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Wang C, Lu C, Wang J, Liu X, Wei Z, Qin Y, Zhang H, Wang X, Wei B, Lv W, Mu G. Molecular mechanisms regulating glucose metabolism in quinoa (Chenopodium quinoa Willd.) seeds under drought stress. BMC PLANT BIOLOGY 2024; 24:796. [PMID: 39174961 PMCID: PMC11342610 DOI: 10.1186/s12870-024-05510-w] [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: 01/13/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND Abiotic stress seriously affects the growth and yield of crops. It is necessary to search and utilize novel abiotic stress resistant genes for 2.0 breeding programme in quinoa. In this study, the impact of drought stress on glucose metabolism were investigated through transcriptomic and metabolomic analyses in quinoa seeds. Candidate drought tolerance genes on glucose metabolism pathway were verified by qRT-PCR combined with yeast expression system. RESULTS From 70 quinoa germplasms, drought tolerant material M059 and drought sensitive material M024 were selected by comprehensive evaluation of drought resistance. 7042 differentially expressed genes (DEGs) were indentified through transcriptomic analyses. Gene Ontology (GO) analysis revealed that these DEGs were closely related to carbohydrate metabolic process, phosphorus-containing groups, and intracellular membrane-bounded organelles. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis detected that DEGs were related to pathways involving carbohydrate metabolisms, glycolysis and gluconeogenesis. Twelve key differentially accumulated metabolites (DAMs), (D-galactose, UDP-glucose, succinate, inositol, D-galactose, D-fructose-6-phosphate, D-glucose-6-phosphate, D-glucose-1-phosphate, dihydroxyacetone phosphate, ribulose-5-phosphate, citric acid and L-malate), and ten key candidate DEGs (CqAGAL2, CqINV, CqFrK7, CqCELB, Cqbg1x, CqFBP, CqALDO, CqPGM, CqIDH3, and CqSDH) involved in drought response were identified. CqSDH, CqAGAL2, and Cqβ-GAL13 were candidate genes that have been validated in both transcriptomics and yeast expression screen system. CONCLUSION These findings provide a foundation for elucidating the molecular regulatory mechanisms governing glucose metabolism in quinoa seeds under drought stress, providing insights for future research exploring responses to drought stress in quinoa.
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Affiliation(s)
- Chunmei Wang
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Chuan Lu
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Junling Wang
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Xiaoqing Liu
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Zhimin Wei
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals(Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, The Key Research Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Yan Qin
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Huilong Zhang
- Shijiazhuang Fubao Ecological Technology Co., LTD, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Xiaoxia Wang
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Boxiang Wei
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Wei Lv
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, 050000, Hebei Province, P. R. China.
| | - Guojun Mu
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China.
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China.
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Wang A, Guo W, Wang S, Wang Y, Kong D, Li W. Transcriptome analysis unveiled the genetic basis of rapid seed germination strategies in alpine plant Rheum pumilum. Sci Rep 2024; 14:19194. [PMID: 39160287 PMCID: PMC11333768 DOI: 10.1038/s41598-024-70320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/14/2024] [Indexed: 08/21/2024] Open
Abstract
Rheum pumilum stands as both a quintessential alpine plant and a significant traditional Chinese and Tibetan medicinal herb. Unraveling the molecular intricacies of seed germination in Rh. pumilum not only unveils the genetic foundations of plant seed germination strategies in high-altitude environments but also offers insights for cultivating Rh. pumilum medicinal materials. Employing transcriptome sequencing and the Weighted Gene Co-expression Network Analysis, this study delved into the shifts in gene expression levels across various stages of seed germination in Rh. pumilum. The process of seed germination in Rh. pumilum entails a cascade of complex physiological events. Six hormones (ABA, IAA, ETH, GA, BR, CK) emerged as pivotal players in seeds breaking in shells and the facilitation of rapid seed germination in Rh. pumilum. Fourteen transcription factor families (LOB, GRAS, B3, bHLH, bZIP, EIL, MYB, MYB related, NAC, TCP, WRKY, HSF, PLATZ, and SBP) along with four key genes (E2.4.1.13, EIN3, BZR, and BIN2) were identified that may be associated with both biotic and abiotic environmental stress. The ETR, ACACA and ATPeV0C genes were linked with energy accumulation during the initial stages of seed germination, CYP707A may play an important role in breaking seed dormancy, while the BRI1 gene may be correlated with swift seed germination. Additionally, several unidentified genes were recognized to play key roles in seed germination of Rh. pumilum, warranting further investigation. Moreover, Rh. pumilum demonstrates full activation of crucial physiological functions such as energy metabolism, signal transduction, and responses to biological and abiotic stresses during the seed breaking in shells. This study provides molecular evidence elucidating the swift seed germination strategies adopted by alpine plants to thrive in high-altitude environments. Furthermore, it serves as a foundational reference for enhancing seed germination rates and breeding practices to promote the sustainable development of Rh. pumilum medicinal materials.
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Affiliation(s)
- Ailan Wang
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Wenjie Guo
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Shimeng Wang
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Yanfang Wang
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Dongrui Kong
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Weiwei Li
- School of Life Sciences, Ludong University, Yantai, Shandong, China.
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García-Vázquez JL, Quijada-Rivera M, Hernández-Oñate MÁ, Tiznado-Hernández ME, Lazo-Javalera MF, Martínez-Téllez MÁ, Astorga-Cienfuegos KR, Rivera-Domínguez M. Effect of Vitis vinifera zygotic embryo cryopreservation and post-cryopreservation on the gene expression of DNA demethylases. Cryobiology 2024; 116:104947. [PMID: 39084504 DOI: 10.1016/j.cryobiol.2024.104947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/24/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
Grapevine (Vitis vinifera L.) crops are continuously exposed to biotic and abiotic stresses, which can cause genetic and epigenetic alterations. To determine the possible effects of grapevine cryopreservation on the regulation of DNA demethylase genes, this work studied the expression of DNA demethylase genes in cryopreserved and post-cryopreserved grapevine tissues. V. vinifera DNA demethylases were characterized by in silico analysis, and gene expression quantification was conducted by RT‒qPCR. Three DNA demethylase sequences were found: VIT_13s0074g00450 (VvDMT), VIT_08s0007g03920 (VvROS1), and VIT_06s0061g01270 (VvDML3). Phylogenetic analysis revealed that the sequences from V. vinifera and A. thaliana had a common ancestry. In the promoters of responsive elements to transcription factors such as AP-2, Myb, bZIP, TBP, and GATA, the conserved domains RRM DME and Perm CXXC were detected. These responsive elements play roles in the response to abiotic stress and the regulation of cell growth. These data helped us characterize the V. vinifera DNA demethylase genes. Gene expression analysis indicated that plant vitrification solution 2 (PVS2) treatment does not alter the expression of DNA demethylase genes. The expression levels of VvDMT and VvROS1 increased in response to cryopreservation by vitrification. Furthermore, in post-cryopreservation, VvROS1 was highly induced, and VvDML3 was repressed in all the treatment groups. Gene expression differences between different treatments and tissues may play roles in controlling methylation patterns during gene regulation in tissues stressed by cryopreservation procedures and in the post-cryopreservation period during plant growth and development.
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Affiliation(s)
- Juan Luis García-Vázquez
- Food Science Coordination, Center for Food Research and Development A.C, Hermosillo, Sonora, 83000, Mexico
| | - Mariana Quijada-Rivera
- Food Science Coordination, Center for Food Research and Development A.C, Hermosillo, Sonora, 83000, Mexico
| | - Miguel Ángel Hernández-Oñate
- Vegetal Food Origin Coordination, Center for Food Research and Development A.C, Hermosillo, Sonora, 83000, Mexico
| | | | | | - Miguel Ángel Martínez-Téllez
- Vegetal Food Origin Coordination, Center for Food Research and Development A.C, Hermosillo, Sonora, 83000, Mexico
| | | | - Marisela Rivera-Domínguez
- Food Science Coordination, Center for Food Research and Development A.C, Hermosillo, Sonora, 83000, Mexico.
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Wang Y, Ye H, Ren F, Ren X, Zhu Y, Xiao Y, He J, Wang B. Comparative Transcriptome Analysis Revealed Candidate Gene Modules Involved in Salt Stress Response in Sweet Basil and Overexpression of ObWRKY16 and ObPAL2 Enhanced Salt Tolerance of Transgenic Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1487. [PMID: 38891295 PMCID: PMC11174604 DOI: 10.3390/plants13111487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Sweet basil (Ocimum basilicum L.) is an important aromatic plant with high edibility and economic value, widely distributed in many regions of the tropics including the south of China. In recent years, environmental problems, especially soil salinization, have seriously restricted the planting and spread of sweet basil. However, the molecular mechanism of the salt stress response in sweet basil is still largely unknown. In this study, seed germination, seedling growth, and chlorophyll synthesis in sweet basil were inhibited under salt stress conditions. Through comparative transcriptome analysis, the gene modules involved in the metabolic processes, oxidative response, phytohormone signaling, cytoskeleton, and photosynthesis were screened out. In addition, the landscape of transcription factors during salt treatment in sweet basil was displayed as well. Moreover, the overexpression of the WRKY transcription factor-encoding gene, ObWRKY16, and the phenylalanine ammonia-lyase-encoding gene, ObPAL2, enhanced the seed germination, seedling growth, and survival rate, respectively, of transgenic Arabidopsis, suggesting that they might be important candidates for the creation of salt-tolerant sweet basil cultivars. Our data enrich the study on salt responses in sweet basil and provide essential gene resources for genetic improvements in sweet basil in the future.
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Affiliation(s)
- Yukun Wang
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; (Y.W.); (Y.Z.); (Y.X.)
- College of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (H.Y.); (F.R.); (X.R.)
- Engineering and Technology Research Center of Shaoguan Horticulture in Shaoguan University, Shaoguan 512005, China
| | - Hong Ye
- College of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (H.Y.); (F.R.); (X.R.)
- Engineering and Technology Research Center of Shaoguan Horticulture in Shaoguan University, Shaoguan 512005, China
| | - Fei Ren
- College of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (H.Y.); (F.R.); (X.R.)
- Engineering and Technology Research Center of Shaoguan Horticulture in Shaoguan University, Shaoguan 512005, China
| | - Xiaoqiang Ren
- College of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (H.Y.); (F.R.); (X.R.)
- Engineering and Technology Research Center of Shaoguan Horticulture in Shaoguan University, Shaoguan 512005, China
| | - Yunna Zhu
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; (Y.W.); (Y.Z.); (Y.X.)
- College of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (H.Y.); (F.R.); (X.R.)
- Engineering and Technology Research Center of Shaoguan Horticulture in Shaoguan University, Shaoguan 512005, China
| | - Yanhui Xiao
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; (Y.W.); (Y.Z.); (Y.X.)
- College of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (H.Y.); (F.R.); (X.R.)
- Engineering and Technology Research Center of Shaoguan Horticulture in Shaoguan University, Shaoguan 512005, China
| | - Jinming He
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; (Y.W.); (Y.Z.); (Y.X.)
- College of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (H.Y.); (F.R.); (X.R.)
- Engineering and Technology Research Center of Shaoguan Horticulture in Shaoguan University, Shaoguan 512005, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; (Y.W.); (Y.Z.); (Y.X.)
- College of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China; (H.Y.); (F.R.); (X.R.)
