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Zheng M, Wang X, Luo J, Ma B, Li D, Chen X. The pleiotropic functions of GOLDEN2-LIKE transcription factors in plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1445875. [PMID: 39224848 PMCID: PMC11366661 DOI: 10.3389/fpls.2024.1445875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
The regulation of gene expression is crucial for biological plant growth and development, with transcription factors (TFs) serving as key switches in this regulatory mechanism. GOLDEN2-LIKE (GLK) TFs are a class of functionally partially redundant nuclear TFs belonging to the GARP superfamily of MYB TFs that play a key role in regulating genes related to photosynthesis and chloroplast biogenesis. Here, we summarized the current knowledge of the pleiotropic roles of GLKs in plants. In addition to their primary functions of controlling chloroplast biogenesis and function maintenance, GLKs have been proven to regulate the photomorphogenesis of seedlings, metabolite synthesis, flowering time, leaf senescence, and response to biotic and abiotic stress, ultimately contributing to crop yield. This review will provide a comprehensive understanding of the biological functions of GLKs and serve as a reference for future theoretical and applied studies of GLKs.
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Affiliation(s)
- Mengyi Zheng
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Xinyu Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Jie Luo
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Bojun Ma
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Dayong Li
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Xifeng Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
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2
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Wang H, Xia L, Chen J, Cheng C. Transcriptome Analysis Reveals the Molecular Mechanism of the Leaf Yellowing in Allotriploid Cucumber. Genes (Basel) 2024; 15:825. [PMID: 39062604 PMCID: PMC11275418 DOI: 10.3390/genes15070825] [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: 04/25/2024] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 07/28/2024] Open
Abstract
Yellowing leaves are ideal materials for studying the metabolic pathways of photosynthetic pigment chloroplast development, and the mechanism of photosynthetic systems. Here, we obtained a triploid material HCC (2n = 3x = 26), which was derived from hybridization between the artificial tetraploid Cucumis × hytivus (2n = 4x = 38, HHCC) and the cultivated cucumber Cucumis sativus (2n = 2x = 14, CC), and this triploid HCC showed obvious leaf yellowing characteristics. Phenotypic observation results showed that chloroplast development was impaired, the chlorophyll content decreased, and photosynthesis decreased in yellowing HCC leaves. The transcriptome results indicated that HCC-GLK is significantly downregulated in HCC and participates in the regulation of leaf yellowing. GO enrichment analysis revealed that differential genes were enriched in the heme binding and tetrapyrrole binding pathways related to leaf color. KEGG enrichment analysis revealed that differential genes were predominantly enriched in photosynthesis-related pathways. The experimental results of VIGS and yeast hybridization showed that silencing the GLK gene can induce leaf yellowing in cucumber plants, and the GLK protein can affect plant chloroplast development by interacting with the CAB3C protein (light-harvesting chlorophyll a/b binding) in the plant chlorophyll synthesis pathway. The current findings have not only enhanced our understanding of the regulatory mechanism of the GLK transcription factor in cucumber but also introduced novel insights and directions for investigating the molecular mechanism underlying polyploid leaf yellowing.
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Affiliation(s)
| | | | | | - Chunyan Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (L.X.); (J.C.)
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3
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Wang H, Xu F. Identification and expression analysis of the GLK gene family in tea plant (Camellia sinensis) and a functional study of CsGLK54 under low-temperature stress. Sci Rep 2024; 14:12465. [PMID: 38816567 PMCID: PMC11139860 DOI: 10.1038/s41598-024-63323-1] [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: 03/22/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
The Golden2-like (GLK) transcription factor family is a significant group of transcription factors in plantae. The currently available studies have shown that GLK transcription factors have been studied mainly in chloroplast growth and development, with fewer studies in abiotic stress regulation. In this study, all tea plant GLK transcription factors were identified for the first time in tea plants, and genome-wide identification, phylogenetic analysis, and thematic characterization were performed to identify 66 GLK transcription factors in tea plants. These genes are categorized into seven groups, and an amino acid sequence comparison analysis is performed. This study revealed that the structure of GLK genes in tea plants is highly conserved and that these genes are distributed across 14 chromosomes. Collinearity analysis revealed 17 pairs of genes with fragment duplications and one pair of genes with tandem duplications, and the analysis of Ka/Ks ratios indicated that most of the genes underwent negative purifying selection. Analysis of promoter cis-elements revealed that the promoters of tea plant GLK genes contain a large number of cis-acting elements related to phytohormones and stress tolerance. In addition, a large number of genes contain LTR elements, suggesting that tea plant GLK genes are involved in low-temperature stress. qRT‒PCR analysis revealed that the expression of CsGLK17, CsGLK38, CsGLK54, CsGLK11 and CsGLK60 significantly increased and that the expression of CsGLK7 and CsGLK13 decreased in response to low-temperature induction. Taken together, the results of the transcription profile analysis suggested that CsGLK54 may play an important regulatory role under low-temperature stress. The subcellular localization of CsGLK54 was in the nucleus. Furthermore, CsGLK54 positively regulated the transcription levels of the NbPOD and NbSOD genes under low-temperature stress, which led to an increase in POD and SOD enzyme activities and a decrease in MDA content. These findings provide valuable insights into the regulatory mechanism of low-temperature stress in tea plants.
