1
|
Lou H, Zhu J, Zhao Z, Han Z, Zhang W. Chitinase Gene FoChi20 in Fusarium oxysporum Reduces Its Pathogenicity and Improves Disease Resistance in Cotton. Int J Mol Sci 2024; 25:8517. [PMID: 39126085 PMCID: PMC11312659 DOI: 10.3390/ijms25158517] [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: 05/16/2024] [Revised: 07/08/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Chitinase genes, as a class of cell wall hydrolases, are essential for the development and pathogenesis of Fusarium oxysporum f.sp. vasinfectum (F. ox) in cotton, but related research focused on chitinase genes are limited. This study explored two island cotton root secretions from the highly resistant cultivar Xinhai 41 and sensitive cultivar Xinhai 14 to investigate their interaction with F. ox by a weighted correlation network analysis (WGCNA). As a result, two modules that related to the fungal pathogenicity emerged. Additionally, a total of twenty-five chitinase genes were identified. Finally, host-induced gene silencing (HIGS) of FoChi20 was conducted, and the cotton plants showed noticeably milder disease with a significantly lower disease index than the control. This study illuminated that chitinase genes play crucial roles in the pathogenicity of cotton wilt fungi, and the FoChi20 gene could participate in the pathogenesis of F. ox and host-pathogen interactions, which establishes a theoretical framework for disease control in Sea Island cotton.
Collapse
Affiliation(s)
- Hui Lou
- The Key Laboratory of Oasis Eco-Agriculture, Agriculture College, Shihezi University, Shihezi 832000, China; (H.L.); (J.Z.); (Z.Z.)
| | - Jincheng Zhu
- The Key Laboratory of Oasis Eco-Agriculture, Agriculture College, Shihezi University, Shihezi 832000, China; (H.L.); (J.Z.); (Z.Z.)
| | - Zengqiang Zhao
- The Key Laboratory of Oasis Eco-Agriculture, Agriculture College, Shihezi University, Shihezi 832000, China; (H.L.); (J.Z.); (Z.Z.)
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310000, China
| | - Wei Zhang
- The Key Laboratory of Oasis Eco-Agriculture, Agriculture College, Shihezi University, Shihezi 832000, China; (H.L.); (J.Z.); (Z.Z.)
| |
Collapse
|
2
|
Kumar T, Wang JG, Xu CH, Lu X, Mao J, Lin XQ, Kong CY, Li CJ, Li XJ, Tian CY, Ebid MHM, Liu XL, Liu HB. Genetic Engineering for Enhancing Sugarcane Tolerance to Biotic and Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:1739. [PMID: 38999579 PMCID: PMC11244436 DOI: 10.3390/plants13131739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024]
Abstract
Sugarcane, a vital cash crop, contributes significantly to the world's sugar supply and raw materials for biofuel production, playing a significant role in the global sugar industry. However, sustainable productivity is severely hampered by biotic and abiotic stressors. Genetic engineering has been used to transfer useful genes into sugarcane plants to improve desirable traits and has emerged as a basic and applied research method to maintain growth and productivity under different adverse environmental conditions. However, the use of transgenic approaches remains contentious and requires rigorous experimental methods to address biosafety challenges. Clustered regularly interspaced short palindromic repeat (CRISPR) mediated genome editing technology is growing rapidly and may revolutionize sugarcane production. This review aims to explore innovative genetic engineering techniques and their successful application in developing sugarcane cultivars with enhanced resistance to biotic and abiotic stresses to produce superior sugarcane cultivars.
Collapse
Affiliation(s)
- Tanweer Kumar
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
- Sugar Crops Research Institute, Agriculture, Fisheries and Co-Operative Department, Charsadda Road, Mardan 23210, Khyber Pakhtunkhwa, Pakistan
| | - Jun-Gang Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
| | - Chao-Hua Xu
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Xin Lu
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Jun Mao
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Xiu-Qin Lin
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Chun-Yan Kong
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Chun-Jia Li
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Xu-Juan Li
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Chun-Yan Tian
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Mahmoud H. M. Ebid
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Xin-Long Liu
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| | - Hong-Bo Liu
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (T.K.)
| |
Collapse
|
3
|
Zhang C, Li Z, Sun T, Zang S, Wang D, Su Y, Wu Q, Que Y. Sugarcane ScCAX4 is a Negative Regulator of Resistance to Pathogen Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13205-13216. [PMID: 38809782 DOI: 10.1021/acs.jafc.4c00805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Calcium (Ca2+) is a second messenger in various physiological processes within plants. The significance of the Ca2+/H+ exchanger (CAX) has been established in facilitating Ca2+ transport in plants; however, disease resistance functions of the CAX gene remain elusive. In this study, we conducted sequence characterization and expression analysis for a sugarcane CAX gene, ScCAX4 (GenBank Accession Number: MW206380). In order to further investigate the disease resistance functions, this gene was then transiently overexpressed in Nicotiana benthamiana leaves, which were subsequently inoculated with Fusarium solani var. coeruleum. Results showed that ScCAX4 overexpression increased the susceptibility of N. benthamiana to pathogen infection by regulating the expression of genes related to salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) pathways, suggesting its negative role in disease resistance. Furthermore, we genetically transformed the ScCAX4 gene into N. benthamiana and obtained three positive T2 generation lines. Interestingly, the symptomatology of transgenic plants was consistent with that of transient overexpression after pathogen inoculation. Notably, the JA content in transgenic overexpression lines was significantly higher than that in the wild-type. RNA-seq revealed that ScCAX4 could mediate multiple signaling pathways, and the JA signaling pathway played a key role in modulating disease resistance. Finally, a regulatory model was depicted for the increased susceptibility to pathogen infection conferred by the ScCAX4 gene. This study provides genetic resources for sugarcane molecular breeding and the research direction for plant CAX genes.