- Engineering and Technology Research Center of Shaoguan Horticulture in Shaoguan University, Shaoguan 512005, China
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Li Y, Zhu J, Xu J, Zhang X, Xie Z, Li Z. Effect of cold stress on photosynthetic physiological characteristics and molecular mechanism analysis in cold-resistant cotton (ZM36) seedlings. FRONTIERS IN PLANT SCIENCE 2024; 15:1396666. [PMID: 38803600 PMCID: PMC11128660 DOI: 10.3389/fpls.2024.1396666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024]
Abstract
Low temperature and cold damage seriously hinder the growth, development, and morphogenesis of cotton seedlings. However, the response mechanism of cotton seedlings under cold stress still lacks research. In this study, transcriptome sequencing, gas exchange parameters, and rapid chlorophyll fluorescence parameters were analyzed in leaves of cold-tolerant upland cotton variety "ZM36" under different temperature stress [25°C (T25, CK), 15°C (T15), 10°C (T10), and 4°C (T4)]. The results showed that the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), PSII potential maximum photochemical efficiency (Fv/Fm), and performance index (PIabs) of cotton leaves significantly decreased, and the intercellular CO2 concentration (Ci) and Fo/Fm significantly increased under cold stress. The transcriptome sequencing analysis showed that a total of 13,183 DEGs were involved in the response of cotton seedlings at each temperature point (T25, T15, T10, and T4), mainly involving five metabolic pathways-the phosphatidylinositol signaling system, photosynthesis, photosynthesis antenna protein, carbon fixation in photosynthetic organisms, and carotenoid synthesis. The 1,119 transcription factors were discovered among all the DEGs. These transcription factors involve 59 families, of which 15.8% of genes in the NAC family are upregulated. Through network regulatory analysis, the five candidate genes GhUVR8 (GH_A05G3668), GhPLATZ (GH_A09G2161), GhFAD4-1 (GH_A01G0758), GhNFYA1 (GH_A02G1336), and GhFAD4-2 (GH_D01G0766) were identified in response to cold stress. Furthermore, suppressing the expression level of GhPLATZ by virus-induced gene silencing led to the reduction of low temperature resistance, implying GhPLATZ as a positive regulator of low temperature tolerance. The findings of the study revealed a piece of the complex response mechanism of the cold-tolerant variety "ZM36" to different cold stresses and excavated key candidate genes for low temperature response, which provided support for accelerating the selection and breeding of cotton varieties with low temperature tolerance.
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Affiliation(s)
- Youzhong Li
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shihezi, Xinjiang, China
| | - Jincheng Zhu
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang, China
| | - Jianwei Xu
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Xianliang Zhang
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji, China
| | - Zongming Xie
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shihezi, Xinjiang, China
| | - Zhibo Li
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
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Xu S, Chen S, Cai J, Yan T, Tu M, Wang R, Hua S, Jiang L. Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:129. [PMID: 38740615 DOI: 10.1007/s00122-024-04642-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE Through comprehensive genomic and transcriptomic analyses, we identified a set of 23 genes that act up- or downstream of erucic acid content (EAC) production in rapeseed seeds. We selected example genes to showcase the distribution of single nucleotide polymorphisms, haplotypes associated with EAC phenotypes, and the creation of molecular markers differentiating low EAC and high EAC genotypes. Erucic acid content (EAC) is a crucial trait in rapeseed, with low LEAC oil recognized for its health benefits and high EA oil holding industrial value. Despite its significance, the genomic consequences of intensive LEAC-cultivar selection and the genetic basis underlying EA regulation remain largely unexplored. To address this knowledge gap, we conducted selective signal analyses, genome-wide association studies (GWAS), and transcriptome analyses. Our investigation unveiled the genetic footprints resulting from LEAC selection in germplasm populations, drawing attention to specific loci that contribute to enriching diversity. By integrating GWAS and transcriptome analyses, we identified a set of 23 genes that play a significant role in determining EAC in seeds or are downstream consequences of EA-level alterations. These genes have emerged as promising candidates for elucidating the potential mechanisms governing EAC in rapeseed. To exemplify the findings, we selected specific genes to demonstrate the distribution of single nucleotide polymorphisms and haplotypes associated with different EAC phenotypes. Additionally, we showcased to develop molecular markers distinguishing between LEAC and high EAC genotypes.
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Affiliation(s)
- Shiqi Xu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Shan Chen
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Jialing Cai
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Tao Yan
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Mengxin Tu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Ruisen Wang
- Jaixing Academy of Agricultural Sciences, Jiaxing, 314000, China
| | - Shuijin Hua
- Zhejiang Academy of Agricultural Sciences, Desheng Zhong Road 298, Hangzhou, 310022, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China.
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Ruan Q, Bai X, Wang Y, Zhang X, Wang B, Zhao Y, Zhu X, Wei X. Regulation of endogenous hormone and miRNA in leaves of alfalfa (Medicago sativa L.) seedlings under drought stress by endogenous nitric oxide. BMC Genomics 2024; 25:229. [PMID: 38429670 PMCID: PMC10908014 DOI: 10.1186/s12864-024-10024-8] [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: 01/20/2023] [Accepted: 01/17/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Alfalfa (Medicago sativa. L) is one of the best leguminous herbage in China and even in the world, with high nutritional and ecological value. However, one of the drawbacks of alfalfa is its sensitivity to dry conditions, which is a global agricultural problem. The objective of this study was to investigate the regulatory effects of endogenous nitric oxide (NO) on endogenous hormones and related miRNAs in alfalfa seedling leaves under drought stress. The effects of endogenous NO on endogenous hormones such as ABA, GA3, SA, and IAA in alfalfa leaves under drought stress were studied. In addition, high-throughput sequencing technology was used to identify drought-related miRNAs and endogenous NO-responsive miRNAs in alfalfa seedling leaves under drought stress. RESULT By measuring the contents of four endogenous hormones in alfalfa leaves, it was found that endogenous NO could regulate plant growth and stress resistance by inducing the metabolism levels of IAA, ABA, GA3, and SA in alfalfa, especially ABA and SA in alfalfa. In addition, small RNA sequencing technology and bioinformatics methods were used to analyze endogenous NO-responsive miRNAs under drought stress. It was found that most miRNAs were enriched in biological pathways and molecular functions related to hormones (ABA, ETH, and JA), phenylpropane metabolism, and plant stress tolerance. CONCLUSION In this study, the analysis of endogenous hormone signals and miRNAs in alfalfa leaves under PEG and PEG + cPTIO conditions provided an important basis for endogenous NO to improve the drought resistance of alfalfa at the physiological and molecular levels. It has important scientific value and practical significance for endogenous NO to improve plant drought resistance.
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Affiliation(s)
- Qian Ruan
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Pratacultural College, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaoming Bai
- Pratacultural College, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Yizhen Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of agronomy, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaofang Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Baoqiang Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Ying Zhao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaolin Zhu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of agronomy, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaohong Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China.
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China.
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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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Chen X, Yao C, Liu J, Liu J, Fang J, Deng H, Yao Q, Kang T, Guo X. Basic helix-loop-helix (bHLH) gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses. BMC Genomics 2024; 25:67. [PMID: 38233751 PMCID: PMC10792839 DOI: 10.1186/s12864-023-09911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Rye (Secale cereale), one of the drought and cold-tolerant crops, is an important component of the Triticae Dumortier family of Gramineae plants. Basic helix-loop-helix (bHLH), an important family of transcription factors, has played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, no systemic analysis of the bHLH transcription factor family has yet been reported in rye. RESULTS In this study, 220 bHLH genes in S. cereale (ScbHLHs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these ScbHLH genes are systematically analyzed. These 220 ScbHLH members are divided into 21 subfamilies and one unclassified gene. Throughout evolution, the subfamilies 5, 9, and 18 may have experienced stronger expansion. The segmental duplications may have contributed significantly to the expansion of the bHLH family. To systematically analyze the evolutionary relationships of the bHLH family in different plants, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression response characteristics of 22 ScbHLH genes in various biological processes and stress responses were analyzed. Some candidate genes, such as ScbHLH11, ScbHLH48, and ScbHLH172, related to tissue developments and environmental stresses were screened. CONCLUSIONS The results indicate that these ScbHLH genes exhibit characteristic expression in different tissues, grain development stages, and stress treatments. These findings provided a basis for a comprehensive understanding of the bHLH family in rye.
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Affiliation(s)
- Xingyu Chen
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Caimei Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jiahao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jintao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jingmei Fang
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Hong Deng
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Qian Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Tairan Kang
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China.
| | - Xiaoqiang Guo
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China.
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10
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Joubert M, van den Berg N, Theron J, Swart V. Global transcriptomic analysis in avocado nursery trees reveals differential gene expression during asymptomatic infection by avocado sunblotch viroid (ASBVd). Virus Res 2024; 339:199263. [PMID: 37940077 PMCID: PMC10682261 DOI: 10.1016/j.virusres.2023.199263] [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: 08/23/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/10/2023]
Abstract
Avocado sunblotch viroid (ASBVd) is the type species of the family Avsunviroidae and the causal agent of avocado sunblotch disease. The disease is characterised by the presence of chlorotic lesions on avocado fruit, leaves and/or stems. Infected trees may remain without chlorosis for extended periods of time, though distorted growth and reduced yield has been observed in these cases. The molecular effects of ASBVd on avocado, and members of the Avsunviroidae on their respective hosts in general, remain poorly understood. Host global transcriptomic studies within the family Pospiviroidae have identified several host pathways that are affected during these plant-pathogen interactions. In this study, we used RNA sequencing to investigate host gene expression in asymptomatic avocado nursery trees infected with ASBVd. Transcriptome data showed that 631 genes were differentially expressed, 63 % of which were upregulated during infection. Plant defence responses, phytohormone networks, gene expression pathways, secondary metabolism, cellular transport as well as protein modification and degradation were all significantly affected by ASBVd infection. This work represents the first global gene expression study of ASBVd-infected avocado, and the transcriptional reprogramming observed during this asymptomatic infection improves our understanding of the molecular interactions underlying broader avsunviroid-host interactions.
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Affiliation(s)
- M Joubert
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa; Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - N van den Berg
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa; Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - J Theron
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| | - V Swart
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa; Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa.
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11
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Waseem M, Peng J, Basharat S, Peng Q, Li Y, Yang G, Cheng S, Liu P. A comprehensive analysis of transcriptomic data for comparison of cold tolerance in two Brassica napus genotypes. PHYSIOLOGIA PLANTARUM 2024; 176:e14213. [PMID: 38353135 DOI: 10.1111/ppl.14213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/16/2024]
Abstract
Brassica napus is an important oil crop and cold stress severely limits its productivity. To date, several studies have reported the regulatory genes and pathways involved in cold-stress responses in B. napus. However, transcriptome-scale identification of the regulatory genes is still lacking. In this study, we performed comparative transcriptome analysis of cold-tolerant C18 (CT - C18) and cold-sensitive C6 (CS - C6) Brassica napus genotypes under cold stress for 7 days, with the primary purpose of identifying cold-responsive transcription in B. napus. A total of 6061 TFs belonging to 58 families were annotated in the B. napus genome, of which 3870 were expressed under cold stress in both genotypes. Among these, 451 TFs were differentially expressed (DE), with 21 TF genes expressed in both genotypes. Most TF members of the MYB (26), bHLH (23), and NAC (17) families were significantly expressed in the CT - C18 genotype compared with the CS - C6 B. napus genotype. GO classification showed a significant role in transcription regulation, DNA-binding transcription factor activity, response to chitin, and the ethylene-activated signaling pathway. KEGG pathway annotation revealed these TFs are involved in regulating more pathways, resulting in more tolerance. In conclusion, the results provide insights into the molecular regulation mechanisms of B. napus in response to freezing treatment, expanding our understanding of the complex molecular mechanisms in plants' response to freezing stress.
