs to be under the influence of strong purifying selection, and segmental duplication events were found to play the dominant roles in the AvNAC TF family expansion. Cis-elements analysis demonstrated that the light-, stress-, and phytohormone-responsive elements being dominant in the AvNAC promoters, and potential TFs including Dof, BBR-BPC, ERF and MIKC_MADS were visualized in the TF regulatory network. Among these AvNACs, AvNAC58 and AvNAC69 exhibited significant differential expression in response to drought and salt stresses. The protein interaction prediction further confirmed their potential roles in the trehalose metabolism pathway with respect to drought and salt resistance. This study provides a reference for further understanding the functional characteristics of NAC genes in the stress-response mechanism and development of A. venetum.
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Affiliation(s)
- Xiaoyu Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Xiaojun Qiu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Yue Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Aminu Shehu Abubakar
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- Department of Agronomy, Bayero University Kano, Kano PMB 3011, Nigeria
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Xiaofei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- National Breeding Center for Bast Fiber Crops, Changsha 410221, China
- Key Laboratory of Genetic Breeding and Microbial Processing for Bast Fiber Product of Hunan Province, Changsha 410221, China
- Correspondence: (G.G.); (A.Z.); Tel.: +86-0731-8899-8511 (G.G.); +86-0731-8899-8586 (A.Z.)
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- National Breeding Center for Bast Fiber Crops, Changsha 410221, China
- Key Laboratory of Genetic Breeding and Microbial Processing for Bast Fiber Product of Hunan Province, Changsha 410221, China
- Correspondence: (G.G.); (A.Z.); Tel.: +86-0731-8899-8511 (G.G.); +86-0731-8899-8586 (A.Z.)
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Sustek-Sánchez F, Rognli OA, Rostoks N, Sõmera M, Jaškūnė K, Kovi MR, Statkevičiūtė G, Sarmiento C. Improving abiotic stress tolerance of forage grasses - prospects of using genome editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1127532. [PMID: 36824201 PMCID: PMC9941169 DOI: 10.3389/fpls.2023.1127532] [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: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Due to an increase in the consumption of food, feed, and fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to obtain high-yielding crops that can adapt to future climate changes. Currently, the main feed source used for ruminant livestock production is forage grasses. In temperate climate zones, perennial grasses grown for feed are widely distributed and tend to suffer under unfavorable environmental conditions. Genome editing has been shown to be an effective tool for the development of abiotic stress-resistant plants. The highly versatile CRISPR-Cas system enables increasingly complex modifications in genomes while maintaining precision and low off-target frequency mutations. In this review, we provide an overview of forage grass species that have been subjected to genome editing. We offer a perspective view on the generation of plants resilient to abiotic stresses. Due to the broad factors contributing to these stresses the review focuses on drought, salt, heat, and cold stresses. The application of new genomic techniques (e.g., CRISPR-Cas) allows addressing several challenges caused by climate change and abiotic stresses for developing forage grass cultivars with improved adaptation to the future climatic conditions. Genome editing will contribute towards developing safe and sustainable food systems.
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Affiliation(s)
- Ferenz Sustek-Sánchez
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Odd Arne Rognli
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Nils Rostoks
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Latvia, Riga, Latvia
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kristina Jaškūnė
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Mallikarjuna Rao Kovi
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gražina Statkevičiūtė
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
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Malambane G, Madumane K, Sewelo LT, Batlang U. Drought stress tolerance mechanisms and their potential common indicators to salinity, insights from the wild watermelon (Citrullus lanatus): A review. FRONTIERS IN PLANT SCIENCE 2023; 13:1074395. [PMID: 36815012 PMCID: PMC9939662 DOI: 10.3389/fpls.2022.1074395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
Climate change has escalated the effect of drought on crop production as it has negatively altered the environmental condition. Wild watermelon grows abundantly in the Kgalagadi desert even though the environment is characterized by minimal rainfall, high temperatures and intense sunshine during growing season. This area is also characterized by sandy soils with low water holding capacity, thus bringing about drought stress. Drought stress affects crop productivity through its effects on development and physiological functions as dictated by molecular responses. Not only one or two physiological process or genes are responsible for drought tolerance, but a combination of various factors do work together to aid crop tolerance mechanism. Various studies have shown that wild watermelon possess superior qualities that aid its survival in unfavorable conditions. These mechanisms include resilient root growth, timely stomatal closure, chlorophyll fluorescence quenching under water deficit as key physiological responses. At biochemical and molecular level, the crop responds through citrulline accumulation and expression of genes associated with drought tolerance in this species and other plants. Previous salinity stress studies involving other plants have identified citrulline accumulation and expression of some of these genes (chloroplast APX, Type-2 metallothionein), to be associated with tolerance. Emerging evidence indicates that the upstream of functional genes are the transcription factor that regulates drought and salinity stress responses as well as adaptation. In this review we discuss the drought tolerance mechanisms in watermelons and some of its common indicators to salinity at physiological, biochemical and molecular level.