Collapse
Affiliation(s)
- Chang Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenxiang Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
4
|
Zou W, Sun T, Chen Y, Wang D, You C, Zang S, Lin P, Wu Q, Su Y, Que Y. Sugarcane ScOPR1 gene enhances plant disease resistance through the modulation of hormonal signaling pathways. PLANT CELL REPORTS 2024; 43:158. [PMID: 38822833 DOI: 10.1007/s00299-024-03241-8] [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: 03/16/2024] [Accepted: 05/21/2024] [Indexed: 06/03/2024]
Abstract
KEY MESSAGE Transgenic plants stably overexpressing ScOPR1 gene enhanced disease resistance by increasing the accumulation of JA, SA, and GST, as well as up-regulating the expression of genes related to signaling pathways. 12-Oxo-phytodienoate reductase (OPR) is an oxidoreductase that depends on flavin mononucleotide (FMN) and catalyzes the conversion of 12-oxophytodienoate (12-OPDA) into jasmonic acid (JA). It plays a key role in plant growth and development, and resistance to adverse stresses. In our previous study, we have obtained an OPR gene (ScOPR1, GenBank Accession Number: MG755745) from sugarcane. This gene showed positive responses to methyl jasmonate (MeJA), salicylic acid (SA), abscisic acid (ABA), and Sporisorium scitamineum, suggesting its potential for pathogen resistance. Here, in our study, we observed that Nicotiana benthamiana leaves transiently overexpressing ScOPR1 exhibited weaker disease symptoms, darker 3,3-diaminobenzidine (DAB) staining, higher accumulation of reactive oxygen species (ROS), and higher expression of hypersensitive response (HR) and SA pathway-related genes after inoculation with Ralstonia solanacearum and Fusarium solanacearum var. coeruleum. Furthermore, the transgenic N. benthamiana plants stably overexpressing the ScOPR1 gene showed enhanced resistance to pathogen infection by increasing the accumulation of JA, SA, and glutathione S-transferase (GST), as well as up-regulating genes related to HR, JA, SA, and ROS signaling pathways. Transcriptome analysis revealed that the specific differentially expressed genes (DEGs) in ScOPR1-OE were significantly enriched in hormone transduction signaling and plant-pathogen interaction pathways. Finally, a functional mechanism model of the ScOPR1 gene in response to pathogen infection was depicted. This study provides insights into the molecular mechanism of ScOPR1 and presents compelling evidence supporting its positive involvement in enhancing plant disease resistance.
Collapse
Affiliation(s)
- Wenhui Zou
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yao Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chuihuai You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| |
Collapse
|
5
|
Qin T, Wang Y, Pu Z, Shi N, Dormatey R, Wang H, Sun C. Comprehensive Transcriptome and Proteome Analyses Reveal the Drought Responsive Gene Network in Potato Roots. PLANTS (BASEL, SWITZERLAND) 2024; 13:1530. [PMID: 38891338 PMCID: PMC11175002 DOI: 10.3390/plants13111530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
The root system plays a decisive role in the growth and development of plants. The water requirement of a root system depends strongly on the plant species. Potatoes are an important food and vegetable crop grown worldwide, especially under irrigation in arid and semi-arid regions. However, the expected impact of global warming on potato yields calls for an investigation of genes related to root development and drought resistance signaling pathways in potatoes. In this study, we investigated the molecular mechanisms of different drought-tolerant potato root systems in response to drought stress under controlled water conditions, using potato as a model. We analyzed the transcriptome and proteome of the drought-sensitive potato cultivar Atlantic (Atl) and the drought-tolerant cultivar Qingshu 9 (Q9) under normal irrigation (CK) and weekly drought stress (D). The results showed that a total of 14,113 differentially expressed genes (DEGs) and 5596 differentially expressed proteins (DEPs) were identified in the cultivars. A heat map analysis of DEGs and DEPs showed that the same genes and proteins in Atl and Q9 exhibited different expression patterns under drought stress. Weighted gene correlation network analysis (WGCNA) showed that in Atl, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG)-enriched pathways were related to pyruvate metabolism and glycolysis, as well as cellular signaling and ion transmembrane transporter protein activity. However, GO terms and KEGG-enriched pathways related to phytohormone signaling and the tricarboxylic acid cycle were predominantly enriched in Q9. The present study provides a unique genetic resource to effectively explore the functional genes and uncover the molecular regulatory mechanism of the potato root system in response to drought stress.