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Affiliation(s)
- Hongtao Wang
- Key Laboratory of Landscape Architecture, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Fangfang Xu
- College of Forestry, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
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Yang D, Chen T, Wu Y, Tang H, Yu J, Dai X, Zheng Y, Wan X, Yang Y, Tan X. Genome-wide analysis of the peanut CaM/CML gene family reveals that the AhCML69 gene is associated with resistance to Ralstonia solanacearum. BMC Genomics 2024; 25:200. [PMID: 38378471 PMCID: PMC10880322 DOI: 10.1186/s12864-024-10108-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Calmodulins (CaMs)/CaM-like proteins (CMLs) are crucial Ca2+-binding sensors that can decode and transduce Ca2+ signals during plant development and in response to various stimuli. The CaM/CML gene family has been characterized in many plant species, but this family has not yet been characterized and analyzed in peanut, especially for its functions in response to Ralstonia solanacearum. In this study, we performed a genome-wide analysis to analyze the CaM/CML genes and their functions in resistance to R. solanacearum. RESULTS Here, 67, 72, and 214 CaM/CML genes were identified from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively. The genes were divided into nine subgroups (Groups I-IX) with relatively conserved exon‒intron structures and motif compositions. Gene duplication, which included whole-genome duplication, tandem repeats, scattered repeats, and unconnected repeats, produced approximately 81 pairs of homologous genes in the AhCaM/CML gene family. Allopolyploidization was the main reason for the greater number of AhCaM/CML members. The nonsynonymous (Ka) versus synonymous (Ks) substitution rates (less than 1.0) suggested that all homologous pairs underwent intensive purifying selection pressure during evolution. AhCML69 was constitutively expressed in different tissues of peanut plants and was involved in the response to R. solanacearum infection. The AhCML69 protein was localized in the cytoplasm and nucleus. Transient overexpression of AhCML69 in tobacco leaves increased resistance to R. solanacearum infection and induced the expression of defense-related genes, suggesting that AhCML69 is a positive regulator of disease resistance. CONCLUSIONS This study provides the first comprehensive analysis of the AhCaM/CML gene family and potential genetic resources for the molecular design and breeding of peanut bacterial wilt resistance.
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Affiliation(s)
- Dong Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Ting Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Yushuang Wu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Huiquan Tang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Junyi Yu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Xiaoqiu Dai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Yixiong Zheng
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Xiaorong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Yong Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China.
| | - Xiaodan Tan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China.
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Kumar D, Kirti PB. The genus Arachis: an excellent resource for studies on differential gene expression for stress tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1275854. [PMID: 38023864 PMCID: PMC10646159 DOI: 10.3389/fpls.2023.1275854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Peanut Arachis hypogaea is a segmental allotetraploid in the section Arachis of the genus Arachis along with the Section Rhizomataceae. Section Arachis has several diploid species along with Arachis hypogaea and A. monticola. The section Rhizomataceae comprises polyploid species. Several species in the genus are highly tolerant to biotic and abiotic stresses and provide excellent sets of genotypes for studies on differential gene expression. Though there were several studies in this direction, more studies are needed to identify more and more gene combinations. Next generation RNA-seq based differential gene expression study is a powerful tool to identify the genes and regulatory pathways involved in stress tolerance. Transcriptomic and proteomic study of peanut plants under biotic stresses reveals a number of differentially expressed genes such as R genes (NBS-LRR, LRR-RLK, protein kinases, MAP kinases), pathogenesis related proteins (PR1, PR2, PR5, PR10) and defense related genes (defensin, F-box, glutathione S-transferase) that are the most consistently expressed genes throughout the studies reported so far. In most of the studies on biotic stress induction, the differentially expressed genes involved in the process with enriched pathways showed plant-pathogen interactions, phenylpropanoid biosynthesis, defense and signal transduction. Differential gene expression studies in response to abiotic stresses, reported the most commonly expressed genes are transcription factors (MYB, WRKY, NAC, bZIP, bHLH, AP2/ERF), LEA proteins, chitinase, aquaporins, F-box, cytochrome p450 and ROS scavenging enzymes. These differentially expressed genes are in enriched pathways of transcription regulation, starch and sucrose metabolism, signal transduction and biosynthesis of unsaturated fatty acids. These identified differentially expressed genes provide a better understanding of the resistance/tolerance mechanism, and the genes for manipulating biotic and abiotic stress tolerance in peanut and other crop plants. There are a number of differentially expressed genes during biotic and abiotic stresses were successfully characterized in peanut or model plants (tobacco or Arabidopsis) by genetic manipulation to develop stress tolerance plants, which have been detailed out in this review and more concerted studies are needed to identify more and more gene/gene combinations.