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Affiliation(s)
- Muhammad Waseem
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication) Hainan University, Sanya, Hainan
- School of Tropical Agriculture and Forestry (School of Agriculture and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, Hainan
- Fang Zhiyuan Academician Team Innovation Center of Hainan Province
| | - Jiantao Peng
- School of Tropical Agriculture and Forestry (School of Agriculture and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, Hainan
| | - Sana Basharat
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Qiqi Peng
- College of Agronomy, Guangxi University, Guangxi, China
| | - Yun Li
- College of Agronomy, Guangxi University, Guangxi, China
| | - Guangsheng Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication) Hainan University, Sanya, Hainan
- School of Tropical Agriculture and Forestry (School of Agriculture and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, Hainan
| | - Shanhan Cheng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication) Hainan University, Sanya, Hainan
- School of Tropical Agriculture and Forestry (School of Agriculture and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, Hainan
- Fang Zhiyuan Academician Team Innovation Center of Hainan Province
| | - Pingwu Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication) Hainan University, Sanya, Hainan
- School of Tropical Agriculture and Forestry (School of Agriculture and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, Hainan
- Fang Zhiyuan Academician Team Innovation Center of Hainan Province
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12
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Guo P, Yang Q, Wang Y, Yang Z, Xie Q, Chen G, Chen X, Hu Z. Overexpression of SlPRE3 alters the plant morphologies in Solanum lycopersicum. PLANT CELL REPORTS 2023; 42:1907-1925. [PMID: 37776371 DOI: 10.1007/s00299-023-03070-1] [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: 07/27/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
KEY MESSAGE Overexpression of SlPRE3 is detrimental to the photosynthesis and alters plant morphology and root development. SlPRE3 interacts with SlAIF1/SlAIF2/SlPAR1/SlIBH1 to regulate cell expansion. Basic helix-loop-helix (bHLH) transcription factors play crucial roles as regulators in plant growth and development. In this study, we isolated and characterized SlPRE3, an atypical bHLH transcription factor gene. SlPRE3 exhibited predominant expression in the root and moderate expression in the senescent leaves. Comparative analysis with the wild type revealed significant differences in plant morphology in the 35S:SlPRE3 lines. These differences included increased internode length, rolling leaves with reduced chlorophyll accumulation, and elongated yet fewer adventitious roots. Additionally, 35S:SlPRE3 lines displayed elevated levels of GA3 (gibberellin A3) and reduced starch accumulation. Furthermore, utilizing the Y2H (Yeast two-hybrid) and the BiFC (Bimolecular Fluorescent Complimentary) techniques, we identified physical interactions between SlPRE3 and SlAIF1 (ATBS1-interacting factor 1)/SlAIF2 (ATBS1-interacting factor 2)/SlPAR1 (PHYTOCHROME RAPIDLY REGULATED 1)/SlIBH1 (ILI1-binding bHLH 1). RNA-seq analysis of root tissues revealed significant alterations in transcript levels of genes involved in gibberellin metabolism and signal transduction, cell expansion, and root development. In summary, our study sheds light on the crucial regulatory role of SlPRE3 in determining plant morphology and root development.
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Affiliation(s)
- Pengyu Guo
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Room 521, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Qingling Yang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Room 521, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Yunshu Wang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Room 521, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Zhijie Yang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Room 521, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Room 521, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Room 521, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Xuqing Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, 11 Shuguanghuayuan Middle Road, Haidian, Beijing, 100097, People's Republic of China.
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Room 521, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China.
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13
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Li J, Chen S, Yin Y, Shan Q, Zheng C, Chen Y. Genome-Wide Analysis of bHLH Family Genes and Identification of Members Associated with Cold/Drought-Induced Photoinhibition in Kandelia obovata. Int J Mol Sci 2023; 24:15942. [PMID: 37958925 PMCID: PMC10647802 DOI: 10.3390/ijms242115942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Plant basic helix-loop-helix (bHLH) transcription factors play pivotal roles in responding to stress, including cold and drought. However, it remains unclear how bHLH family genes respond to these stresses in Kandelia obovata. In this study, we identified 75 bHLH members in K. obovata, classified into 11 subfamilies and unevenly distributed across its 18 chromosomes. Collineation analysis revealed that segmental duplication primarily drove the expansion of KobHLH genes. The KobHLH promoters were enriched with elements associated with light response. Through RNA-seq, we identified several cold/drought-associated KobHLH genes. This correlated with decreased net photosynthetic rates (Pn) in the leaves of cold/drought-treated plants. Weighted gene co-expression network analysis (WGCNA) confirmed that 11 KobHLH genes were closely linked to photoinhibition in photosystem II (PS II). Among them, four Phytochrome Interacting Factors (PIFs) involved in chlorophyll metabolism were significantly down-regulated. Subcellular localization showed that KobHLH52 and KobHLH30 were located in the nucleus. Overall, we have comprehensively analyzed the KobHLH family and identified several members associated with photoinhibition under cold or drought stress, which may be helpfulfor further cold/drought-tolerance enhancement and molecular breeding through genetic engineering in K. obovata.
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Affiliation(s)
- Junjian Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Siyi Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yaxin Yin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Qiaobo Shan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Chunfang Zheng
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yan Chen
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
- Forestry College, Inner Mongolia Agricultural University, Hohhot 010018, China
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14
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Shang L, Zhou Y, Wen S, Wang K, Li Y, Zhang M, Jian H, Lyu D. Construction of heat stress regulation networks based on Illumina and SMRT sequencing data in potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1271084. [PMID: 38023929 PMCID: PMC10651764 DOI: 10.3389/fpls.2023.1271084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
Potato (Solanum tuberosum L.) is one of the most important tuber food crops in the world; however, the cultivated potatoes are susceptible to high temperature, by which potato production is adversely affected. Understanding the coping mechanism of potato to heat stress is essential to secure yield and expand adaptability under environmental conditions with rising temperature. However, the lack of heat-related information has significantly limited the identification and application of core genes. To gain deeper insights into heat tolerance genes, next-generation sequencing and single-molecule real-time sequencing were used to learn the transcriptional response of potato to heat stress and 13,159 differentially expressed genes (DEGs) were identified in this study. All DEGs were grouped into 12 clusters using the K-means clustering algorithm. Gene Ontology enrichment analysis revealed that they were involved in temperature signaling, phytohormone, and protein modification. Among them, there were 950 differentially expressed transcription factors (DETFs). According to the network analysis of DETFs at the sixth hour under heat stress, we found some genes that were previously reported to be associated with photoperiodic tuberization, StCO (CONSTANS), tuber formation, StBEL11 (BEL1-LIKE 11), and earliness in potato, StCDF1 (CYCLING DOF FACTOR 1) responding to temperature. Furthermore, we verified the relative expression levels using quantitative real-time polymerase chain reaction, and the results were consistent with the inferences from transcriptomes. In addition, there were 22,125 alternative splicing events and 2,048 long non-coding RNAs. The database and network established in this study will extend our understanding of potato response to heat stress. It ultimately provided valuable resources for molecular analysis of heat stress response in potato and cultivation of potato varieties with heat tolerance.
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Affiliation(s)
- Lina Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yonghong Zhou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Ke Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yang Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Meihua Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hongju Jian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
| | - Dianqiu Lyu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
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15
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Zhao L, Bi W, Jia Y, Shi J, Chi Y, Yu M, Wang C. Genome-Wide Characterization of bHLH Family Genes and Expression Analysis in Response to Osmotic Stress in Betula platyphylla. PLANTS (BASEL, SWITZERLAND) 2023; 12:3687. [PMID: 37960044 PMCID: PMC10649471 DOI: 10.3390/plants12213687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
The bHLH family, as a superfamily of transcription factors (TFs), has special functional characteristics in plants and plays a crucial role in a plant's growth and development and helping the plant cope with various stresses. In this study, 128 bHLH family genes were screened in the birch (B. platyphylla) genome using conservative domain scan and blast analysis. These genes are clustered into 21 subfamilies based on the phylogenetic tree construction and are unevenly distributed among the 14 birch chromosomes. In all, 22 segmental duplication pairs with 27 BpbHLH genes were identified. The duplications were distributed on eight chromosomes. Analysis of gene structures and protein motifs revealed intra-group conservation of BpbHLHs. Of the BpbHLH family genes, 16 contain only one intron each. The BPChr14G06667 gene contains the most introns, that is, 19. The cis-elements, which respond to plant hormones, light, defense, and stress, were found on the promoter of BHLH family genes. As per RNA-seq data analysis, under PEG osmotic stress, most BpbHLH genes were differentially expressed, and eight were highly differentially expressed. The qRT-PCR analysis results further indicated that BPChr06G09475 was the gene with the highest expression level in leaves, roots, and stems, and that the expression of these eight genes was higher in leaves than in roots and stems and upregulated in all three tissues under osmotic stress compared to the controls. The above analysis suggests that the BpbHLH family genes have a certain biological effect under drought stress that provides a basis for molecular breeding for stress resistance in birch.
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Affiliation(s)
| | | | | | | | | | | | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.Z.); (W.B.); (Y.J.); (Y.C.); (M.Y.)
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16
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Liu Y, Lin L, Liu Y, Mo Q, Zhang D, Li W, Xiong X, Yu X, Li Y. Genome-Wide Analysis of the bHLH Gene Family in Loropetalum chinense var. rubrum: Identification, Classification, Evolution, and Diversity of Expression Patterns under Cultivation. PLANTS (BASEL, SWITZERLAND) 2023; 12:3392. [PMID: 37836132 PMCID: PMC10574408 DOI: 10.3390/plants12193392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 10/15/2023]
Abstract
The basic helix-loop-helix (bHLH) transcription factor family is the second-largest transcription factor family in plants. Members of this family are involved in the processes of growth and development, secondary metabolic biosynthesis, signal transduction, and plant resistance. Loropetalum chinense var. rubrum is a critical woody plant with higher ornamental and economic values, which has been used as ornamental architecture and traditional Chinese herbal medicine plants. However, the bHLH transcription factors in Loropetalum chinense var. rubrum (L. chinense var. rubrum) have not yet been systematically demonstrated, and their role in the biosynthesis of anthocyanin is still unclear. Here, we identified 165 potential LcbHLHs genes by using two methods, and they were unequally distributed on chromosomes 1 to 12 of the genome of L. chinense var. rubrum. Based on an evolutionary comparison with proteins from Arabidopsis and Oryza sativa, these bHLH proteins were categorized into 21 subfamilies. Most LcbHLHs in a particular subfamily had similar gene structures and conserved motifs. The Gene Ontology annotation and Cis-elements predicted that LcbHLHs had many molecular functions and were involved in processes of plant growth, including the biosynthesis of flavonoids and anthocyanins. Transcriptomic analysis revealed different expression patterns among different tissues and cultivars of L. chinense var. rubrum. Many LcbHLHs were expressed in the leaves, and only a few genes were highly expressed in the flowers. Six LcbHLHs candidate genes were identified by bioinformatics analysis and expression analysis. Further Real-time quantitative PCR analysis and protein interaction network analysis showed that LcbHLH156, which is one of the candidate proteins belonging to the IIIf subfamily, could interact with proteins related to anthocyanin synthesis. Therefore, LcbHLH156 was transiently expressed in L. chinense var. rubrum to verify its function in regulating anthocyanin synthesis. Compared with the control group, red pigment accumulation appeared at the wound after injection, and the total anthocyanin content increased at the wound of leaves. These results lay a foundation for the research of the regulation mechanism of leaf colors in L. chinense var. rubrum and also provide a basis for the function of the LcbHLH family.
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Affiliation(s)
- Yang Liu
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Ling Lin
- School of Economics, Hunan Agricultural University, Changsha 410128, China;
| | - Yang Liu
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Qiong Mo
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Damao Zhang
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Weidong Li
- Hunan Key Laboratory of Germplasm Innovation and Comprehensive Utilization of Garden Flowers, Hunan Horticulture Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China;
| | - Xingyao Xiong
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Kunpeng Institute of Modern Agriculture, Foshan 528225, China
| | - Xiaoying Yu
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
| | - Yanlin Li
- College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (Y.L.); (Q.M.); (D.Z.)
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Kunpeng Institute of Modern Agriculture, Foshan 528225, China
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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Liu Q, Wen J, Wang S, Chen J, Sun Y, Liu Q, Li X, Dong S. Genome-wide identification, expression analysis, and potential roles under low-temperature stress of bHLH gene family in Prunus sibirica. FRONTIERS IN PLANT SCIENCE 2023; 14:1267107. [PMID: 37799546 PMCID: PMC10548393 DOI: 10.3389/fpls.2023.1267107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
The basic helix-loop-helix (bHLH) family is one of the most well-known transcription factor families in plants, and it regulates growth, development, and abiotic stress responses. However, systematic analyses of the bHLH gene family in Prunus sibirica have not been reported to date. In this study, 104 PsbHLHs were identified and classified into 23 subfamilies that were unevenly distributed on eight chromosomes. Nineteen pairs of segmental replication genes and ten pairs of tandem replication genes were identified, and all duplicated gene pairs were under purifying selection. PsbHLHs of the same subfamily usually share similar motif compositions and exon-intron structures. PsbHLHs contain multiple stress-responsive elements. PsbHLHs exhibit functional diversity by interacting and coordinating with other members. Twenty PsbHLHs showed varying degrees of expression. Eleven genes up-regulated and nine genes down-regulated in -4°C. The majority of PsbHLHs were highly expressed in the roots and pistils. Transient transfection experiments demonstrated that transgenic plants with overexpressed PsbHLH42 have better cold tolerance. In conclusion, the results of this study have significant implications for future research on the involvement of bHLH genes in the development and stress responses of Prunus sibirica.