Collapse
Affiliation(s)
- Tianyuan Qin
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Yihao Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Zhuanfang Pu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Ningfan Shi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Richard Dormatey
- CSIR—Crops Research Institute, P.O. Box 3785, Kumasi 00233, Ghana;
| | - Huiqiong Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (Y.W.); (Z.P.); (N.S.); (H.W.)
| |
Collapse
|
6
|
Wu Q, Li A, Zhao P, Xia H, Zhang Y, Que Y. Theory to practice: a success in breeding sugarcane variety YZ08-1609 known as the King of Sugar. FRONTIERS IN PLANT SCIENCE 2024; 15:1413108. [PMID: 38807781 PMCID: PMC11130468 DOI: 10.3389/fpls.2024.1413108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 05/01/2024] [Indexed: 05/30/2024]
Abstract
Sugarcane, a significant cash crop in tropical and subtropical regions, contributes to 80% of sugar production and 40% of bioethanol production in the world. It is a key sugar crop, accounting for 85% of sugar production in China. Developing new varieties with high yield, high sugar, and better stress resistance is crucial for the sustainable growth of sugar industry. Hybrid breeding is the most widely used and effective method, with over 98% of Chinese sugarcane varieties resulting from this approach. Over the past two decades, Chinese breeders have developed the theory of high-heterogeneous composite high-sugar breeding, leading to the successful breeding of the fifth-generation sugarcane varieties. Among them, YZ08-1609, a complex hybrid of Saccharum spp., was developed by Sugarcane Research Institute (YSRI) of Yunnan Academy of Agricultural Sciences. The average cane yield of YZ08-1609 was 14.4% higher than ROC22. It is highly resistant to mosaic disease, and highly tolerant to drought stress, but moderately susceptible to smut disease. Notably, YZ08-1609 stands out with a sucrose content of 20.3%, setting an international record, earning the reputation as "King of Sugar". To summarize experience and inspire breeding, we provided here the detailed insights into the selection of parents, breeding process, and characteristics of YZ08-1609. Besides, the biological mechanisms underlying its high yield and high sugar was excavated at both transcriptional and metabolic levels. The challenges and prospects in breeding sugarcane varieties especially with high sugar were also discussed, offering a foundation for the future development of high-sugar varieties.
Collapse
Affiliation(s)
- Qibin Wu
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Aomei Li
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Peifang Zhao
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Hongming Xia
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Yuebin Zhang
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Youxiong Que
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
7
|
Wu Q, Zhang C, Xu F, Zang S, Wang D, Sun T, Su Y, Yang S, Ding Y, Que Y. Transcriptional Regulation of SugarCane Response to Sporisorium scitamineum: Insights from Time-Course Gene Coexpression and Ca 2+ Signaling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10506-10520. [PMID: 38651833 PMCID: PMC11082935 DOI: 10.1021/acs.jafc.4c02123] [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: 03/07/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Sugarcane response to Sporisorium scitamineum is determined by multiple major genes and numerous microeffector genes. Here, time-ordered gene coexpression networks were applied to explore the interaction between sugarcane and S. scitamineum. Totally, 2459 differentially expressed genes were identified and divided into 10 levels, and several stress-related subnetworks were established. Interestingly, the Ca2+ signaling pathway was activated to establish the response to sugarcane smut disease. Accordingly, two CAX genes (ScCAX2 and ScCAX3) were cloned and characterized from sugarcane. They were significantly upregulated under ABA stress but inhibited by MeJA treatment. Furthermore, overexpression of ScCAX2 and ScCAX3 enhanced the susceptibility of transgenic plants to the pathogen infection, suggesting its negative role in disease resistance. A regulatory model for ScCAX genes in disease response was thus depicted. This work helps to clarify the transcriptional regulation of sugarcane response to S. scitamineum stress and the function of the CAX gene in disease response.