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Wei J, Luo B, Kong S, Liu W, Zhang C, Wei Z, Min X. Screening and identification of multiple abiotic stress responsive candidate genes based on hybrid-sequencing in Vicia sativa. Heliyon 2023; 9:e13536. [PMID: 36816321 PMCID: PMC9929474 DOI: 10.1016/j.heliyon.2023.e13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Common vetch is an important leguminous forage for both livestock fodder and green manure and has a tremendous latent capacity in a sustainable agroecosystem. In the present study, a comprehensive transcriptome analysis of the aboveground leaves and underground roots of common vetch under multiple abiotic stress treatments, including NaCl, drought, cold, and cold drought, was performed using hybrid-sequencing technology, i. e. single-molecule real-time sequencing technology (SMRT) and supplemented by next-generation sequencing (NGS) technology. A total of 485,038 reads of insert (ROIs) with a mean length of 2606 bp and 228,261 full-length nonchimeric (FLNC) reads were generated. After deduplication, 39,709 transcripts were generated. Of these transcripts, we identified 1059 alternative splicing (AS) events, 17,227 simple sequence repeats (SSRs), and 1647 putative transcription factors (TFs). Furthermore, 640 candidates long noncoding RNAs (lncRNAs) and 28,256 complete coding sequences (CDSs) were identified. In gene annotation analyses, a total of 38,826 transcripts (97.78%) were annotated in eight public databases. Finally, seven multiple abiotic stress-responsive candidate genes were obtained through gene expression, annotation information, and protein-protein interaction (PPI) networks. Our research not only enriched the structural information of FL transcripts in common vetch, but also provided useful information for exploring the molecular mechanism of multiple abiotic stress tolerance between aboveground and underground tissues in common vetch and related legumes.
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Affiliation(s)
- Jia Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Bo Luo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Shiyi Kong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People’s Republic of China
| | - Chuanjie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
| | - Xueyang Min
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
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Chang S, Li Q, Huang B, Chen W, Tan H. Genome-wide identification and characterisation of bHLH transcription factors in Artemisia annua. BMC PLANT BIOLOGY 2023; 23:63. [PMID: 36721100 PMCID: PMC9890702 DOI: 10.1186/s12870-023-04063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND A. annua (also named Artemisia annua, sweet wormwood) is the main source of the anti-malarial drug artemisinin, which is synthesised and stored in its trichomes. Members of the basic Helix-Loop-Helix (bHLH) family of transcription factors (TFs) have been implicated in artemisinin biosynthesis in A. annua and in trichome development in other plant species. RESULTS Here, we have systematically identified and characterised 226 putative bHLH TFs in A. annua. All of the proteins contain a HLH domain, 213 of which also contain the basic motif that mediates DNA binding of HLH dimers. Of these, 22 also contained a Myc domain that permits dimerisation with other families of TFs; only two proteins lacking the basic motif contained a Myc domain. Highly conserved GO annotations reflected the transcriptional regulatory role of the identified TFs, and suggested conserved roles in biological processes such as iron homeostasis, and guard cell and endosperm development. Expression analysis revealed that three genes (AabHLH80, AabHLH96, and AaMyc-bHLH3) exhibited spatiotemporal expression patterns similar to genes encoding key enzymes in artemisinin synthesis. CONCLUSIONS This comprehensive analysis of bHLH TFs provides a new resource to direct further analysis into key molecular mechanisms underlying and regulating artemisinin biosynthesis and trichome development, as well as other biological processes, in the key medicinal plant A. annua.