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Affiliation(s)
- Quangang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Jiaxing Wen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Shipeng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Jianhua Chen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Yongqiang Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Qingbai Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Xi Li
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Shengjun Dong
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
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18
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Godbole RC, Kadam SB, Pable AA, Singh S, Barvkar VT. Phylogenomics of transcriptionally active AP2/ERF and bHLH transcription factors and study of their promoter regions in Nothapodytes nimmoniana (J.Graham) Mabb. Genome 2023; 66:235-250. [PMID: 37163758 DOI: 10.1139/gen-2023-0009] [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] [Indexed: 05/12/2023]
Abstract
Nothapodytes nimmoniana is a medicinally important plant producing anticancer monoterpene indole alkaloid (MIA), camptothecin (CPT). The CPT is synthesised through the strictosidine intermediate following the MIA pathway; however, transcriptional regulation of CPT pathway is still elusive in N. nimmoniana. Biosynthesis of MIA is regulated by various transcription factors (TFs) belonging to AP2/ERF, bHLH, MYB, and WRKY families. The present study identified transcriptionally active full-length 105 AP2/ERF and 68 bHLH family TFs from the N. nimmoniana. AP2/ERF TFs were divided into three subfamilies along with a soloist, while bHLH TFs were divided into 10 subfamilies according to their phylogenetic similarities. Three group IXa ERFs, Nn-ERF22, Nn-ERF29, and Nn-ERF41, one subfamily IVa TF Nn-bHLH7, and three subfamilies IIIe Nn-bHLH33, Nn-bHLH51, and Nn-bHLH52 clustered with the TFs regulating alkaloid biosynthesis in Catharanthus roseus, tomato, tobacco, and Artemisia annua. Expression of these TFs in N. nimmoniana was higher in roots, which is a primary CPT accumulating tissue. Moreover, genome skimming approach was used to reconstruct the promoter regions of candidate ERF genes to identify the cis-regulatory elements. The presence of G-boxes and other jasmonic acid-responsive elements in the promoter suggests the regulation of ERFs by bHLHs. The present study effectively generated and used genomics resource for characterisation of regulatory TFs from non-model medicinal plant.
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Affiliation(s)
- Rucha C Godbole
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Swapnil B Kadam
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India
| | - Sudhir Singh
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre (BARC), Mumbai, 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
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Liu S, Zhang Y, Pan X, Li B, Yang Q, Yang C, Zhang J, Wu F, Yang A, Li Y. PIF1, a phytochrome-interacting factor negatively regulates drought tolerance and carotenoids biosynthesis in tobacco. Int J Biol Macromol 2023; 247:125693. [PMID: 37419268 DOI: 10.1016/j.ijbiomac.2023.125693] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/09/2023]
Abstract
The phytochrome-interacting factors (PIFs) function crucially in multiple physiological processes, but the biological functions of some PIFs remain elusive in some species. Here, a PIF transcription factor NtPIF1 was cloned and characterized in tobacco (Nicotiana tabacum L.). The transcript of NtPIF1 was significantly induced by drought stress treatments, and it localized in the nuclear. Knockout of NtPIF1 by CRISPR/Cas9 system led to the improved drought tolerance of tobacco with increased osmotic adjustment, antioxidant activity, photosynthetic efficiency and decreased water loss rate. On the contrary, NtPIF1-overexpression plants displays drought-sensitive phenotypes. In addition, NtPIF1 reduced the biosynthesis of abscisic acid (ABA) and its upstream carotenoids by regulating the expression of genes involved in ABA and carotenoids biosynthetic pathway upon drought stress. Electrophoretic mobility shift and dual-luciferase assays illustrated that, NtPIF1 directly bind to the E-box elements within the promoters of NtNCED3, NtABI5, NtZDS and Ntβ-LCY to repress their transcription. Overall, these data suggested that NtPIF1 negatively regulate tobacco adaptive response to drought stress and carotenoids biosynthesis; moreover, NtPIF1 has the potential to develop drought-tolerant tobacco plants using CRISPR/Cas9 system.
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Affiliation(s)
- Shaohua Liu
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, China; Shenzhen Yupeng Technology Co., Ltd, Shenzhen 518110, China
| | - Yinchao Zhang
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, China
| | - Xuhao Pan
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, China
| | - Bin Li
- Sichuan Tobacco Corporation, Chengdu 610014, China
| | - Qing Yang
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, China
| | - Changqing Yang
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, China
| | | | - Fengyan Wu
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, China
| | - Aiguo Yang
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, China.
| | - Yiting Li
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, China.
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20
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Xu J, Du R, Wang Y, Chen J. Wound-Induced Temporal Reprogramming of Gene Expression during Agarwood Formation in Aquilaria sinensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:2901. [PMID: 37631113 PMCID: PMC10459772 DOI: 10.3390/plants12162901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/27/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023]
Abstract
Agarwood is a resinous heartwood of Aquilaria sinensis that is formed in response to mechanical wounding. However, the transcriptional response of A. sinensis to mechanical wounding during the agarwood formation process is still unclear. Here, three five-year-old A. sinensis trees were mechanically damaged by a chisel, and time-series transcriptomic analysis of xylem tissues in the treated area (TA) was performed at 15 (TA1), 70 (TA2) and 180 days after treatment (TA3). Samples from untreated areas at the corresponding time points (UA1, UA2, UA3, respectively) were collected as controls. A total of 1862 (TA1 vs. UA1), 961 (TA2 vs. UA2), 1370 (TA3 vs. UA3), 3305 (TA2 vs. TA1), 2625 (TA3 vs. TA1), 2899 (TA3 vs. TA2), 782 (UA2 vs. UA1), 4443 (UA3 vs. UA1) and 4031 (UA3 vs. UA2) genes were differentially expressed (DEGs). Functional enrichment analysis showed that DEGs were significantly enriched for secondary metabolic processes, signal transduction and transcriptional regulation processes. Most of the genes involved in lignin biosynthesis were more abundant in the TA groups, which included phenylalanine ammonia-lyase, 4-coumarate CoA ligase, cinnamate 4-hydroxylase, caffeoyl-CoA O-methyltransferase and cinnamoyl-CoA reductase. DEGs involved in sesquiterpene biosynthesis were also identified. Hydroxymethylglutaryl-CoA synthase, 3-hydroxy-3-methylglutaryl-coenzyme A reductase, phosphomevalonate kinase and terpene synthase genes were significantly increased in the TA groups, promoting sesquiterpene biosynthesis in the wounded xylem tissues. The TF-gene transcriptomic networks suggested that MYB DNA-binding, NAM, WRKY, HLH and AP2 TFs co-expressed with genes related to lignin and sesquiterpene synthesis, indicating their critical regulatory roles in the biosynthesis of these compounds. Overall, our study reveals a dynamic transcriptional response of A. sinensis to mechanical wounding, provides a resource for identifying candidate genes for molecular breeding of agarwood quality, and sheds light on the molecular mechanisms of agarwood formation in A. sinensis.
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Affiliation(s)
- Jieru Xu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Hainan University, Sanya 572019, China; (J.X.); (R.D.); (Y.W.)
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Ruyue Du
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Hainan University, Sanya 572019, China; (J.X.); (R.D.); (Y.W.)
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yue Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Hainan University, Sanya 572019, China; (J.X.); (R.D.); (Y.W.)
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Jinhui Chen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Hainan University, Sanya 572019, China; (J.X.); (R.D.); (Y.W.)
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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21
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Li X, Ma Z, Song Y, Shen W, Yue Q, Khan A, Tahir MM, Wang X, Malnoy M, Ma F, Bus V, Zhou S, Guan Q. Insights into the molecular mechanisms underlying responses of apple trees to abiotic stresses. HORTICULTURE RESEARCH 2023; 10:uhad144. [PMID: 37575656 PMCID: PMC10421731 DOI: 10.1093/hr/uhad144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/13/2023] [Indexed: 08/15/2023]
Abstract
Apple (Malus[Formula: see text]domestica) is a popular temperate fruit crop worldwide. However, its growth, productivity, and quality are often adversely affected by abiotic stresses such as drought, extreme temperature, and high salinity. Due to the long juvenile phase and highly heterozygous genome, the conventional breeding approaches for stress-tolerant cultivars are time-consuming and resource-intensive. These issues may be resolved by feasible molecular breeding techniques for apples, such as gene editing and marker-assisted selection. Therefore, it is necessary to acquire a more comprehensive comprehension of the molecular mechanisms underpinning apples' response to abiotic stress. In this review, we summarize the latest research progress in the molecular response of apples to abiotic stressors, including the gene expression regulation, protein modifications, and epigenetic modifications. We also provide updates on new approaches for improving apple abiotic stress tolerance, while discussing current challenges and future perspectives for apple molecular breeding.
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Affiliation(s)
- Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ziqing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Song
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenyun Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qianyu Yue
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Abid Khan
- Department of Horticulture, The University of Haripur, Haripur 22620, Pakistan
| | - Muhammad Mobeen Tahir
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaofei Wang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271000, China
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige 38098, Italy
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Vincent Bus
- The New Zealand Institute for Plant and Food Research Limited, Havelock North 4157, New Zealand
| | - Shuangxi Zhou
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Yadav IS, Rawat N, Chhuneja P, Kaur S, Uauy C, Lazo G, Gu YQ, Doležel J, Tiwari VK. Comparative genomic analysis of 5M g chromosome of Aegilops geniculata and 5U u chromosome of Aegilops umbellulata reveal genic diversity in the tertiary gene pool. FRONTIERS IN PLANT SCIENCE 2023; 14:1144000. [PMID: 37521926 PMCID: PMC10373596 DOI: 10.3389/fpls.2023.1144000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Wheat is one of the most important cereal crops for the global food security. Due to its narrow genetic base, modern bread wheat cultivars face challenges from increasing abiotic and biotic stresses. Since genetic improvement is the most sustainable approach, finding novel genes and alleles is critical for enhancing the genetic diversity of wheat. The tertiary gene pool of wheat is considered a gold mine for genetic diversity as novel genes and alleles can be identified and transferred to wheat cultivars. Aegilops geniculata and Ae. umbellulata are the key members of the tertiary gene pool of wheat and harbor important genes against abiotic and biotic stresses. Homoeologous-group five chromosomes (5Uu and 5Mg) have been extensively studied from Ae. geniculata and Ae. umbellulata as they harbor several important genes including Lr57, Lr76, Yr40, Yr70, Sr53 and chromosomal pairing loci. In the present study, using chromosome DNA sequencing and RNAseq datasets, we performed comparative analysis to study homoeologous gene evolution in 5Mg, 5Uu, and group 5 wheat chromosomes. Our findings highlight the diversity of transcription factors and resistance genes, resulting from the differential expansion of the gene families. Both the chromosomes were found to be enriched with the "response to stimulus" category of genes providing resistance against biotic and abiotic stress. Phylogenetic study positioned the M genome closer to the D genome, with higher proximity to the A genome than the B genome. Over 4000 genes were impacted by SNPs on 5D, with 4-5% of those genes displaying non-disruptive variations that affect gene function.