Collapse
Affiliation(s)
- Qibin Wu
- National
Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience
and Biotechnology, Chinese Academy of Tropical
Agricultural Sciences, Sanya 572024, Haikou 571101, Hainan, China
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang Zhang
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Fu Xu
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongjiao Wang
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Tingting Sun
- National
Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience
and Biotechnology, Chinese Academy of Tropical
Agricultural Sciences, Sanya 572024, Haikou 571101, Hainan, China
| | - Yachun Su
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Shaolin Yang
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
- Yunnan
Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research
Institute, Yunnan Academy of Agricultural
Sciences, Kaiyuan 661600, China
| | - Yinghong Ding
- College
of Landscape Architecture and Art, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Youxiong Que
- National
Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience
and Biotechnology, Chinese Academy of Tropical
Agricultural Sciences, Sanya 572024, Haikou 571101, Hainan, China
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
8
|
Niu J, Zhao J, Guo Q, Zhang H, Yue A, Zhao J, Yin C, Wang M, Du W. WGCNA Reveals Hub Genes and Key Gene Regulatory Pathways of the Response of Soybean to Infection by Soybean mosaic virus. Genes (Basel) 2024; 15:566. [PMID: 38790195 PMCID: PMC11120672 DOI: 10.3390/genes15050566] [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: 03/27/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Soybean mosaic virus (SMV) is one of the main pathogens that can negatively affect soybean production and quality. To study the gene regulatory network of soybeans in response to SMV SC15, the resistant line X149 and susceptible line X97 were subjected to transcriptome analysis at 0, 2, 8, 12, 24, and 48 h post-inoculation (hpi). Differential expression analysis revealed that 10,190 differentially expressed genes (DEGs) responded to SC15 infection. Weighted gene co-expression network analysis (WGCNA) was performed to identify highly related resistance gene modules; in total, eight modules, including 2256 DEGs, were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of 2256 DEGs revealed that the genes significantly clustered into resistance-related pathways, such as the plant-pathogen interaction pathway, mitogen-activated protein kinases (MAPK) signaling pathway, and plant hormone signal transduction pathway. Among these pathways, we found that the flg22, Ca2+, hydrogen peroxide (H2O2), and abscisic acid (ABA) regulatory pathways were fully covered by 36 DEGs. Among the 36 DEGs, the gene Glyma.01G225100 (protein phosphatase 2C, PP2C) in the ABA regulatory pathway, the gene Glyma.16G031900 (WRKY transcription factor 22, WRKY22) in Ca2+ and H2O2 regulatory pathways, and the gene Glyma.04G175300 (calcium-dependent protein kinase, CDPK) in Ca2+ regulatory pathways were highly connected hub genes. These results indicate that the resistance of X149 to SC15 may depend on the positive regulation of flg22, Ca2+, H2O2, and ABA regulatory pathways. Our study further showed that superoxide dismutase (SOD) activity, H2O2 content, and catalase (CAT) and peroxidase (POD) activities were significantly up-regulated in the resistant line X149 compared with those in 0 hpi. This finding indicates that the H2O2 regulatory pathway might be dependent on flg22- and Ca2+-pathway-induced ROS generation. In addition, two hub genes, Glyma.07G190100 (encoding F-box protein) and Glyma.12G185400 (encoding calmodulin-like proteins, CMLs), were also identified and they could positively regulate X149 resistance. This study provides pathways for further investigation of SMV resistance mechanisms in soybean.
Collapse
Affiliation(s)
- Jingping Niu
- College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China;
| | - Jing Zhao
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Qian Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Hanyue Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Aiqin Yue
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Jinzhong Zhao
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (C.Y.)
| | - Congcong Yin
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (C.Y.)
| | - Min Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Weijun Du
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| |
Collapse
|
9
|
Li R, Wang X, Hu Y, Huang G. Analysis of huanglongbing-associated RNA-seq data reveals disturbances in biological processes within Citrus spp. triggered by Candidatus Liberibacter asiaticus infection. FRONTIERS IN PLANT SCIENCE 2024; 15:1388163. [PMID: 38660443 PMCID: PMC11039969 DOI: 10.3389/fpls.2024.1388163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Introduction Huanglongbing (HLB), a disease that's ubiquitous worldwide, wreaks havoc on the citrus industry. The primary culprit of HLB is the gram-negative bacterium Candidatus Liberibacter asiaticus (CLas) that infects the phloem, but its damaging mechanism is yet to be fully understood. Methods and results In this study, a multitude of tools including weighted correlation network analysis (WGCNA), protein-protein interaction (PPI) network analysis and gene expression profiling are employed to unravel the intricacies of its pathogenesis. The investigation pinpoints various central genes, such as the ethylene-responsive transcription factor 9 (ERF9) and thioredoxin reductase 1 (TrxR1), that are associated with CLas invasion and resultant disturbances in numerous biological operations. Additionally, the study uncovers a range of responses through the detection of differential expressed genes (DEGs) across different experiments. The discovery of core DEGs leads to the identification of pivotal genes such as the sieve element occlusion (SEO) and the wall-associated receptor kinase-like 15 (WAKL15). PPI network analysis highlights potential vital proteins, while GO and KEGG pathway enrichment analysis illustrate a significant impact on multiple defensive and metabolic pathways. Gene set enrichment analysis (GSEA) indicates significant alterations in biological processes such as leaf senescence and response to biotic stimuli. Discussion This all-encompassing approach extends valuable understanding into the pathogenesis of CLas, potentially aiding future research and therapeutic strategies for HLB.
Collapse
Affiliation(s)
- Ruimin Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Xinyou Wang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Yanan Hu
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Guiyan Huang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| |
Collapse
|
10
|
Hu X, Luo Z, Xu C, Wu Z, Wu C, Ebid MHM, Zan F, Zhao L, Liu X, Liu J. A Comprehensive Analysis of Transcriptomics and Metabolomics Revealed Key Pathways Involved in Saccharum spontaneum Defense against Sporisorium scitamineum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4476-4492. [PMID: 38373255 DOI: 10.1021/acs.jafc.3c07768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Sugarcane smut, caused by Sporisorium scitamineum, poses a severe threat to sugarcane production. The genetic basis of sugarcane resistance to S. scitamineum remains elusive. A comparative transcriptomic and metabolomic study was conducted on two wild Saccharum species of S. spontaneum with contrast smut resistance. Following infection, the resistant line exhibited greater down-regulation of genes and metabolites compared to the susceptible line, indicating distinct biological processes. Lignan and lignin biosynthesis and SA signal transduction were activated in the resistant line, while flavonoid biosynthesis and auxin signal transduction were enhanced in the susceptible line. TGA2.2 and ARF14 were identified as playing positive and negative roles, respectively, in plant defense. Exogenous auxin application significantly increased the susceptibility of S. spontaneum to S. scitaminum. This study established the significant switching of defense signaling pathways in contrast-resistant S. spontaneum following S. scitamineum infection, offering a hypothetical model and candidate genes for further research into sugarcane smut disease.