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Affiliation(s)
- Dilip Kumar
- Department of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Pulugurtha Bharadwaja Kirti
- Agri Biotech Foundation, Professor Jayashankar Telangana State (PJTS) Agricultural University, Hyderabad, Telangana, India
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6
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Huang R, Li H, Gao C, Yu W, Zhang S. Advances in omics research on peanut response to biotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1101994. [PMID: 37284721 PMCID: PMC10239885 DOI: 10.3389/fpls.2023.1101994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/18/2023] [Indexed: 06/08/2023]
Abstract
Peanut growth, development, and eventual production are constrained by biotic and abiotic stresses resulting in serious economic losses. To understand the response and tolerance mechanism of peanut to biotic and abiotic stresses, high-throughput Omics approaches have been applied in peanut research. Integrated Omics approaches are essential for elucidating the temporal and spatial changes that occur in peanut facing different stresses. The integration of functional genomics with other Omics highlights the relationships between peanut genomes and phenotypes under specific stress conditions. In this review, we focus on research on peanut biotic stresses. Here we review the primary types of biotic stresses that threaten sustainable peanut production, the multi-Omics technologies for peanut research and breeding, and the recent advances in various peanut Omics under biotic stresses, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics and phenomics, for identification of biotic stress-related genes, proteins, metabolites and their networks as well as the development of potential traits. We also discuss the challenges, opportunities, and future directions for peanut Omics under biotic stresses, aiming sustainable food production. The Omics knowledge is instrumental for improving peanut tolerance to cope with various biotic stresses and for meeting the food demands of the exponentially growing global population.
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Affiliation(s)
- Ruihua Huang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Hongqing Li
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Caiji Gao
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Weichang Yu
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Liaoning Peanut Research Institute, Liaoning Academy of Agricultural Sciences, Fuxing, China
- China Good Crop Company (Shenzhen) Limited, Shenzhen, China
| | - Shengchun Zhang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
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Luo W, Tan J, Li T, Feng Z, Ding Z, Xie X, Chen Y, Chen L, Liu YG, Zhu Q, Guo J. Overexpression of maize GOLDEN2 in rice and maize calli improves regeneration by activating chloroplast development. SCIENCE CHINA. LIFE SCIENCES 2023; 66:340-349. [PMID: 35982378 DOI: 10.1007/s11427-022-2149-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/21/2022] [Indexed: 11/25/2022]
Abstract
Golden2 (G2), a member of the GARP transcription factor superfamily, regulates several biological processes and phytohormone signaling pathways in plants. In this study, we used a rice codon-optimized maize G2 gene (rZmG2) to improve the regeneration efficiency of rice and maize calli for genetic transformation. We isolated a promoter driving strong and callus-specific expression from rice to drive rZmG2 transcription from a transgene after transformation of two indica and two japonica rice cultivars. The resulting rZmG2 transgenic calli turned green in advance at the differentiation stage, thus significantly raising the regeneration rates of the transgenic indica and japonica rice plants relative to control transformations. Similar effect of this gene on improving maize transformation was also observed. Transcriptome sequencing and RT-qPCR analyses showed that many rice genes related to chloroplast development and phytohormones are upregulated in rZmG2-transgenic calli. These results demonstrate that rZmG2 can promote embryogenic callus differentiation and improve regeneration efficiency by activating chloroplast development and phytohormone pathways. We also established a heat-inducible Cre/loxP-based gene-excision system to remove rZmG2 and the antibiotic selectable gene after obtaining the transgenic plants. This study provides a useful tool for functional genomics work and biotechnology in plants.