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Affiliation(s)
- Inderjit S. Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Gerard Lazo
- Agricultural Research Service, United States Department of Agriculture (USDA), Albany, CA, United States
| | - Yong Q. Gu
- Agricultural Research Service, United States Department of Agriculture (USDA), Albany, CA, United States
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Olomouc, Czechia
| | - Vijay K. Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
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Bai Y, Zhang T, Zheng X, Li B, Qi X, Xu Y, Li L, Liang C. Overexpression of a WRKY transcription factor McWRKY57-like from Mentha canadensis L. enhances drought tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2023; 23:216. [PMID: 37098465 PMCID: PMC10126992 DOI: 10.1186/s12870-023-04213-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Drought has become a major environmental problem affecting crop production. Members of the WRKY family play important roles in plant development and stress responses. However, their roles in mint have been barely explored. RESULTS In this study, we isolated a drought-inducible gene McWRKY57-like from mint and investigated its function. The gene encodes a group IIc WRKY transcription factor, McWRKY57-like, which is a nuclear protein with a highly conserved WRKY domain and a C2H2 zinc-finger structure, and has transcription factor activity. Its expression levels were examined in different tissues of mint and under the treatment of mannitol, NaCl, abscisic acid, and methyl jasmonate. We found that McWRKY57-like overexpression in Arabidopsis significantly increased drought tolerance. Further studies showed that under drought stress, McWRKY57-like-overexpressing plants had higher chlorophyll, soluble sugar, soluble protein, and proline contents but lower water loss rate and malondialdehyde content than wild-type plants. Moreover, the activities of antioxidant enzymes catalase, superoxide dismutase, and peroxidase were enhanced in McWRKY57-like transgenic plants. Furthermore, qRT-PCR analysis revealed that the drought-related genes AtRD29A, AtRD29B, AtRD20, AtRAB18, AtCOR15A, AtCOR15B, AtKIN2, and AtDREB1A were upregulated in McWRKY57-like transgenic plants than in wild-type Arabidopsis under simulated drought conditions. CONCLUSION These data demonstrated that McWRKY57-like conferred drought tolerance in transgenic Arabidopsis by regulating plant growth, osmolyte accumulation and antioxidant enzyme activities, and the expression of stress-related genes. The study indicates that McWRKY57-like plays a positive role in drought response in plants.
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Affiliation(s)
- Yang Bai
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Ting Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Xiaowei Zheng
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Bingxuan Li
- The key laboratory of quality improvement of agriculture products of Zhejiang province, college of advanced agriculture sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xiwu Qi
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Yu Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Li Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Chengyuan Liang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China.
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Feng Z, Sun L, Dong M, Fan S, Shi K, Qu Y, Zhu L, Shi J, Wang W, Liu Y, Chen X, Weng Y, Liu X, Ren H. Identification and Functional Characterization of CsMYCs in Cucumber Glandular Trichome Development. Int J Mol Sci 2023; 24:ijms24076435. [PMID: 37047408 PMCID: PMC10094329 DOI: 10.3390/ijms24076435] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Glandular trichomes (GTs), specialized structures formed by the differentiation of plant epidermal cells, are known to play important roles in the resistance of plants to external biotic and abiotic stresses. These structures are capable of storing and secreting secondary metabolites, which often have important agricultural and medicinal values. In order to better understand the molecular developmental mechanisms of GTs, studies have been conducted in a variety of crops, including tomato (Solanum lycopersicum), sweetworm (Artemisia annua), and cotton (Gossypium hirsutum). The MYC transcription factor of the basic helix-loop-helix (bHLH) transcription factor family has been found to play an important role in GT development. In this study, a total of 13 cucumber MYC transcription factors were identified in the cucumber (Cucumis sativus L.) genome. After performing phylogenetic analyses and conserved motifs on the 13 CsMYCs in comparison to previously reported MYC transcription factors that regulate trichome development, seven candidate MYC transcription factors were selected. Through virus-induced gene silencing (VIGS), CsMYC2 is found to negatively regulate GT formation while CsMYC4, CsMYC5, CsMYC6, CsMYC7, and CsMYC8 are found to positively regulate GT formation. Furthermore, the two master effector genes, CsMYC2 and CsMYC7, are observed to have similar expression patterns indicating that they co-regulate the balance of GT development in an antagonistic way.
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Affiliation(s)
- Zhongxuan Feng
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Lei Sun
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Mingming Dong
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shanshan Fan
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Kexin Shi
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yixin Qu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Liyan Zhu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Jinfeng Shi
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Wujun Wang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yihan Liu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xiaofeng Chen
- Yantai Institute, China Agricultural University, Yantai 264670, China
| | - Yiqun Weng
- USDA-ARS, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
| | - Xingwang Liu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572019, China
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Huazhong Ren
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572019, China
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing 100193, 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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Sharaf A, Nuc P, Ripl J, Alquicer G, Ibrahim E, Wang X, Maruthi MN, Kundu JK. Transcriptome Dynamics in Triticum aestivum Genotypes Associated with Resistance against the Wheat Dwarf Virus. Viruses 2023; 15:v15030689. [PMID: 36992398 PMCID: PMC10054045 DOI: 10.3390/v15030689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Wheat dwarf virus (WDV) is one of the most important pathogens of cereal crops worldwide. To understand the molecular mechanism of resistance, here we investigated the comparative transcriptome of wheat genotypes with different levels of resistance (Svitava and Fengyou 3) and susceptibility (Akteur) to WDV. We found a significantly higher number of differentially expressed transcripts (DETs) in the susceptible genotype than in the resistant one (e.g., Svitava). The number of downregulated transcripts was also higher in the susceptible genotype than in the resistant one (Svitava) and the opposite was true for the upregulated transcripts. Further functional analysis of gene ontology (GO) enrichment identified a total of 114 GO terms for the DETs. Of these, 64 biological processes, 28 cellular components and 22 molecular function GO terms were significantly enriched. A few of these genes appear to have a specific expression pattern related to resistance or susceptibility to WDV infection. Validation of the expression pattern by RT-qPCR showed that glycosyltransferase was significantly downregulated in the susceptible genotype compared to the resistant genotypes after WDV infection, while CYCLIN-T1-3, a regulator of CDK kinases (cyclin-dependent kinase), was upregulated. On the other hand, the expression pattern of the transcription factor (TF) MYB (TraesCS4B02G174600.2; myeloblastosis domain of transcription factor) was downregulated by WDV infection in the resistant genotypes compared to the susceptible genotype, while a large number of TFs belonging to 54 TF families were differentially expressed due to WDV infection. In addition, two transcripts (TraesCS7A02G341400.1 and TraesCS3B02G239900.1) were upregulated with uncharacterised proteins involved in transport and regulation of cell growth, respectively. Altogether, our findings showed a clear gene expression profile associated with resistance or susceptibility of wheat to WDV. In future studies, we will explore the regulatory network within the same experiment context. This knowledge will broaden not only the future for the development of virus-resistant wheat genotypes but also the future of genetic improvement of cereals for resilience and WDV-resistance breeding.
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Affiliation(s)
- Abdoallah Sharaf
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Przemysław Nuc
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Jan Ripl
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Glenda Alquicer
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Emad Ibrahim
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Midatharahally N. Maruthi
- Agriculture, Health and Environment Department, Natural Resources Institute, Medway Campus, University of Greenwich, Chatham, Kent ME4 4TB, UK;
| | - Jiban Kumar Kundu
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
- Correspondence: ; Tel.: +420-233-022-410
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Kajla M, Roy A, Singh IK, Singh A. Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs. FRONTIERS IN PLANT SCIENCE 2023; 14:1126567. [PMID: 36938003 PMCID: PMC10017880 DOI: 10.3389/fpls.2023.1126567] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.
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Affiliation(s)
- Mohini Kajla
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Jagdish Chandra Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India
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28
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Praveen A, Dubey S, Singh S, Sharma VK. Abiotic stress tolerance in plants: a fascinating action of defense mechanisms. 3 Biotech 2023; 13:102. [PMID: 36866326 PMCID: PMC9971429 DOI: 10.1007/s13205-023-03519-w] [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: 09/15/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Climate fluctuation mediated abiotic stress consequences loss in crop yields. These stresses have a negative impact on plant growth and development by causing physiological and molecular changes. In this review, we have attempted to outline recent studies (5 years) associated with abiotic stress resistance in plants. We investigated the various factors that contribute to coping with abiotic challenges, such as transcription factors (TFs), microRNAs (miRNAs), epigenetic changes, chemical priming, transgenic breeding, autophagy, and non-coding RNAs. Stress responsive genes are regulated mostly by TFs, and these can be used to enhance stress resistance in plants. Plants express some miRNA during stress imposition that act on stress-related target genes to help them survive. Epigenetic alterations govern gene expression and facilitate stress tolerance. Chemical priming enhances growth in plants by modulating physiological parameters. Transgenic breeding enables identification of genes involved in precise plant responses during stressful situations. In addition to protein coding genes, non-coding RNAs also influence the growth of the plant by causing alterations at gene expression levels. For achieving sustainable agriculture for a rising world population, it is crucial to develop abiotic-resistant crops with anticipated agronomical traits. To achieve this objective, understanding the diverse mechanisms by which plants protect themselves against abiotic stresses is imperative. This review emphasizes on recent progress and future prospects for abiotic stress tolerance and productivity in plants.
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Affiliation(s)
- Afsana Praveen
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Yamuna Expressway, Sector 17A, Gautam Budh Nagar, Uttar Pradesh 203201 India
| | - Sonali Dubey
- National Botanical Research Institute, Uttar Pradesh, Lukhnow, 226001 India
| | - Shilpy Singh
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Yamuna Expressway, Sector 17A, Gautam Budh Nagar, Uttar Pradesh 203201 India
| | - Varun Kumar Sharma
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Yamuna Expressway, Sector 17A, Gautam Budh Nagar, Uttar Pradesh 203201 India
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Wang Y, Zhao H, Xu L, Zhang H, Xing H, Fu Y, Zhu L. PUB30-mediated downregulation of the HB24-SWEET11 module is involved in root growth inhibition under salt stress by attenuating sucrose supply in Arabidopsis. THE NEW PHYTOLOGIST 2023; 237:1667-1683. [PMID: 36444526 DOI: 10.1111/nph.18635] [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: 10/29/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
One of the strategies that plants adopt to cope with an unfavorable environment is to sacrifice their growth for tolerance. Although moderate salt stress can induce root growth inhibition, the molecular mechanisms regulating this process have yet to be elucidated. Here, we found that overexpression of a zinc finger-homeodomain family transcription factor, HOMEOBOX PROTEIN 24 (HB24), led to longer primary roots than in the wild-type in the presence of 125 mM NaCl, whereas this phenotype was reversed for the hb24 loss-of-function mutant, indicating a negative impact of HB24 on salt-induced root growth inhibition. We then found that salt stress triggered the degradation of HB24 via the ubiquitin-proteasome pathway, as mediated by a plant U-box type E3 ubiquitin ligase 30 (PUB30) that directly targets HB24. We verified that HB24 is able to directly bind to the promoters of Sugars Will Eventually be Exported Transporter 11/12 (SWEET11/12) to regulate their expression in roots. Through genetic and biochemical assays, we further demonstrated that the HB24-SWEET11 module plays a negative role in salt-induced root growth inhibition. Therefore, we propose that under salt stress, PUB30 mediates HB24's degradation, thereby downregulating the expression of SWEET11, resulting in reduced sucrose supply and root growth inhibition.
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Affiliation(s)
- Yutao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huan Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Liyuan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hantao Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hongjie Xing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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30
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Chen N, Pan L, Yang Z, Su M, Xu J, Jiang X, Yin X, Wang T, Wan F, Chi X. A MYB-related transcription factor from peanut, AhMYB30, improves freezing and salt stress tolerance in transgenic Arabidopsis through both DREB/CBF and ABA-signaling pathways. FRONTIERS IN PLANT SCIENCE 2023; 14:1136626. [PMID: 36925750 PMCID: PMC10013196 DOI: 10.3389/fpls.2023.1136626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/14/2023] [Indexed: 06/12/2023]
Abstract
Abiotic stresses such as salinity and low temperature have serious impact on peanut growth and yield. The present work investigated the function of a MYB-related transcription factor gene AhMYB30 obtained from peanut under salt and low temperature stresses by transgenic methods. The results indicated that the overexpression of AhMYB30 in Arabidopsis could enhance the resistance of transgenic plants to freezing and salt stresses. The expression of stress-response genes RD29A (Response-to-Dehydration 29A), COR15A (Cold-Regulated 15A), KIN1 (Kinesin 1) and ABI2 (Abscisic acid Insensitive 2) increased in transgenic plants compared with in wild-type. Subcellular localization and transcriptional autoactivation validation demonstrated that AhMYB30 has essential features of transcription factors. Therefore, AhMYB30 may increase salt and freezing stress tolerance as the transcription factor (TF) in Arabidopsis through both DREB/CBF and ABA-signaling pathways. Our results lay the theoretical foundation for exploring stress resistance mechanisms of peanut and offering novel genetic resources for molecular breeding.