Collapse
Affiliation(s)
- Xin Hu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Zhengying Luo
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Chaohua Xu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Zhuandi Wu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Caiwen Wu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Mahmoud H M Ebid
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Fengang Zan
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Liping Zhao
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Xinlong Liu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Jiayong Liu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| |
Collapse
|
11
|
Sicilia A, Russo R, Catara V, Lo Piero AR. Hub Genes and Pathways Related to Lemon ( Citrus limon) Leaf Response to Plenodomus tracheiphilus Infection and Influenced by Pseudomonas mediterranea Biocontrol Activity. Int J Mol Sci 2024; 25:2391. [PMID: 38397068 PMCID: PMC10889467 DOI: 10.3390/ijms25042391] [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: 02/02/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
The lemon industry in the Mediterranean basin is strongly threatened by "mal secco" disease (MSD) caused by the fungus Plenodomus tracheiphlilus. Leaf pretreatments with Pseudomonas mediterranea 3C have been proposed as innovative tools for eco-sustainable interventions aimed at controlling the disease. In this study, by exploiting the results of previously performed RNAseq analysis, WCGNA was conducted among gene expression patterns in both inoculated (Pt) and pretreated and fungus-inoculated lemon plants (Citrus limon L.) (3CPt), and two indicators of fungal infection, i.e., the amount of fungus DNA measured in planta and the disease index (DI). The aims of this work were (a) to identify gene modules significantly associated with those traits, (b) to construct co-expression networks related to mal secco disease; (c) to define the effect and action mechanisms of P. mediterranea by comparing the networks. The results led to the identification of nine hub genes in the networks, with three of them belonging to receptor-like kinases (RLK), such as HERK1, CLAVATA1 and LRR, which play crucial roles in plant-pathogen interaction. Moreover, the comparison between networks indicated that the expression of those receptors is not induced in the presence of P. mediterranea, suggesting how powerful WCGNA is in discovering crucial genes that must undergo further investigation and be eventually knocked out.
Collapse
Affiliation(s)
| | | | | | - Angela Roberta Lo Piero
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy; (A.S.); (R.R.); (V.C.)
| |
Collapse
|
12
|
Wan G, Wang Z, Zhang X, Tian Y, Zhou X, Ge L, Xiong G, Wang X, Hu Y. Genomic and transcriptome insight into the structure and immunity role of TRIM proteins in Chinese soft-shelled turtles (Pelodiscus sinensis) after Aeromonas hydrophila infection. Mol Biol Rep 2024; 51:263. [PMID: 38302771 DOI: 10.1007/s11033-023-09139-0] [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: 10/09/2023] [Accepted: 12/11/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND TRIM proteins, recognized as a class of E3 ubiquitin ligases, are increasingly acknowledged for their antipathogen immune functions in mammals and fish. In the Chinese soft-shelled turtle (Pelodiscus sinensis), a secondary aquatic reptile that occupies a unique evolutionary position, the TRIM gene has rarely been reported. METHODS AND RESULTS In the present study, 48 PsTRIM proteins were identified from the genome of Pelodiscus sinensis via Hidden Markov Model (HMM) searches and Signal Transduction ATPases with Numerous Domains (SMART) analysis. These PsTRIMs were found across 43 distinct scaffolds, and phylogenetic analyses classified them into three principal clades. The PsTRIMs feature a conserved assembly of either RING-B-box-coiled-coil (RBCC) or B-box-coiled-coil (BBC) domains at the N-terminus, in addition to eight unique domains at the C-terminus, including the B30.2 domain, 19 of which were identified. Expression profiling revealed ubiquitous expression of the 48 PsTRIMs across various P. sinensis tissues. Notably, seven PsTRIMs exhibited significant differential expression in liver transcriptomes following infection with Aeromonas hydrophila. Weighted gene coexpression network analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis implicated PsTRIM14 and PsTRIM28 as key players in host defense against bacterial invasion. Real-time quantitative PCR results indicated that PsTRIM1, PsTRIM2, PsTRIM14, and PsTRIM28 experienced marked upregulation in P. sinensis livers at 12 h post-infection with A. hydrophila. CONCLUSIONS Our study is the first to comprehensively identify and analyze the functions of TRIM genes in P. sinensis, unveiling their considerable diversity and potential roles in modulating immune responses.