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Affiliation(s)
- Shuwei Chang
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pharmacy, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Qi Li
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Baokang Huang
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wansheng Chen
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hexin Tan
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pharmacy, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
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Wang Y, Xi Z, Wang X, Zhang Y, Liu Y, Yuan S, Zhao S, Sheng J, Meng D. Identification of bHLH family genes in Agaricus bisporus and transcriptional regulation of arginine catabolism-related genes by AbbHLH1 after harvest. Int J Biol Macromol 2023; 226:496-509. [PMID: 36521696 DOI: 10.1016/j.ijbiomac.2022.12.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/23/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022]
Abstract
Basic helix-loop-helix (bHLH) transcription factors (TFs) are widely distributed in eukaryotes and play an important role in biological growth and development. The identification and functional analyses of bHLH genes/proteins in edible mushrooms (Agaricus bisporus) have yet to be reported. In the present study, we identified 10 putative bHLH members carrying the conserved bHLH domains. Phylogenetic analyses revealed that the 10 AbbHLHs were the closest to sequences of species belonging to 7 different fungal subgroups, which was supported by loop length, intron patterns, and key amino acid residues. The substantial increase after harvest and continuously elevated expression of AbbHLH1 during the development until the disruption of mushroom velum, and the preferential expression in cap and gill tissues suggest the important function of AbbHLH1 in postharvest development of A. bisporus. The relationship of arginine catabolism-related genes with the early stage of postharvest continuing development also was revealed by expression determination. Subcellular localization showed that AbbHLH1 could be localized in nucleus. Importantly, the electrophoretic mobility shift and dual-luciferase reporter assays showed that AbbHLH1 activated the promoters of AbOAT, AbSPDS, and AbSAMDC and suppressed the expression of AbARG, AbUREA, and AbODC, probably for the modulation of arginine catabolism and thus control of postharvest mushroom development. Taken together, the available data provide valuable functional insight into the role of AbbHLH proteins in postharvest mushrooms.
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Affiliation(s)
- Yating Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Zhiai Xi
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Xiuhong Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Yuyu Zhang
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing 100048, People's Republic of China
| | - Yongguo Liu
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing 100048, People's Republic of China
| | - Shuai Yuan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Shirui Zhao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Jiping Sheng
- School of Agricultural Economics and Rural Development, Renmin University of China, Beijing 100872, People's Republic of China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China; Tianjin Gasin-DH Preservation Technology Co., Ltd, Tianjin 300300, People's Republic of China.
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Wang N, Shu X, Zhang F, Wang Z. Transcriptome-wide characterization of bHLH transcription factor genes in Lycoris radiata and functional analysis of their response to MeJA. FRONTIERS IN PLANT SCIENCE 2023; 13:975530. [PMID: 36704164 PMCID: PMC9872026 DOI: 10.3389/fpls.2022.975530] [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: 06/22/2022] [Accepted: 12/12/2022] [Indexed: 06/18/2023]
Abstract
As one of the biggest plant specific transcription factor (TF) families, basic helix-loop-helix (bHLH) protein, plays significant roles in plant growth, development, and abiotic stress responses. However, there has been minimal research about the effects of methyl jasmonate (MeJA) treatment on the bHLH gene family in Lycoris radiata (L'Her.) Herb. In this study, based on transcriptome sequencing data, 50 putative L. radiata bHLH (LrbHLH) genes with complete open reading frames (ORFs), which were divided into 20 bHLH subfamilies, were identified. The protein motif analyses showed that a total of 10 conserved motifs were found in LrbHLH proteins and motif 1 and motif 2 were the most highly conserved motifs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of LrbHLH genes revealed their involvement in regulation of plant growth, jasmonic acid (JA) mediated signaling pathway, photoperiodism, and flowering. Furthermore, subcellular localization revealed that most LrbHLHs were located in the nucleus. Expression pattern analysis of LrbHLH genes in different tissues and at flower developmental stages suggested that their expression differed across lineages and might be important for plant growth and organ development in Lycoris. In addition, all LrbHLH genes exhibited specific spatial and temporal expression patterns under MeJA treatment. Moreover, protein-protein interaction (PPI) network analysis and yeast two-hybrid assay showed that numerous LrbHLHs could interact with jasmonate ZIM (zinc-finger inflorescence meristem) domain (JAZ) proteins. This research provides a theoretical basis for further investigation of LrbHLHs to find their functions and insights for their regulatory mechanisms involved in JA signaling pathway.