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Affiliation(s)
- Wanni Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China
| | - Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China
| | - Tie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China
| | - Ziting Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China
| | - Zhi Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yuanling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Jinxing Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, SCAU, Guangzhou, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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Yang Q, Sharif Y, Zhuang Y, Chen H, Zhang C, Fu H, Wang S, Cai T, Chen K, Raza A, Wang L, Zhuang W. Genome-wide identification of germin-like proteins in peanut ( Arachis hypogea L.) and expression analysis under different abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 13:1044144. [PMID: 36756235 PMCID: PMC9901545 DOI: 10.3389/fpls.2022.1044144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
Peanut is an important food and feed crop, providing oil and protein nutrients. Germins and germin-like proteins (GLPs) are ubiquitously present in plants playing numerous roles in defense, growth and development, and different signaling pathways. However, the GLP members have not been comprehensively studied in peanut at the genome-wide scale. We carried out a genome-wide identification of the GLP genes in peanut genome. GLP members were identified comprehensively, and gene structure, genomic positions, motifs/domains distribution patterns, and phylogenetic history were studied in detail. Promoter Cis-elements, gene duplication, collinearity, miRNAs, protein-protein interactions, and expression were determined. A total of 84 GLPs (AhGLPs ) were found in the genome of cultivated peanut. These GLP genes were clustered into six groups. Segmental duplication events played a key role in the evolution of AhGLPs, and purifying selection pressure was underlying the duplication process. Most AhGLPs possessed a well-maintained gene structure and motif organization within the same group. The promoter regions of AhGLPs contained several key cis-elements responsive to 'phytohormones', 'growth and development', defense, and 'light induction'. Seven microRNAs (miRNAs) from six families were found targeting 25 AhGLPs. Gene Ontology (GO) enrichment analysis showed that AhGLPs are highly enriched in nutrient reservoir activity, aleurone grain, external encapsulating structure, multicellular organismal reproductive process, and response to acid chemicals, indicating their important biological roles. AhGLP14, AhGLP38, AhGLP54, and AhGLP76 were expressed in most tissues, while AhGLP26, AhGLP29, and AhGLP62 showed abundant expression in the pericarp. AhGLP7, AhGLP20, and AhGLP21, etc., showed specifically high expression in embryo, while AhGLP12, AhGLP18, AhGLP40, AhGLP78, and AhGLP82 were highly expressed under different hormones, water, and temperature stress. The qRT-PCR results were in accordance with the transcriptome expression data. In short, these findings provided a foundation for future functional investigations on the AhGLPs for peanut breeding programs.
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Affiliation(s)
- Qiang Yang
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Yasir Sharif
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Yuhui Zhuang
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Hua Chen
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Chong Zhang
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Huiwen Fu
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Shanshan Wang
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Tiecheng Cai
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Kun Chen
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Ali Raza
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Lihui Wang
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Weijian Zhuang
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
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9
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Yang Y, Chen T, Dai X, Yang D, Wu Y, Chen H, Zheng Y, Zhi Q, Wan X, Tan X. Comparative transcriptome analysis revealed molecular mechanisms of peanut leaves responding to Ralstonia solanacearum and its type III secretion system mutant. Front Microbiol 2022; 13:998817. [PMID: 36090119 PMCID: PMC9453164 DOI: 10.3389/fmicb.2022.998817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease that limits peanut production and quality, but the molecular mechanisms of the peanut response to R. solanacearum remain unclear. In this study, we reported the first work analyzing the transcriptomic changes of the resistant and susceptible peanut leaves infected with R. solanacearum HA4-1 and its type III secretion system mutant strains by the cutting leaf method at different timepoints (0, 24, 36, and 72 h post inoculation). A total of 125,978 differentially expressed genes (DEGs) were identified and subsequently classified into six groups to analyze, including resistance-response genes, susceptibility-response genes, PAMPs induced resistance-response genes, PAMPs induced susceptibility-response genes, T3Es induced resistance-response genes, and T3Es induced susceptibility-response genes. KEGG enrichment analyses of these DEGs showed that plant-pathogen interaction, plant hormone signal transduction, and MAPK signaling pathway were the outstanding pathways. Further analysis revealed that CMLs/CDPKs-WRKY module, MEKK1-MKK2-MPK3 cascade, and auxin signaling played important roles in the peanut response to R. solanacearum. Upon R. solanacearum infection (RSI), three early molecular events were possibly induced in peanuts, including Ca2+ activating CMLs/CDPKs-WRKY module to regulate the expression of resistance/susceptibility-related genes, auxin signaling was induced by AUX/IAA-ARF module to activate auxin-responsive genes that contribute to susceptibility, and MEKK1-MKK2-MPK3-WRKYs was activated by phosphorylation to induce the expression of resistance/susceptibility-related genes. Our research provides new ideas and abundant data resources to elucidate the molecular mechanism of the peanut response to R. solanacearum and to further improve the bacterial wilt resistance of peanuts.