Collapse
Affiliation(s)
- Gang Wan
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China
| | - Ziao Wang
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, China
| | - Xingyue Zhang
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China
| | - Yu Tian
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China
| | - Xianwen Zhou
- Affair Center of Animal Husbandry and Aquaculture in Xiang Xi Autonomous Prefecture, Jishou, 416000, Hunan, China
| | - Lingrui Ge
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, China
| | - Gang Xiong
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, China
| | - Xiaoqing Wang
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China.
| | - Yazhou Hu
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China.
| |
Collapse
|
13
|
Que Y, Wu Q, Zhang H, Luo J, Zhang Y. Developing new sugarcane varieties suitable for mechanized production in China: principles, strategies and prospects. FRONTIERS IN PLANT SCIENCE 2024; 14:1337144. [PMID: 38259907 PMCID: PMC10802142 DOI: 10.3389/fpls.2023.1337144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
The sugar industry, which relates to people's livelihood, is strategic and fundamental in the development of agricultural economy. In China, sugar derived from sugarcane accounts for approximately 85% of total sugar production. Mechanization is the "flower" of sugarcane industry. As the saying goes "when there are blooming flowers, there will be sweet honey." However, due to limitations in land resources, technology, equipment, organization, and management, mechanization throughout the sugarcane production process has not yet brought about the economic benefits that a mechanized system should provide and has not reached an ideal yield through the integration of agricultural machinery and agronomic practice. This paper briefly describes how to initiate the mechanization of Chinese sugarcane production to promote the sound, healthy, and rapid development of the sugarcane industry, and how to ultimately achieve the transformation of sugarcane breeding in China and the modernization of the sugarcane industry from three perspectives, namely, requirements of mechanized production for sugarcane varieties, breeding strategies for selecting new sugarcane varieties suitable for mechanized production, and screening for sugarcane varieties that are suitable for mechanization and diversification in variety distribution or arrangement in China. We also highlight the current challenges surrounding this topic and look forward to its bright prospects.
Collapse
Affiliation(s)
- Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunan Academy of Agricultural Sciences, Kaiyuan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- National Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunan Academy of Agricultural Sciences, Kaiyuan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun Luo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuebin Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| |
Collapse
|
14
|
Zhao C, Liu W, Zhang Y, Li Y, Ma C, Tian R, Li R, Li M, Huang L. Two transcription factors, AcREM14 and AcC3H1, enhance the resistance of kiwifruit Actinidiachinensis var. chinensis to Pseudomonas syringae pv. actinidiae. HORTICULTURE RESEARCH 2024; 11:uhad242. [PMID: 38222821 PMCID: PMC10782502 DOI: 10.1093/hr/uhad242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/12/2023] [Indexed: 01/16/2024]
Abstract
Kiwifruit bacterial canker is a global disease caused by Pseudomonas syringae pv. actinidiae (Psa), which poses a major threat to kiwifruit production worldwide. Despite the economic importance of Actinidia chinensis var. chinensis, only a few resistant varieties have been identified to date. In this study, we screened 44 kiwifruit F1 hybrid lines derived from a cross between two A. chinensis var. chinensis lines and identified two offspring with distinct resistance to Psa: resistant offspring RH12 and susceptible offspring SH14. To identify traits associated with resistance, we performed a comparative transcriptomic analysis of these two lines. We identified several highly differentially expressed genes (DEGs) associated with flavonoid synthesis, pathogen interactions, and hormone signaling pathways, which play essential roles in disease resistance. Additionally, using weighted gene co-expression network analysis, we identified six core transcription factors. Moreover, qRT-PCR results demonstrated the high expression of AcC3H1 and AcREM14 in Psa-induced highly resistant hybrid lines. Ultimately, Overexpression of AcC3H1 and AcREM14 in kiwifruit enhanced disease resistance, and this was associated with upregulation of enzymatic activity and gene expression in the salicylic acid (SA) signaling pathway. Our study elucidates a molecular mechanism underlying disease resistance in kiwifruit and contributes to the advancement of research on kiwifruit breeding.