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Affiliation(s)
- Na Chen
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Lijuan Pan
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Zhen Yang
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Maowen Su
- Department of Animal and Plant Quarantine, Qingdao Customs, Qingdao, China
| | - Jing Xu
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Xiao Jiang
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Xiangzhen Yin
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Tong Wang
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
| | - Feifei Wan
- Division for Guidance of Cooperative Economy, Binzhou Agricultural Technology Extension Center, Binzhou, China
| | - Xiaoyuan Chi
- Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Peanut Research Institute, Qingdao, China
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Liu H, Zhou C, Nisa ZU, El-Kassaby YA, Li W. Exogenous 6-BA inhibited hypocotyl elongation under darkness in Picea crassifolia Kom revealed by transcriptome profiling. FRONTIERS IN PLANT SCIENCE 2023; 14:1086879. [PMID: 36923127 PMCID: PMC10009258 DOI: 10.3389/fpls.2023.1086879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Hypocotyl elongation is an important process in plant growth and development, and is under hormonal regulatory signaling pathways. In our study, exogenous 6-BA significantly inhibited Picea crassifolia hypocotyl elongation more than ethylene in the dark, indicating the existence of different regulatory strategies in conifers, therefore, the P. crassifolia transcriptome was studied to explore the responsive genes and their regulatory pathways for exogenous N6-benzyladenine (6-BA) inhibition of hypocotyl elongation using RNA-Sequencing approach. We present the first transcriptome assembly of P. crassifolia obtained from 24.38 Gb clean data. With lowly-expressed and short contigs excluded, the assembly contains roughly 130,612 unigenes with an N50 length of 1,278 bp. Differential expression analysis found 3,629 differentially expressed genes (DEGs) and found that the differential expression fold of genes was mainly concentrated between 2 and 8 (1 ≤ log2FoldChange ≤ 3). Functional annotation showed that the GO term with the highest number of enriched genes (83 unigenes) was the shoot system development (GO: 0048367) and the KEGG category, plant hormone signal transduction (ko04075), was enriched 30 unigenes. Further analysis revealed that several cytokinin dehydrogenase genes (PcCTD1, PcCTD3 and PcCTD6) catabolized cytokinins, while xyloglucan endotransglucosylase hydrolase gene (PcXTH31), WALLS ARE THIN 1-like gene (PcWAT1-1) and Small auxin-induced gene (PcSAUR15) were strongly repressed thus synergistically completing the inhibition of hypocotyl elongation in P. crassifolia. Besides, PcbHLH149, PcMYB44 and PcERF14 were predicted to be potential core TFs that may form a multi-layered regulatory network with the above proteins for the regulation of hypocotyl growth.
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Affiliation(s)
- Hongmei Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Chengcheng Zhou
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zaib Un Nisa
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Cotton Research Institute, Multan, Punjab, Pakistan
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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32
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Jia S, Liu X, Wen X, Waheed A, Ding Y, Kahar G, Li X, Zhang D. Genome-Wide Identification of bHLH Transcription Factor Family in Malus sieversii and Functional Exploration of MsbHLH155.1 Gene under Valsa Canker Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:620. [PMID: 36771705 PMCID: PMC9919239 DOI: 10.3390/plants12030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/15/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Xinjiang wild apple (Malus sieversii) is an ancient relic; a plant with abundant genetic diversity and disease resistance. Several transcription factors were studied in response to different biotic and abiotic stresses on the wild apple. Basic/helix-loop-helix (bHLH) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, no study has yet been conducted on the bHLH gene in M. sieversii. Based on the genome of M. sieversii, 184 putative MsbHLH genes were identified, and their physicochemical properties were studied. MsbHLH covered 23 subfamilies and lacked two subfamily genes of Arabidopsis thaliana based on the widely used classification method. Moreover, MsbHLH exon-intron structures matched subfamily classification, as evidenced by the analysis of their protein motifs. The analysis of cis-acting elements revealed that many MsbHLH genes share stress- and hormone-related cis-regulatory elements. These MsbHLH transcription factors were found to be involved in plant defense responses based on the protein-protein interactions among the differentially expressed MsbHLHs. Furthermore, 94 MsbHLH genes were differentially expressed in response to pathogenic bacteria. The qRT-PCR results also showed differential expression of MsbHLH genes. To further verify the gene function of bHLH, our study used the transient transformation method to obtain the overexpressed MsbHLH155.1 transgenic plants and inoculated them. Under Valsa canker infection, the lesion phenotype and physiological and biochemical indexes indicated that the antioxidant capacity of plants could increase and reduce the damage caused by membrane peroxidation. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of bHLH genes in M. sieversii and lays a foundation for a better understanding disease resistance in plants, as well as providing candidate genes for the development of M. sieversii resistance breeding.
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Affiliation(s)
- Shanshan Jia
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xiaojie Liu
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Xuejing Wen
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Abdul Waheed
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Yu Ding
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Gulnaz Kahar
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xiaoshuang Li
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Daoyuan Zhang
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
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Ding Y, Wang X, Wang D, Jiang L, Xie J, Wang T, Song L, Zhao X. Identification of CmbHLH Transcription Factor Family and Excavation of CmbHLHs Resistant to Necrotrophic Fungus Alternaria in Chrysanthemum. Genes (Basel) 2023; 14:genes14020275. [PMID: 36833202 PMCID: PMC9957535 DOI: 10.3390/genes14020275] [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: 12/22/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
Chrysanthemum morifolium Ramat. 'Huaihuang' is a traditional Chinese medicinal plant. However, a black spot disease caused by Alternaria sp., a typical necrotrophic fungus, has a serious damaging influence on the field growth, yield, and quality of the plant. 'Huaiju 2#' being bred from 'Huaihuang', shows resistance to Alternaria sp. bHLH transcription factor has been widely studied because of their functions in growth development, signal transduction, and abiotic stress. However, the function of bHLH in biotic stress has rarely been studied. To characterize the resistance genes, the CmbHLH family was surveyed in 'Huaiju 2#'. On the basis of the transcriptome database of 'Huaiju 2#' after Alternaria sp. inoculation, with the aid of the Chrysanthemum genome database, 71 CmbHLH genes were identified and divided into 17 subfamilies. Most (64.8%) of the CmbHLH proteins were rich in negatively charged amino acids. CmbHLH proteins are generally hydrophilic proteins with a high aliphatic amino acid content. Among the 71 CmbHLH proteins, five CmbHLHs were significantly upregulated by Alternaria sp. infection, and the expression of CmbHLH18 was the most significant. Furthermore, heterologous overexpression of CmbHLH18 could improve the resistance of Arabidopsis thaliana to necrotrophic fungus Alternaria brassicicola by enhancing callose deposition, preventing spores from entering leaves, reducing ROS accumulation, increasing the activities of antioxidant enzymes and defense enzymes, and promoting their gene expression levels. These results indicate that the five CmbHLHs, especially CmbHLH18, may be considered candidate genes for resistance to necrotrophic fungus. These findings not only increase our understanding of the role CmbHLHs play in biotic stress but also provide a basis by using CmbHLHs to breed a new variety of Chrysanthemum with high resistance to necrotrophic fungus.
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Affiliation(s)
- Yifeng Ding
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xiaomeng Wang
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Dandan Wang
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Liwei Jiang
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Jing Xie
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Tianle Wang
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Lingyu Song
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xiting Zhao
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, Xinxiang 453007, China
- Engineering Laboratory of Biotechnology for Green Medicinal Plant of Henan Province, Xinxiang 453007, China
- Correspondence: or ; Tel.: +86-182-3739-1085 or +86-135-6988-6182
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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: 7] [Impact Index Per Article: 7.0] [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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Zhang S, Gao H, Wang L, Zhang Y, Zhou D, Anwar A, Li J, Wang F, Li C, Zhang Y, Gao J. Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage ( Brassica rapa L. ssp. Pekinensis). PLANTS (BASEL, SWITZERLAND) 2022; 11:3555. [PMID: 36559667 PMCID: PMC9785529 DOI: 10.3390/plants11243555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Chinese cabbage tipburn is characterized by the formation of necrotic lesions on the margin of leaves, including on the insides of the leafy head. This physiological disorder is associated with a localized calcium deficiency during leaf development. However, little information is available regarding the molecular mechanisms governing Ca-deficiency-triggered tipburn. This study comprehensively analysed the transcriptomic comparison between control and calcium treatments (CK and 0 mM Ca) in Chinese cabbage to determine its molecular mechanism in tipburn. Our analysis identified that the most enriched gene ontology (GO) categories are photosynthesis, thylakoid and cofactor binding. Moreover, the KEGG pathway was most enriched in photosynthesis, carbon metabolism and carbon fixation. We also analyzed the co-expression network by functional categories and identified ten critical hub differentially expressed genes (DEGs) in each gene regulatory network (GRN). These DEGs might involve abiotic stresses, developmental processes, cell wall metabolism, calcium distribution, transcription factors, plant hormone biosynthesis and signal transduction pathways. Under calcium deficiency, CNX1, calmodulin-binding proteins and CMLs family proteins were downregulated compared to CK. In addition, plant hormones such as GA, JA, BR, Auxin and ABA biosynthesis pathways genes were downregulated under calcium treatment. Likewise, HATs, ARLs and TCP transcription factors were reported as inactive under calcium deficiency, and potentially involved in the developmental process. This work explores the specific DEGs' significantly different expression levels in 0 mM Ca and the control involved in plant hormones, cell wall developments, a light response such as chlorophylls and photosynthesis, transport metabolism and defence mechanism and redox. Our results provide critical evidence of the potential roles of the calcium signal transduction pathway and candidate genes governing Ca-deficiency-triggered tipburn in Chinese cabbage.
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Affiliation(s)
- Shu Zhang
- Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Hanzhong Gao
- Columbian College of Arts & Sciences, Phillips Hall, The George Washington University, 801 22nd St. NW., Washington, DC 20052, USA
| | - Lixia Wang
- Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yihui Zhang
- Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Life Sciences, Shandong Normal University, Jinan 250061, China
| | - Dandan Zhou
- College of Life Sciences, Shandong Normal University, Jinan 250061, China
| | - Ali Anwar
- Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jingjuan Li
- Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Fengde Wang
- Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Cheng Li
- Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ye Zhang
- College of Life Science, Huangshan University, Huangshan 245061, China
| | - Jianwei Gao
- Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China
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Cao H, Yang Z, Song S, Xue M, Liang G, Li N. Transcriptome analysis reveals genes potentially related to maize resistance to Rhizoctonia solani. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 193:78-89. [PMID: 36343463 DOI: 10.1016/j.plaphy.2022.10.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 08/31/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Banded leaf and sheath blight (BLSB) is a devasting disease caused by the necrotrophic fungus Rhizoctonia solani that affects maize (Zea mays L.) fields worldwide, especially in China and Southeast Asia. Understanding how maize plants respond to R. solani infection is a key step towards controlling the spread of this fungal pathogen. In this study, we determined the transcriptome of maize plants infected by a low-virulence strain (LVS) and a high-virulence strain (HVS) of R. solani for 3 and 5 days by transcriptome deep-sequencing (RNA-seq). We identified 3,015 (for LVS infection) and 1,628 (for HVS infection) differentially expressed genes (DEGs). We confirmed the expression profiles of 10 randomly selected DEGs by quantitative reverse transcription PCR. We also performed a Gene Ontology (GO) enrichment analysis to establish which biological processes are associated with these DEGs, which revealed the enrichment of defense-related GO terms in LVS- and HVS-regulated genes. We selected 388 DEGs upregulated upon fungal infection as possible candidate genes. Among them, the overexpression of ZmNAC41 (encoding NAC transcription factor 41) or ZmBAK1 (encoding BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) in rice enhanced resistance to R. solani. In addition, overexpressing ZmBAK1 in rice also increased plant height, plant weight, thousand-grain weight, and grain length. The identification of 388 potential key maize genes related to resistance to R. solani provides significant insights into improving BLSB resistance.