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Affiliation(s)
- Yong Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ting Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiaoqiu Dai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Dong Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yushuang Wu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Huilan Chen
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Yixiong Zheng
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Qingqing Zhi
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiaorong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- *Correspondence: Xiaorong Wan,
| | - Xiaodan Tan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Xiaodan Tan,
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Full-Length Transcriptome Sequencing Reveals the Impact of Cold Stress on Alternative Splicing in Quinoa. Int J Mol Sci 2022; 23:ijms23105724. [PMID: 35628539 PMCID: PMC9144462 DOI: 10.3390/ijms23105724] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Quinoa is a cold-resistant and nutrient-rich crop. To decipher the cold stress response of quinoa, the full-length transcriptomes of the cold-resistant quinoa variety CRQ64 and the cold-sensitive quinoa variety CSQ5 were compared. We identified 55,389 novel isoforms and 6432 novel genes in these transcriptomes. Under cold stress, CRQ64 had more differentially expressed genes (DEGs) and differentially alternative splicing events compared to non-stress conditions than CSQ5. DEGs that were specifically present only in CRQ64 were significantly enriched in processes which contribute to osmoregulation and ROS homeostasis in plants, such as sucrose metabolism and phenylpropanoid biosynthesis. More genes with differential alternative splicing under cold stress were enriched in peroxidase functions in CRQ64. In total, 5988 transcription factors and 2956 long non-coding RNAs (LncRNAs) were detected in this dataset. Many of these had altered expression patterns under cold stress compared to non-stress conditions. Our transcriptome results demonstrate that CRQ64 undergoes a wider stress response than CSQ5 under cold stress. Our results improved the annotation of the quinoa genome and provide new insight into the mechanisms of cold resistance in quinoa.
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Tan X, Dai X, Chen T, Wu Y, Yang D, Zheng Y, Chen H, Wan X, Yang Y. Complete Genome Sequence Analysis of Ralstonia solanacearum Strain PeaFJ1 Provides Insights Into Its Strong Virulence in Peanut Plants. Front Microbiol 2022; 13:830900. [PMID: 35273586 PMCID: PMC8904134 DOI: 10.3389/fmicb.2022.830900] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/12/2022] [Indexed: 11/22/2022] Open
Abstract
The bacterial wilt of peanut (Arachis hypogaea L.) caused by Ralstonia solanacearum is a devastating soil-borne disease that seriously restricted the world peanut production. However, the molecular mechanism of R. solanacearum–peanut interaction remains largely unknown. We found that R. solanacearum HA4-1 and PeaFJ1 isolated from peanut plants showed different pathogenicity by inoculating more than 110 cultivated peanuts. Phylogenetic tree analysis demonstrated that HA4-1 and PeaFJ1 both belonged to phylotype I and sequevar 14M, which indicates a high degree of genomic homology between them. Genomic sequencing and comparative genomic analysis of PeaFJ1 revealed 153 strain-specific genes compared with HA4-1. The PeaFJ1 strain-specific genes consisted of diverse virulence-related genes including LysR-type transcriptional regulators, two-component system-related genes, and genes contributing to motility and adhesion. In addition, the repertoire of the type III effectors of PeaFJ1 was bioinformatically compared with that of HA4-1 to find the candidate effectors responsible for their different virulences. There are 79 effectors in the PeaFJ1 genome, only 4 of which are different effectors compared with HA4-1, including RipS4, RipBB, RipBS, and RS_T3E_Hyp6. Based on the virulence profiles of the two strains against peanuts, we speculated that RipS4 and RipBB are candidate virulence effectors in PeaFJ1 while RipBS and RS_T3E_Hyp6 are avirulence effectors in HA4-1. In general, our research greatly reduced the scope of virulence-related genes and made it easier to find out the candidates that caused the difference in pathogenicity between the two strains. These results will help to reveal the molecular mechanism of peanut–R. solanacearum interaction and develop targeted control strategies in the future.