Collapse
Affiliation(s)
- Chao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Wei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Yali Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Yuanzhe Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Chao Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Runze Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Rui Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| |
Collapse
|
15
|
Chen C, Ren H, Li H, Deng Y, Cui Q, Zhu J, Zhang S, Yu J, Wang H, Yu X, Yang S, Hu X, Peng Y. Identification of crucial modules and genes associated with backfat tissue development by WGCNA in Ningxiang pigs. Front Genet 2023; 14:1234757. [PMID: 37662841 PMCID: PMC10469685 DOI: 10.3389/fgene.2023.1234757] [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: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Fat deposition is an economically important trait in pigs. Ningxiang pig, one of the four famous indigenous breeds in China, is characterized by high fat content. The underlying gene expression pattern in different developmental periods of backfat tissue remains unclear, and the purpose of this investigation is to explore the potential molecular regulators of backfat tissue development in Ningxiang pigs. Backfat tissue (three samples for each stage) was initially collected from different developmental stages (60, 120, 180, 240, 300, and 360 days after birth), and histological analysis and RNA sequencing (RNA-seq) were then conducted. Fragments per kilobase of transcript per million (FPKM) method was used to qualify gene expressions, and differentially expressed genes (DEGs) were identified. Furthermore, strongly co-expressed genes in modules, which were named by color, were clustered by Weighted gene co-expression network analysis (WGCNA) based on dynamic tree cutting algorithm. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment were subsequently implemented, and hub genes were described in each module. Finally, QPCR analysis was employed to validate RNA-seq data. The results showed that adipocyte area increased and adipocyte number decreased with development of backfat tissue. A total of 1,024 DEGs were identified in five comparison groups (120 days vs. 60 days, 180 days vs. 120 days, 240 days vs. 180 days, 300 days vs. 240 days, and 360 days vs. 300 days). The turquoise, red, pink, paleturquoise, darkorange, and darkgreen module had the highest correlation coefficient with 60, 120, 180, 240, 300, and 360 days developmental stage, while the tan, black and turquoise module had strong relationship with backfat thickness, adipocyte area, and adipocyte number, respectively. Thirteen hub genes (ACSL1, ACOX1, FN1, DCN, CHST13, COL1A1, COL1A2, COL6A3, COL5A1, COL14A1, OAZ3, DNM1, and SELP) were recognized. ACSL1 and ACOX1 might perform function in the early developmental stage of backfat tissue (60 days), and FN1, DCN, COL1A1, COL1A2, COL5A1, COL6A3, and COL14A1 have unignorable position in backfat tissue around 120 days developmental stage. Besides, hub genes SELP and DNM1 in modules significantly associated with backfat thickness and adipocyte area might be involved in the process of backfat tissue development. These findings contribute to understand the integrated mechanism underlying backfat tissue development and promote the progress of genetic improvement in Ningxiang pigs.
Collapse
Affiliation(s)
- Chen Chen
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Huibo Ren
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Huali Li
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Yuan Deng
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Qingming Cui
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Ji Zhu
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Siyang Zhang
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Jine Yu
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Huiming Wang
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Xiaodan Yu
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Shiliu Yang
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Xionggui Hu
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Yinglin Peng
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| |
Collapse
|
16
|
Zhang S, Liu J, Shi L, Wang Q, Zhang P, Wang H, Liu J, Li H, Li L, Li X, Huang L, Qin P. Identification of core genes associated with different phosphorus levels in quinoa seedlings by weighted gene co-expression network analysis. BMC Genomics 2023; 24:399. [PMID: 37454047 DOI: 10.1186/s12864-023-09507-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: 03/19/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Quinoa is a highly nutritious and novel crop that is resistant to various abiotic stresses. However, its growth and development is restricted due to its limited utilization of soil phosphorus. Studies on the levels of phosphorus in quinoa seedlings are limited; therefore, we analyzed transcriptome data from quinoa seedlings treated with different concentrations of phosphorus. RESULTS To identify core genes involved in responding to various phosphorus levels, the weighted gene co-expression network analysis method was applied. From the 12,085 expressed genes, an analysis of the gene co-expression network was done. dividing the expressed genes into a total of twenty-five different modules out of which two modules were strongly correlated with phosphorus levels. Subsequently we identified five core genes that correlated strongly either positively or negatively with the phosphorus levels. Gene ontology and assessments of the Kyoto Encyclopedia of Genes and Genomes have uncovered important biological processes and metabolic pathways that are involved in the phosphorus level response. CONCLUSIONS We discovered crucial new core genes that encode proteins from various transcription factor families, such as MYB, WRKY, and ERF, which are crucial for abiotic stress resistance. This new library of candidate genes associated with the phosphorus level responses in quinoa seedlings will help in breeding varieties that are tolerant to phosphorus levels.
Collapse
Affiliation(s)
- Shan Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jian Liu
- Institute of Agricultural Sciences of the Lixiache District, Yangzhou, 225007, China
| | - Lian Shi
- Yuxi Academy of Agricultural Sciences, Yuxi, 653100, China
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongxin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hanxue Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xinyi Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Liubin Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
| |
Collapse
|
17
|
Wu Q, Li Z, Yang J, Xu F, Fu X, Xu L, You C, Wang D, Su Y, Que Y. Deciphering the Atlas of Post-Translational Modification in Sugarcane. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37339007 DOI: 10.1021/acs.jafc.3c01886] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
In plants, lysine acetylation (Kac), 2-hydroxyisobutyrylation (Khib), and lysine lactylation (Kla), the three new types of post-translational modification (PTM), play very important roles in growth, development, and resistance to adverse environmental stresses. Herein, we report the first global acetylome, 2-hydroxyisobutyrylome, and lactylome in sugarcane. A total of 8573 Kac, 4637 Khib, and 215 Kla sites across 3903, 1507, and 139 modified proteins were identified. Besides, homology analyses revealed the Kac, Khib, and Kla sites on histones were conserved between sugarcane and rice or poplar. Functional annotations demonstrated that the Kac, Khib, and Kla proteins were mainly involved in energy metabolism. In addition, a number of modified transcription factors and stress-related proteins, which were constitutively expressed in different tissues of sugarcane and induced by drought, cold or Sporisorium scitamineum stress, were identified. Finally, a proposed working mode on how PTM functions in sugarcane was depicted. We thus concluded that PTM should play a role in sugarcane growth, development, and response to biotic and abiotic stresses, but the mechanisms require further investigation. The present study provided the all-new comprehensive profile of proteins Kac, Khib, and Kla and a new perspective to understand the molecular mechanisms of protein PTMs in sugarcane.