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Gautam H, Sharma A, Trivedi PK. Plant microProteins and miPEPs: Small molecules with much bigger roles. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111519. [PMID: 36330966 DOI: 10.1016/j.plantsci.2022.111519] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/30/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The plant science community has identified various regulatory components involved in gene expression. With the advancement of approaches and technologies, new layers of gene regulation have been identified, which play essential roles in fine-tuning biological processes. In this area, recently, small peptides emerged as key regulators in gene regulation to control developmental and physiological processes in plants. Various small peptides have also been identified and characterized to elucidate their roles. A class of small peptides, microProteins (miPs), have been shown to contain at least a protein-protein interaction domain with the potential to regulate multi-domain proteins by becoming a part of protein complexes. Recent studies suggest that some pri-miRNAs encode peptides (miPEPs), which are essential components in plant growth and development. This review provides updates about these small peptides, in general, summarizing their potential role in gene regulation and possible mechanism(s) in plants. We also propose that in-depth research on newly identified plant peptides in crops help to provide solutions enabling sustainable agriculture and food production.
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Affiliation(s)
- Himanshi Gautam
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashish Sharma
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
| | - Prabodh Kumar Trivedi
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India.
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Du L, Huang X, Ding L, Wang Z, Tang D, Chen B, Ao L, Liu Y, Kang Z, Mao H. TaERF87 and TaAKS1 synergistically regulate TaP5CS1/TaP5CR1-mediated proline biosynthesis to enhance drought tolerance in wheat. THE NEW PHYTOLOGIST 2023; 237:232-250. [PMID: 36264565 DOI: 10.1111/nph.18549] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Drought stress limits wheat production and threatens food security world-wide. While ethylene-responsive factors (ERFs) are known to regulate plant response to drought stress, the regulatory mechanisms responsible for a tolerant phenotype remain unclear. Here, we describe the positive regulatory role of TaERF87 in mediating wheat tolerance to drought stress. TaERF87 overexpression (OE) enhances drought tolerance, while silencing leads to drought sensitivity in wheat. RNA sequencing with biochemical assays revealed that TaERF87 activates the expression of the proline biosynthesis genes TaP5CS1 and TaP5CR1 via direct binding to GCC-box elements. Furthermore, proline accumulates to higher levels in TaERF87- and TaP5CS1-OE lines than that in wild-type plants under well-watered and drought stress conditions concomitantly with enhanced drought tolerance in these transgenic lines. Moreover, the interaction between TaERF87 and the bHLH transcription factor TaAKS1 synergistically enhances TaP5CS1 and TaP5CR1 transcriptional activation. TaAKS1 OE also increases wheat drought tolerance by promoting proline accumulation. Additionally, our findings verified that TaERF87 and TaAKS1 are targets of abscisic acid-responsive element binding factor 2 (TaABF2). Together, our study elucidates the mechanisms underlying a positive response to drought stress mediated by the TaABF2-TaERF87/TaAKS1-TaP5CS1/TaP5CR1 module, and identifies candidate genes for the development of elite drought-tolerant wheat varieties.