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Affiliation(s)
- Xiaodan Tan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiaoqiu Dai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ting Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yushuang Wu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Dong Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yixiong Zheng
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Huilan Chen
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Xiaorong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yong Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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Sharif Y, Chen H, Deng Y, Ali N, Khan SA, Zhang C, Xie W, Chen K, Cai T, Yang Q, Zhuang Y, Raza A, Zhuang W. Cloning and Functional Characterization of a Pericarp Abundant Expression Promoter (AhGLP17-1P) From Peanut (Arachis hypogaea L.). Front Genet 2022; 12:821281. [PMID: 35126474 PMCID: PMC8811503 DOI: 10.3389/fgene.2021.821281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/31/2021] [Indexed: 12/11/2022] Open
Abstract
Peanut (Arachis hypogaea L.) is an important oil and food legume crop grown in tropical and subtropical areas of the world. As a geocarpic crop, it is affected by many soil-borne diseases and pathogens. The pericarp, an inedible part of the seed, acts as the first layer of defense against biotic and abiotic stresses. Pericarp promoters could drive the defense-related genes specific expression in pericarp for the defense application. Here, we identified a pericarp-abundant promoter (AhGLP17-1P) through microarray and transcriptome analysis. Besides the core promoter elements, several other important cis-elements were identified using online promoter analysis tools. Semiquantitative and qRT-PCR analyses validated that the AhGLP17-1 gene was specifically expressed only in the pericarp, and no expression was detected in leaves, stem, roots, flowers, gynophore/peg, testa, and embryo in peanut. Transgenic Arabidopsis plants showed strong GUS expression in siliques, while GUS staining was almost absent in remaining tissues, including roots, seedlings, leaf, stem, flowers, cotyledons, embryo, and seed coat confirmed its peanut expressions. Quantitative expression of the GUS gene also supported the GUS staining results. The results strongly suggest that this promoter can drive foreign genes’ expression in a pericarp-abundant manner. This is the first study on the functional characterization of the pericarp-abundant promoters in peanut. The results could provide practical significance to improve the resistance of peanut, and other crops for seed protection uses.
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Affiliation(s)
- Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Hua Chen
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Ye Deng
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Niaz Ali
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Shahid Ali Khan
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Wenping Xie
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Kun Chen
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Tiecheng Cai
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Qiang Yang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yuhui Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Ali Raza
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Weijian Zhuang
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- *Correspondence: Weijian Zhuang,
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Liu J, Mehari TG, Xu Y, Umer MJ, Hou Y, Wang Y, Peng R, Wang K, Cai X, Zhou Z, Liu F. GhGLK1 a Key Candidate Gene From GARP Family Enhances Cold and Drought Stress Tolerance in Cotton. FRONTIERS IN PLANT SCIENCE 2021; 12:759312. [PMID: 34992618 PMCID: PMC8725998 DOI: 10.3389/fpls.2021.759312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Drought and low-temperature stresses are the most prominent abiotic stresses affecting cotton. Wild cotton being exposed to harsh environments has more potential to cope with both biotic and abiotic stresses. Exploiting wild cotton material to induce resistant germplasm would be of greater interest. The candidate gene was identified in the BC2F2 population among Gossypium tomentosum and Gossypium hirsutum as wild male donor parent noted for its drought tolerance and the recurrent parent and a high yielding but drought susceptible species by genotyping by sequencing (GBS) mapping. Golden2-like (GLK) gene, which belongs to the GARP family, is a kind of plant-specific transcription factor (TF) that was silenced by virus-induced gene silencing (VIGS). Silencing of GhGLK1 in cotton results in more damage to plants under drought and cold stress as compared with wild type (WT). The overexpression of GhGLK1 in Arabidopsis thaliana showed that the overexpressing plants showed more adaptability than the WT after drought and cold treatments. The results of trypan blue and 3,3'-diaminobenzidine (DAB) staining showed that after drought and cold treatment, the leaf damage in GhGLK1 overexpressed plants was less as compared with the WT, and the ion permeability was also lower. This study suggested that the GhGLK1 gene may be involved in the regulation of drought and cold stress response in cotton. Our current research findings add significantly to the existing knowledge of cold and drought stress tolerance in cotton.
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Affiliation(s)
- Jiangna Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Teame Gereziher Mehari
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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