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Affiliation(s)
- Hongxiang Cao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai an, 271018, China
| | - Zhangshuai Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai an, 271018, China
| | - Shu Song
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai an, 271018, China
| | - Min Xue
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai an, 271018, China
| | - Guanyu Liang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai an, 271018, China
| | - Ning Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai an, 271018, China.
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Pang F, Niu J, Solanki MK, Nosheen S, Liu Z, Wang Z. PHD-finger family genes in wheat ( Triticum aestivum L.): Evolutionary conservatism, functional diversification, and active expression in abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1016831. [PMID: 36578331 PMCID: PMC9791960 DOI: 10.3389/fpls.2022.1016831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Plant homeodomain (PHD) transcription factors (TFs) are a class of proteins with conserved Cys4-His-Cys3 domains that play important roles in plant growth and development and in response to abiotic stresses. Although characterization of PHDs has been performed in plants, little is known about their function in wheat (Triticum aestivum L.), especially under stress conditions. In the present study, 244 TaPHDs were identified in wheat using comparative genomics. We renamed them TaPHD1-244 based on their chromosomal distribution, and almost all PHD proteins were predicted to be located in the nucleus. According to the unrooted neighbor-joining phylogenetic tree, gene structure, and motif analyses, PHD genes were divided into four clades. A total of 149 TaPHD genes were assigned to arise from duplication events. Furthermore, 230 gene pairs came from wheat itself, and 119, 186, 168, 7, 2, and 6 gene pairs came from six other species (Hordeum vulgareto, Zea mays, Oryza sativa, Arabidopsis thaliana, Brassica rapa, and Gossypium raimondii, respectively). A total of 548 interacting protein branches were identified to be involved in the protein interaction network. Tissue-specific expression pattern analysis showed that TaPHDs were highly expressed in the stigma and ovary during flowering, suggesting that the TaPHD gene plays an active role in the reproductive growth of wheat. In addition, the qRT-PCR results further confirmed that these TaPHD genes are involved in the abiotic stress response of wheat. In conclusion, our study provides a theoretical basis for deciphering the molecular functions of TaPHDs, particularly in response to abiotic stress.
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Affiliation(s)
- Fei Pang
- College of Agriculture, Yulin Normal University, Yulin, China
| | - Junqi Niu
- College of Agriculture, Yulin Normal University, Yulin, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Shaista Nosheen
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Zhaoliang Liu
- College of Agriculture, Yulin Normal University, Yulin, China
| | - Zhen Wang
- College of Agriculture, Yulin Normal University, Yulin, China
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Ma D, Cai J, Ma Q, Wang W, Zhao L, Li J, Su L. Comparative time-course transcriptome analysis of two contrasting alfalfa ( Medicago sativa L.) genotypes reveals tolerance mechanisms to salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1070846. [PMID: 36570949 PMCID: PMC9773191 DOI: 10.3389/fpls.2022.1070846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Salt stress is a major abiotic stress affecting plant growth and crop yield. For the successful cultivation of alfalfa (Medicago sativa L.), a key legume forage, in saline-affected areas, it's essential to explore genetic modifications to improve salt-tolerance.Transcriptome assay of two comparative alfalfa genotypes, Adina and Zhaodong, following a 4 h and 8 h's 300 mM NaCl treatment was conducted in this study in order to investigate the molecular mechanism in alfalfa under salt stress conditions. Results showed that we obtained 875,023,571 transcripts and 662,765,594 unigenes were abtained from the sequenced libraries, and 520,091 assembled unigenes were annotated in at least one database. Among them, we identified 1,636 differentially expression genes (DEGs) in Adina, of which 1,426 were up-regulated and 210 down-regulated, and 1,295 DEGs in Zhaodong, of which 565 were up-regulated and 730 down-regulated. GO annotations and KEGG pathway enrichments of the DEGs based on RNA-seq data indicated that DEGs were involved in (1) ion and membrane homeostasis, including ABC transporter, CLC, NCX, and NHX; (2) Ca2+ sensing and transduction, including BK channel, EF-hand domain, and calmodulin binding protein; (3) phytohormone signaling and regulation, including TPR, FBP, LRR, and PP2C; (4) transcription factors, including zinc finger proteins, YABBY, and SBP-box; (5) antioxidation process, including GST, PYROX, and ALDH; (6) post-translational modification, including UCH, ubiquitin family, GT, MT and SOT. The functional roles of DEGs could explain the variations in salt tolerance performance observed between the two alfalfa genotypes Adina and Zhaodong. Our study widens the understanding of the sophisticated molecular response and tolerance mechanism to salt stress, providing novel insights on candidate genes and pathways for genetic modification involved in salt stress adaptation in alfalfa.
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Affiliation(s)
- Dongmei Ma
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jinjun Cai
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Qiaoli Ma
- Agricultural College, Ningxia University, Yinchuan, China
| | - Wenjing Wang
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Lijuan Zhao
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jiawen Li
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Lina Su
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
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Dong R, Luo B, Tang L, Wang QX, Lu ZJ, Chen C, Yang F, Wang S, He J. A comparative transcriptomic analysis reveals a coordinated mechanism activated in response to cold acclimation in common vetch (Vicia sativa L.). BMC Genomics 2022; 23:814. [PMID: 36482290 PMCID: PMC9733113 DOI: 10.1186/s12864-022-09039-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Due to its strong abiotic stress tolerance, common vetch is widely cultivated as a green manure and forage crop in grass and crop rotation systems. The comprehensive molecular mechanisms activated in common vetch during cold adaptation remain unknown. RESULTS We investigated physiological responses and transcriptome profiles of cold-sensitive (Lanjian No. 1) and cold-tolerant (Lanjian No. 3) cultivars during cold acclimation to explore the molecular mechanisms of cold acclimation. In total, 2681 and 2352 differentially expressed genes (DEGs) were identified in Lanjian No. 1 and Lanjian No. 3, respectively; 7532 DEGs were identified in both lines. DEGs involved in "plant hormone signal transduction" were significantly enriched during cold treatment, and 115 DEGs involved in cold-processed hormone signal transduction were identified. Common vetch increased the level of indoleacetic acid (IAA) by upregulating the transcriptional regulator Aux/IAA and downregulating GH3, endowing it with stronger cold tolerance. An auxin-related DEG was overexpressed in yeast and shown to possess a biological function conferring cold tolerance. CONCLUSION This study identifies specific genes involved in Ca2+ signaling, redox regulation, circadian clock, plant hormones, and transcription factors whose transcriptional differentiation during cold acclimation may improve cold tolerance and contributes to the understanding of common and unique molecular mechanisms of cold acclimation in common vetch. The candidate genes identified here also provide valuable resources for further functional genomic and breeding studies.
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Affiliation(s)
- Rui Dong
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Ben Luo
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Li Tang
- grid.428986.90000 0001 0373 6302School of Tropical Crops, Hainan University, Haikou, China
| | - Qiu-xia Wang
- grid.32566.340000 0000 8571 0482State Key Laboratory of Grassland Agro-ecosystems, China, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhong-Jie Lu
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Chao Chen
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Feng Yang
- Grassland Technology Experiment and Extension Station, Guiyang, China
| | - Song Wang
- Grassland Technology Experiment and Extension Station, Guiyang, China
| | - Jin He
- grid.443382.a0000 0004 1804 268XCollege of Agriculture, Guizhou University, Guiyang, China
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Hu Y, Zhang H, Gu B, Zhang J. The transcription factor VaMYC2 from Chinese wild Vitis amurensis enhances cold tolerance of grape (V. vinifera) by up-regulating VaCBF1 and VaP5CS. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 192:218-229. [PMID: 36272189 DOI: 10.1016/j.plaphy.2022.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/26/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Cultivated grapes, one of the most important fruit crops in the world, are sensitive to low temperature. Since Chinese wild grape Vitis amurensis is highly tolerant to cold, it is imperative to study and utilize its cold-tolerance genes for molecular breeding. Here, a VaMYC2 gene from V. amurensis was cloned, and its function was investigated by expressing VaMYC2 in the cold-sensitive V. vinifera cultivar 'Thompson Seedless'. The expression of VaMYC2 could be induced by cold stress, methyl jasmonate and ethylene treatment, but was inhibited by abscisic acid in leaves of V. amurensis. When transgenic grape lines expressing VaMYC2 were subjected to cold stress (-1 °C) for 41 h, the transgenic lines showed less freezing injury and lower electrolyte leakage and malondialdehyde content, but higher contents of soluble sugars, soluble proteins and proline, and antioxidant enzyme activities compared with wild-type. Moreover, the expression of some cold-tolerance related genes increased in transgenic lines. Besides, the interactions of VaMYC2 with VaJAZ1 and VaJAZ7B were confirmed by yeast two-hybrid and bimolecular fluorescence complementation assays. Yeast one-hybrid and dual luciferase assays showed that VaMYC2 can bind to the promoters of VaCBF1 and VaP5CS and activate their expressions. In conclusion, expression of VaMYC2 in V. vinifera enhances cold tolerance of transgenic grapes which is attributed to enhanced accumulation of osmotic regulatory substances, cell membrane stability, antioxidant enzyme activity, and expression of cold tolerance-related genes. Also, VaMYC2 interacts with VaJAZ1 and VaJAZ7, and activates the expression of VaCBF1 and VaP5CS to mediate cold tolerance in grapes.
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Affiliation(s)
- Yafan Hu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Hongjuan Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Bao Gu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jianxia Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Molecular cloning and functional characterization of MhHEC2-like genes in Malus halliana reveals it enhances Fe (iron) deficiency tolerance. Funct Integr Genomics 2022; 22:1283-1295. [DOI: 10.1007/s10142-022-00917-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022]
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Hussain MA, Luo D, Zeng L, Ding X, Cheng Y, Zou X, Lv Y, Lu G. Genome-wide transcriptome profiling revealed biological macromolecules respond to low temperature stress in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2022; 13:1050995. [PMID: 36452101 PMCID: PMC9702069 DOI: 10.3389/fpls.2022.1050995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/14/2022] [Indexed: 06/12/2023]
Abstract
Brassica napus L. (B. napus) is a vital oilseed crop cultivated worldwide; low temperature (LT) is one of the major stress factors that limit its growth, development, distribution, and production. Even though processes have been developed to characterize LT-responsive genes, only limited studies have exploited the molecular response mechanisms in B. napus. Here the transcriptome data of an elite B. napus variety with LT adaptability was acquired and applied to investigate the gene expression profiles of B. napus in response to LT stress. The bioinformatics study revealed a total of 79,061 unigenes, of which 3,703 genes were differentially expressed genes (DEGs), with 2,129 upregulated and 1,574 downregulated. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis pinpointed that the DEGs were enriched in LT-stress-responsive biological functions and metabolic pathways, which included sugar metabolism, antioxidant defense system, plant hormone signal transduction, and photosynthesis. Moreover, a group of LT-stress-responsive transcription factors with divergent expression patterns under LT was summarized. A combined protein interaction suggested that a complex interconnected regulatory network existed in all detected pathways. RNA-seq data was verified using real-time quantitative polymerase chain reaction analysis. Based on these findings, we presented a hypothesis model illustrating valuable information for understanding the LT response mechanisms in B. napus.
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Affiliation(s)
- Muhammad Azhar Hussain
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Dan Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Liu Zeng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiaoyu Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yong Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiling Zou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yan Lv
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Research Institute, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Guangyuan Lu
- School of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
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Deng P, Yan T, Ji W, Zhang G, Wu L, Wu D. Population-level transcriptomes reveal gene expression and splicing underlying cadmium accumulation in barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:847-859. [PMID: 36131686 DOI: 10.1111/tpj.15986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/15/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Abstract
Genetic variation is an important determinant of gene transcription, which in turn contributes to functional and phenotypic diversity. Identification of the genetic variants controlling gene expression and alternative splicing in crops responding to cadmium (Cd), an important issue for food safety and human health, is of great value to improve our understanding of Cd accumulation-related genes. Here we report an in-depth survey of population-level transcriptome variation of barley (Hordeum vulgare) core accessions under Cd exposure. We reveal marked transcriptomic changes in response to Cd exposure, and these are largely independent of tissues. A genome-wide association study (GWAS) revealed 59 498 expression quantitative trait loci (eQTLs) and 23 854 splicing quantitative trait loci (sQTLs), leading to a complex network that covers 66.6% of the expressed genes, including 68 metal transporter genes. On average, 41.0% of sQTLs overlapped with eQTLs across different tissues, indicating that these two dimensions of transcript variation are largely independent. Moreover, we found that 34.5% of GWAS QTLs that underlie 10 Cd accumulation traits in barley are co-localized with eQTLs and sQTLs, which could imply a mechanistic role of different genetic variants affecting gene expression and alternative splicing in these traits. This study highlights the role of distal and proximal genetic effects on gene expression, splicing, and phenotypic plasticity. We anticipate that our results on the genetic control of expression and splicing underlying Cd accumulation provide a bridge to better understand genetic variation and phenotypic diversity to elucidate the mechanisms underlying Cd accumulation in plants.