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Affiliation(s)
- Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xueling Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Li Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhongxue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dongling Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lanjiya Ao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
- Yangling Seed Industry Innovation Center, Yangling, Shaanxi, 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
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Xu W, Ren H, Qi X, Zhang S, Yu Z, Xie J. Conserved hierarchical gene regulatory networks for drought and cold stress response in Myrica rubra. FRONTIERS IN PLANT SCIENCE 2023; 14:1155504. [PMID: 37123838 PMCID: PMC10140524 DOI: 10.3389/fpls.2023.1155504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Stress response in plant is regulated by a large number of genes co-operating in diverse networks that serve multiple adaptive process. To understand how gene regulatory networks (GRNs) modulating abiotic stress responses, we compare the GRNs underlying drought and cold stresses using samples collected at 4 or 6 h intervals within 48 h in Chinese bayberry (Myrica rubra). We detected 7,583 and 8,840 differentially expressed genes (DEGs) under drought and cold stress respectively, which might be responsive to environmental stresses. Drought- and cold-responsive GRNs, which have been built according to the timing of transcription under both abiotic stresses, have a conserved trans-regulator and a common regulatory network. In both GRNs, basic helix-loop-helix family transcription factor (bHLH) serve as central nodes. MrbHLHp10 transcripts exhibited continuous increase in the two abiotic stresses and acts upstream regulator of ASCORBATE PEROXIDASE (APX) gene. To examine the potential biological functions of MrbHLH10, we generated a transgenic Arabidopsis plant that constitutively overexpresses the MrbHLH10 gene. Compared to wild-type (WT) plants, overexpressing transgenic Arabidopsis plants maintained higher APX activity and biomass accumulation under drought and cold stress. Consistently, RNAi plants had elevated susceptibility to both stresses. Taken together, these results suggested that MrbHLH10 mitigates abiotic stresses through the modulation of ROS scavenging.
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Affiliation(s)
- Weijie Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Haiying Ren
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Hangzhou, China
- Xianghu Lab., Hangzhou, China
- *Correspondence: Haiying Ren, ; Jianbo Xie,
| | - Xingjiang Qi
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Hangzhou, China
- Xianghu Lab., Hangzhou, China
| | - Shuwen Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Hangzhou, China
| | - Zheping Yu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Hangzhou, China
| | - Jianbo Xie
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- *Correspondence: Haiying Ren, ; Jianbo Xie,
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Alam MS, Yang ZK, Li C, Yan Y, Liu Z, Nazir MM, Xu JH. Loss-of-function mutations of OsbHLH044 transcription factor lead to salinity sensitivity and a greater chalkiness in rice (Oryza sativa L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 193:110-123. [PMID: 36347113 DOI: 10.1016/j.plaphy.2022.10.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/09/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The most hazardous abiotic stress, salinity, restricted the world crop production, and grain chalkiness affected the grain quality to limit consumers' acceptance. The basic helix-loop-helix (bHLH) proteins modulate massive biological processes in plants. Here the CRISPR/Cas9 gene editing mutants were obtained to detect the function of OsbHLH044. The loss-of-function of OsbHLH044 mutants showed numerous altered plant phenotypes. Notably, the osbhlh044 mutants resulted in prominently reduced morphological and physiological parameters under salt stress. Lower antioxidant activities and higher lipid peroxidation and hydrogen peroxide (H2O2) accumulation in the osbhlh044 mutants caused salinity sensitivity due to elevated reactive oxygen species (ROS). Under salt stress, both shoots and roots of the osbhlh044 mutants acquired higher Na+. Moreover, the expression of ion homeostasis-related genes (OsHKTs, OsHAK, OsSOSs, and OsNHX) and ABA-responsive gene (OsLEA3) was significantly altered in the osbhlh044 mutants after salt stress. The expression levels of genes coding for starch (OsAGPL1, OsSSIIa, OsWx, and OsFLO2) and seed storage proteins (GluA1 and Globulin 1) were significantly decreased, indicating that they synthesize less store starch and proteins, resulting in grain chalkiness in the osbhlh044 mutants. Yeast one Hybrid (Y1H) showed that OsbHLH044 could activate salt- (OsHKT1;3, OsHAK7, OsSOS1, OsSOS2, OsNHX2, and OsLEA3 but not OsHKT2;1), and starch-related genes (OsSSIIa, OsWx, and OsFLO2) by binding to the G-boxes of their promoters. Therefore, the OsbHLH044 gene editing mutants revealed multiple functions, specifically a positive regulator of salt stress and grain quality, which might bring new insights into the breeding of rice varieties.