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Affiliation(s)
- Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guoping Zhang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Liang Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Dezhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
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Zhao L, Zhu Y, Jia H, Han Y, Zheng X, Wang M, Feng W. From Plant to Yeast-Advances in Biosynthesis of Artemisinin. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27206888. [PMID: 36296479 PMCID: PMC9609949 DOI: 10.3390/molecules27206888] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/28/2022]
Abstract
Malaria is a life-threatening disease. Artemisinin-based combination therapy (ACT) is the preferred choice for malaria treatment recommended by the World Health Organization. At present, the main source of artemisinin is extracted from Artemisia annua; however, the artemisinin content in A. annua is only 0.1-1%, which cannot meet global demand. Meanwhile, the chemical synthesis of artemisinin has disadvantages such as complicated steps, high cost and low yield. Therefore, the application of the synthetic biology approach to produce artemisinin in vivo has magnificent prospects. In this review, the biosynthesis pathway of artemisinin was summarized. Then we discussed the advances in the heterologous biosynthesis of artemisinin using microorganisms (Escherichia coli and Saccharomyces cerevisiae) as chassis cells. With yeast as the cell factory, the production of artemisinin was transferred from plant to yeast. Through the optimization of the fermentation process, the yield of artemisinic acid reached 25 g/L, thereby producing the semi-synthesis of artemisinin. Moreover, we reviewed the genetic engineering in A. annua to improve the artemisinin content, which included overexpressing artemisinin biosynthesis pathway genes, blocking key genes in competitive pathways, and regulating the expression of transcription factors related to artemisinin biosynthesis. Finally, the research progress of artemisinin production in other plants (Nicotiana, Physcomitrella, etc.) was discussed. The current advances in artemisinin biosynthesis may help lay the foundation for the remarkable up-regulation of artemisinin production in A. annua through gene editing or molecular design breeding in the future.
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Affiliation(s)
- Le Zhao
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan and Education Ministry of P. R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yunhao Zhu
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan and Education Ministry of P. R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Haoyu Jia
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yongguang Han
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Xiaoke Zheng
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan and Education Ministry of P. R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Min Wang
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
- Beijing Key Laboratory of Plant Research and Development, Beijing Technology and Business University, Beijing 100048, China
- Correspondence: (M.W.); (W.F.); Tel.: +86-134-2629-2115 (M.W.); +86-371-60190296 (W.F.)
| | - Weisheng Feng
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan and Education Ministry of P. R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Correspondence: (M.W.); (W.F.); Tel.: +86-134-2629-2115 (M.W.); +86-371-60190296 (W.F.)
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Godbole RC, Pable AA, Singh S, Barvkar VT. Interplay of transcription factors orchestrating the biosynthesis of plant alkaloids. 3 Biotech 2022; 12:250. [PMID: 36051988 PMCID: PMC9424429 DOI: 10.1007/s13205-022-03316-x] [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: 04/11/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Plants produce a range of secondary metabolites primarily as defence molecules. A plant has to invest considerable energy to synthesise alkaloids, and sometimes they are even toxic to themselves. Hence, the biosynthesis of alkaloids is a spatiotemporally regulated process under quantitative feedback regulation which is accomplished by the signal reception, transcriptional/translational regulation, transport, storage and accumulation. The transcription factors (TFs) initiate the biosynthesis of alkaloids after appropriate cues. The present study recapitulates last decade understanding of the role of TFs in alkaloid biosynthesis. The present review discusses TF families, viz. AP2/ERF, bHLH, WRKY, MYB involved in the biosynthesis of various types of alkaloids. It also highlights the role of the jasmonic acid cascade and post-translational modifications of TF proteins. A thorough understanding of TFs will help us to decide a strategy to facilitate successful pathway manipulation and in vitro production.
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Affiliation(s)
- Rucha C. Godbole
- Department of Botany, Savitribai Phule Pune University, Pune, 411007 India
| | - Anupama A. Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007 India
| | - Sudhir Singh
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre (BARC), Mumbai, 400085 India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094 India
| | - Vitthal T. Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007 India
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Liu W, Yi Y, Zhuang J, Ge C, Cao Y, Zhang L, Liu M. Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree ( Vernicia fordii). PeerJ 2022; 10:e13981. [PMID: 36193421 PMCID: PMC9526410 DOI: 10.7717/peerj.13981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/10/2022] [Indexed: 01/19/2023] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. However, the characteristics of the bHLH gene family in the tung tree genome are still unclear. Hence, VfbHLHs were first searched at a genome-wide level, and their expression levels in various tissues or under low temperature were investigated systematically. In this study, we identified 104 VfbHLHs in the tung tree genome, and these genes were classified into 18 subfamilies according to bHLH domains. Ninety-eight VfbHLHs were mapped to but not evenly distributed on 11 pseudochromosomes. The domain sequences among VfbHLHs were highly conserved, and their conserved residues were also identified. To explore their expression, we performed gene expression profiling using RNA-Seq and RT-qPCR. We identified five, 18 and 28 VfbHLH genes in female flowers, male flowers and seeds, respectively. Furthermore, we found that eight genes (VfbHLH29, VfbHLH31, VfbHLH47, VfbHLH51, VfbHLH57, VfbHLH59, VfbHLH70, VfbHLH72) were significant differential expressed in roots, leaves and petioles under low temperature stress. This study lays the foundation for future studies on bHLH gene cloning, transgenes, and biological mechanisms.
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Affiliation(s)
- Wenjuan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Yaqi Yi
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Jingyi Zhuang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Chang Ge
- School of Urban Design, Wuhan University, Wuhan, Hubei, China
| | - Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Meilan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
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Chen Y, Xiang Y, Hu Z, Gao Y, Zhang Y, Chen M, Khaldun ABM, Yan X, Fan J. Transcriptomic profiling revealed the role of 24-epibrassinolide in alleviating salt stress damage in tall fescue ( Festuca arundinacea). FRONTIERS IN PLANT SCIENCE 2022; 13:976341. [PMID: 36212305 PMCID: PMC9540362 DOI: 10.3389/fpls.2022.976341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Soil salinization is a major problem all over the world. The accumulation of salt in soil reduces the root water uptake and directly affects plant growth and metabolic activities. Brassinosteroid is a plant hormone that plays an important role in regulation of plant growth and physiological process, including promotion of cell expansion and elongation, signal transduction and stress response. Exogenous 24-epibrassinolide (EBL) has been proved to alleviate various environmental stress in plants. However, the role that EBL plays in salt stress response is still unknown in tall fescue (Festuca arundinacea). In this study, the physiology and molecular mechanisms regulated by exogenous EBL of salt stress response in tall fescue was investigated. Tall fescue plants were divided into four groups, including control (CK), NaCl solution (SALT), 24-epibrassinolide (EBL), NaCl solution + 24-epibrassinolide (SE). During the growth period of tall fescue, we found that electrolyte leakage (EL) and malondialdehyde (MDA) were decreased, chlorophyll (Chl) content and antioxidant enzyme activity were increased in leaves of tall fescue in SE group compared with SALT group, indicating that EBL improved the salt tolerance in grasses. Transcriptomic profiling analysis showed that after 12 h of treatments, 10,265, 13,830 and 10,537 differential genes were expressed in EBL, SALT, and SE groups compared with control, respectively. These differentially expressed genes (DEGs) mainly focused on binding, catalytic activity, cellular process, metabolic process, cellular anatomical entity. Moreover, most of the differential genes were expressed in the plant hormone signal transduction pathway. These results helped us to better understand the mechanism of exogenous 24-epibrassinolide to improve the salt tolerance of tall fescue.
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Affiliation(s)
- Yao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yuanhang Xiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhengrong Hu
- Hunan Tobacco Research Institute, Changsha, China
| | - Yang Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Youxin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Minghui Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | | | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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49
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Wang X, Wang Y, Yan S, Sun X, Liu H, Cheng B, Xu X, Wei Z, Zhang G. A multifaceted comparison between the fruit-abscission and fruit-retention cultivars in ornamental crabapple. FRONTIERS IN PLANT SCIENCE 2022; 13:1013263. [PMID: 36212288 PMCID: PMC9535355 DOI: 10.3389/fpls.2022.1013263] [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: 08/06/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
The ornamental crabapple is a multipurpose landscaping tree that bears brilliant fruit throughout the winter. However, whether or not its fruit persists after maturation is specifically correlated to cultivar characteristics. In this work, we screened two different types that display fruit-retention ("Donald Wyman," "Red Jewel," and "Sugar Tyme") and fruit-abscission ("Radiant" and "Flame") in Northern China across the whole winter using multi-year successional records. Fruit-abscission was determined predominantly by the abscission zone established at the base of the pedicel, regardless of fruit size and pedicel length, according to the results of the comparative research. The primary physiological rationale was the accumulation of hydrolases activity (pectinesterase, cellulase, polygalacturonase, and β-glucosidase). Comparative transcriptomics further identified a number of upregulated DEGs involved in the synthesis pathways of canonical phytohormones, such as ethylene, jasmonic acid, abscisic acid, and cytokinin, as well as 12 transcription factors linked in downstream signaling in fruit-abscission cultivars. Finally, a model incorporating multi-layered modulation was proposed for the fruit abscission of ornamental crabapple. This study will serve as the foundation for the development of fruit-viewing crabapples that have an extended ornamental lifetime.
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Affiliation(s)
- Xue Wang
- College of Horticultural Science and Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Institute of Grassland Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shufang Yan
- Hebei Academy of Forestry and Grassland Sciences, Hebei Forest City Construction Technology Innovation Center, Shijiazhuang, China
| | - Xuan Sun
- Institute of Grassland Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hongyan Liu
- Institute of Grassland Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Beibei Cheng
- College of Horticultural Science and Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xingxing Xu
- College of Horticultural Science and Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Zunzheng Wei
- Institute of Grassland Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Guojun Zhang
- College of Horticultural Science and Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Hebei Normal University of Science and Technology, Qinhuangdao, China
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50
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Liu C, Leng J, Li Y, Ge T, Li J, Chen Y, Guo C, Qi J. A spatiotemporal atlas of organogenesis in the development of orchid flowers. Nucleic Acids Res 2022; 50:9724-9737. [PMID: 36095130 PMCID: PMC9508851 DOI: 10.1093/nar/gkac773] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/19/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022] Open
Abstract
Development of floral organs exhibits complex molecular mechanisms involving the co-regulation of many genes specialized and precisely functioning in various tissues and developing stages. Advance in spatial transcriptome technologies allows for quantitative measurement of spatially localized gene abundance making it possible to bridge complex scenario of flower organogenesis with genome-wide molecular phenotypes. Here, we apply the 10× Visium technology in the study of the formation of floral organs through development in an orchid plant, Phalaenopsis Big Chili. Cell-types of early floral development including inflorescence meristems, primordia of floral organs and identity determined tissues, are recognized based on spatial expression distribution of thousands of genes in high resolution. In addition, meristematic cells on the basal position of floral organs are found to continuously function in multiple developmental stages after organ initiation. Particularly, the development of anther, which primordium starts from a single spot to multiple differentiated cell-types in later stages including pollinium and other vegetative tissues, is revealed by well-known MADS-box genes and many other downstream regulators. The spatial transcriptome analyses provide comprehensive information of gene activity for understanding the molecular architecture of flower organogenesis and for future genomic and genetic studies of specific cell-types.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jing Leng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yonglong Li
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Tingting Ge
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Jinglong Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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