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Affiliation(s)
- Mohammad Shah Alam
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhen-Kun Yang
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Chao Li
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China; Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000, China
| | - Yan Yan
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhen Liu
- Hainan Institute, Zhejiang University, Sanya, 572025, China
| | - Muhammad Mudassir Nazir
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jian-Hong Xu
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China; Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000, China; Hainan Institute, Zhejiang University, Sanya, 572025, China.
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Li G, Jin L, Sheng S. Genome-Wide Identification of bHLH Transcription Factor in Medicago sativa in Response to Cold Stress. Genes (Basel) 2022; 13:genes13122371. [PMID: 36553638 PMCID: PMC9777957 DOI: 10.3390/genes13122371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Alfalfa represents one of the most important legume forages, and it is also applied as an organic fertilizer to improve soil quality. However, this perennial plant is native to warmer temperate regions, and its valuable cold-acclimation-related regulatory mechanisms are still less known. In higher plants, the bHLH transcription factors play pleiotropic regulatory roles in response to abiotic stresses. The recently released whole genome sequencing data of alfalfa allowed us to identify 469 MsbHLHs by multi-step homolog search. Herein, we primarily identified 65 MsbHLH genes that significantly upregulated under cold stress, and such bHLHs were classified into six clades according to their expression patterns. Interestingly, the phylogenetic analysis and conserved motif screening of the cold-induced MsbHLHs showed that the expression pattern is relatively varied in each bHLH subfamily, this result indicating that the 65 MsbHLHs may be involved in a complex cold-responsive regulatory network. Hence, we analyzed the TFBSs at promoter regions that unraveled a relatively conserved TFBS distribution with genes exhibiting similar expression patterns. Eventually, to verify the core components involved in long-term cold acclimation, we examined transcriptome data from a freezing-tolerant species (cv. Zhaodong) in the field and compared the expression of cold-sensitive/tolerant subspecies of alfalfa, giving 11 bHLH as candidates, which could be important for further cold-tolerance enhancement and molecular breeding through genetic engineering in alfalfa.
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Zhu L, Yang J, Zhang Y, Hu H, Cui J, Xue J, Xu J. Overexpression of CfICE1 from Cryptomeria fortunei Enhances Cold, Drought and Salt Stress in Poplar. Int J Mol Sci 2022; 23:ijms232315214. [PMID: 36499538 PMCID: PMC9736380 DOI: 10.3390/ijms232315214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
ICE1, a regulator of the cold-inducible transcriptome and freezing tolerance, is currently widely believed to be involved in plant resistance to cold stress. In this study, CfICE1 from Cryptomeria fortunei was transformed into poplar. Physiological indicators of transgenic, empty vector and wild-type poplar after abiotic stress (cold, drought and salt) were determined. Transgenic lines had a higher chlorophyll content, antioxidant enzyme activity and soluble protein content, as well as a lower malondialdehyde and hydrogen peroxide content. The ultrastructure of the plant was observed by transmission electron microscopy, and after stress, the cell structure of the transgenic line was more complete than that of the wild type. CfICE1 was upregulated in transgenic poplar trees after abiotic stress (cold, drought and salt). The CfICE1 transgenic plants improved plant resistance by regulating the CBF gene of poplar under cold and salt stress. In terms of plant responses to abiotic stress, this study showed that overexpression of CfICE1 improved the cold, drought and salt tolerance of poplars.
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Affiliation(s)
| | | | | | | | | | | | - Jin Xu
- Correspondence: ; Tel.: +86-138-1383-1609
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Liang B, Wan S, Ma Q, Yang L, Hu W, Kuang L, Xie J, Huang Y, Liu D, Liu Y. A Novel bHLH Transcription Factor PtrbHLH66 from Trifoliate Orange Positively Regulates Plant Drought Tolerance by Mediating Root Growth and ROS Scavenging. Int J Mol Sci 2022; 23:ijms232315053. [PMID: 36499381 PMCID: PMC9740576 DOI: 10.3390/ijms232315053] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Drought limits citrus yield and fruit quality worldwide. The basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in plant response to drought stress. However, few bHLH TFs related to drought response have been functionally characterized in citrus. In this study, a bHLH family gene, named PtrbHLH66, was cloned from trifoliate orange. PtrbHLH66 contained a highly conserved bHLH domain and was clustered closely with bHLH66 homologs from other plant species. PtrbHLH66 was localized to the nucleus and had transcriptional activation activity. The expression of PtrbHLH66 was significantly induced by polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA) treatments. Ectopic expression of PtrbHLH66 promoted the seed germination and root growth, increased the proline and ABA contents and the activities of antioxidant enzymes, but reduced the accumulation of malondialdehyde (MDA) and reactive oxygen species (ROS) under drought stress, resulting in enhanced drought tolerance of transgenic Arabidopsis. In contrast, silencing the PtrbHLH66 homolog in lemon plants showed the opposite effects. Furthermore, under drought stress, the transcript levels of 15 genes involved in ABA biosynthesis, proline biosynthesis, ROS scavenging and drought response were obviously upregulated in PtrbHLH66 ectopic-expressing Arabidopsis but downregulated in PtrbHLH66 homolog silencing lemon. Thus, our results suggested that PtrbHLH66 acted as a positive regulator of plant drought resistance by regulating root growth and ROS scavenging.
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Liu X, Wei R, Tian M, Liu J, Ruan Y, Sun C, Liu C. Combined Transcriptome and Metabolome Profiling Provide Insights into Cold Responses in Rapeseed ( Brassica napus L.) Genotypes with Contrasting Cold-Stress Sensitivity. Int J Mol Sci 2022; 23:13546. [PMID: 36362332 PMCID: PMC9657917 DOI: 10.3390/ijms232113546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/26/2023] Open
Abstract
Low temperature is a major environmental factor, which limits rapeseed (Brassica napus L.) growth, development, and productivity. So far, the physiological and molecular mechanisms of rapeseed responses to cold stress are not fully understood. Here, we explored the transcriptome and metabolome profiles of two rapeseed genotypes with contrasting cold responses, i.e., XY15 (cold-sensitive) and GX74 (cold-tolerant). The global metabolome profiling detected 545 metabolites in siliques of both genotypes before (CK) and after cold-stress treatment (LW). The contents of several sugar metabolites were affected by cold stress with the most accumulated saccharides being 3-dehydro-L-threonic acid, D-xylonic acid, inositol, D-mannose, D-fructose, D-glucose, and L-glucose. A total of 1943 and 5239 differentially expressed genes were identified from the transcriptome sequencing in XY15CK_vs_XY15LW and GX74CK_vs_GX74LW, respectively. We observed that genes enriched in sugar metabolism and biosynthesis-related pathways, photosynthesis, reactive oxygen species scavenging, phytohormone, and MAPK signaling were highly expressed in GX74LW. In addition, several genes associated with cold-tolerance-related pathways, e.g., the CBF-COR pathway and MAPK signaling, were specifically expressed in GX74LW. Contrarily, genes in the above-mentioned pathways were mostly downregulated in XY15LW. Thus, our results indicate the involvement of these pathways in the differential cold-stress responses in XY15 and GX74.
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Affiliation(s)
- Xinhong Liu
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ran Wei
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Minyu Tian
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory of Crop Physiology and Molecular Biology of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
| | - Jinchu Liu
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Ying Ruan
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Chuanxin Sun
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Chunlin Liu
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory of Crop Physiology and Molecular Biology of Ministry of Education, Hunan Agricultural University, Changsha 410128, China
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Jiang M, Li X, Yuan Y, Zhang G, Pang J, Ren J, Wang J, Yang M. Integrated physiological and transcriptomic analyses reveal the molecular mechanism behind the response to cultivation in Quercus mongolica. FRONTIERS IN PLANT SCIENCE 2022; 13:947696. [PMID: 36003809 PMCID: PMC9393570 DOI: 10.3389/fpls.2022.947696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Quercus mongolica, a common tree species for building and landscaping in northern China, has great commercial and ecological value. The seedlings of Q. mongolica grow poorly and develop chlorosis when introduced from high-altitude mountains to low-altitude plains. Effective cultivation measures are key to improving the quality of seedlings. To investigate the complex responses of Q. mongolica to different cultivation measures, we compared the adaptability of 3-year-old Q. mongolica seedlings to pruning (P), irrigation (W), and fertilization [F (nitro compound fertilizer with 16N-16P-16K)]. Physiological measurements and transcriptome sequencing were performed on leaves collected under the P treatments (control, cutting, removal of all lateral branches, and removal of base branches to one-third of seedling height), the W treatments (0, 1, 2, 3, 4, or 5 times in sequence), and the F treatments (0, 2, 4, and 6 g/plant). Analyses of the physiological data showed that P was more effective than W or F for activating intracellular antioxidant systems. By contrast, W and F were more beneficial than P for inducing the accumulation of soluble sugar. OPLS-DA identified superoxide dismutase, malondialdehyde, and peroxidase as critical physiological indices for the three cultivation measures. Transcriptome analyses revealed 1,012 differentially expressed genes (DEGs) in the P treatment, 1,035 DEGs in the W treatment, and 1,175 DEGs in the F treatment; these DEGs were mainly enriched in Gene Ontology terms related to the stress response and signal transduction. Weighted gene coexpression network analyses indicated that specific gene modules were significantly correlated with MDA (one module) and soluble sugar (four modules). Functional annotation of the hub genes differentially expressed in MDA and soluble sugar-related modules revealed that Q. mongolica responded and adapted to different cultivation measures by altering signal transduction, hormone levels, reactive oxygen species, metabolism, and transcription factors. The hub genes HOP3, CIPK11, WRKY22, and BHLH35 in the coexpression networks may played a central role in responses to the cultivation practices. These results reveal the mechanism behind the response of Q. mongolica to different cultivation measures at the physiological and molecular levels and provide insight into the response of plants to cultivation measures.
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Affiliation(s)
- Min Jiang
- College of Forestry, Hebei Agricultural University, Baoding, China
| | - Xinman Li
- College of Forestry, Hebei Agricultural University, Baoding, China
| | | | - Guowei Zhang
- Hongyashan State-Owned Forest Farm, Baoding, China
| | | | - Junjie Ren
- Hongyashan State-Owned Forest Farm, Baoding, China
| | - Jinmao Wang
- College of Forestry, Hebei Agricultural University, Baoding, China
| | - Minsheng Yang
- College of Forestry, Hebei Agricultural University, Baoding, China
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50
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Zhang X, Liu H, Huang L, Zhou B. Identification of Chilling-Responsive Genes in Litchi chinensis by Transcriptomic Analysis Underlying Phytohormones and Antioxidant Systems. Int J Mol Sci 2022; 23:ijms23158424. [PMID: 35955559 PMCID: PMC9369065 DOI: 10.3390/ijms23158424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/24/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Litchi (Litchi chinensis Sonn.) is an important subtropical and tropical evergreen fruit tree that is seriously affected by chilling stress. In order to identify genes that may be involved in the response to chilling in litchi, we investigate the physiological and biochemical changes under chilling stress and construct 12 RNA-Seq libraries of leaf samples at 0, 4, 8, and 12 days of chilling. The results show that antioxidant enzymes are activated by chilling treatments. Comparing the transcriptome data of the four time points, we screen 2496 chilling-responsive genes (CRGs), from which we identify 63 genes related to the antioxidant system (AO-CRGs) and 54 ABA, 40 IAA, 37 CTK, 27 ETH, 21 BR, 13 GA, 35 JA, 29 SA, and 4 SL signal transduction-related genes. Expression pattern analysis shows that the expression trends of the 28 candidate genes detected by qRT-PCR are similar to those detected by RNA-Seq, indicating the reliability of our RNA-Seq data. Partial Least Squares Structural Equation Modeling (PLS-SEM) analysis of the RNA-Seq data suggests a model for the litchi plants in response to chilling stress that alters the expression of the plant hormone signaling-related genes, the transcription factor-encoding genes LcICE1, LcCBFs, and LcbZIPs, and the antioxidant system-related genes. This study provides candidate genes for the future breeding of litchi cultivars with high chilling resistance, and elucidates possible pathways for litchi in response to chilling using transcriptomic data.
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