Collapse
Affiliation(s)
- Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenxiang Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingtao Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xueqin Fu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National Key Laboratory for Tropical Crop Breeding, Kaiyuan, Yunnan 661699, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National Key Laboratory for Tropical Crop Breeding, Kaiyuan, Yunnan 661699, China
| |
Collapse
|
18
|
Li AM, Liao F, Wang M, Chen ZL, Qin CX, Huang RQ, Verma KK, Li YR, Que YX, Pan YQ, Huang DL. Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors. Int J Mol Sci 2023; 24:ijms24108913. [PMID: 37240257 DOI: 10.3390/ijms24108913] [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: 05/04/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Sugarcane, a C4 plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.
Collapse
Affiliation(s)
- Ao-Mei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Fen Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Miao Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Zhong-Liang Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Cui-Xian Qin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Ruo-Qi Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Krishan K Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - You-Xiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - You-Qiang Pan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Dong-Liang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| |
Collapse
|
19
|
Wu Q, Chen Y, Zou W, Pan YB, Lin P, Xu L, Grisham MP, Ding Q, Su Y, Que Y. Genome-wide characterization of sugarcane catalase gene family identifies a ScCAT1 gene associated disease resistance. Int J Biol Macromol 2023; 232:123398. [PMID: 36702220 DOI: 10.1016/j.ijbiomac.2023.123398] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023]
Abstract
In plants, catalase (CAT) mainly scavenges H2O2 from reactive oxygen species (ROS) and regulates the growth and development. So far, genome-wide identification of CAT gene family in Saccharum has not yet been reported. Here, 16 SsCAT genes were identified based on a Saccharum spontaneum genome. They were clustered into three subfamilies, with closer genes sharing similar structures. Most SsCAT proteins contained three conserved amino acids, one active catalytic site, one heme-ligand signature, and three peroxisomal targeting signal 1 (PTS1) sequences. The cis-regulatory element prediction revealed that SsCAT genes were involved in growth and development, and in response to various hormones and stresses. RNA-Seq databases showed that SsCAT genes were differentially expressed in Saccharum tissues and under cold, drought, and Sporisorium scitamineum stresses. The ScCAT1 gene transcript (GenBank accession number KF664183) and relevant CAT activity were up-regulated under S. scitamineum stress. Overexpression of ScCAT1 gene in Nicotiana benthamiana could enhance its resistance to pathogen infection through scavenging of excessive toxic ROS and up-regulated expressions of genes related to hypersensitive response (HR), ROS and salicylic acid (SA) pathways. This study provides comprehensive information for the CAT gene family and sets up a basis for its function identification in sugarcane.
Collapse
Affiliation(s)
- Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanling Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Bao Pan
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA 70360, USA
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Michael P Grisham
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA 70360, USA
| | - Qiugang Ding
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
20
|
Canales J, Arenas-M A, Medina J, Vidal EA. A Revised View of the LSU Gene Family: New Functions in Plant Stress Responses and Phytohormone Signaling. Int J Mol Sci 2023; 24:ijms24032819. [PMID: 36769138 PMCID: PMC9917515 DOI: 10.3390/ijms24032819] [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: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
LSUs (RESPONSE TO LOW SULFUR) are plant-specific proteins of unknown function that were initially identified during transcriptomic studies of the sulfur deficiency response in Arabidopsis. Recent functional studies have shown that LSUs are important hubs of protein interaction networks with potential roles in plant stress responses. In particular, LSU proteins have been reported to interact with members of the brassinosteroid, jasmonate signaling, and ethylene biosynthetic pathways, suggesting that LSUs may be involved in response to plant stress through modulation of phytohormones. Furthermore, in silico analysis of the promoter regions of LSU genes in Arabidopsis has revealed the presence of cis-regulatory elements that are potentially responsive to phytohormones such as ABA, auxin, and jasmonic acid, suggesting crosstalk between LSU proteins and phytohormones. In this review, we summarize current knowledge about the LSU gene family in plants and its potential role in phytohormone responses.
Collapse
Affiliation(s)
- Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
- Correspondence: (J.C.); (E.A.V.)
| | - Anita Arenas-M
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, INIA-CSIC-Universidad Politécnica de Madrid, 28223 Madrid, Spain
| | - Elena A. Vidal
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Correspondence: (J.C.); (E.A.V.)
| |
Collapse
|
21
|
Cheng W, Wang Z, Xu F, Lu G, Su Y, Wu Q, Wang T, Que Y, Xu L. Screening of Candidate Genes Associated with Brown Stripe Resistance in Sugarcane via BSR-seq Analysis. Int J Mol Sci 2022; 23:ijms232415500. [PMID: 36555141 PMCID: PMC9778799 DOI: 10.3390/ijms232415500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Sugarcane brown stripe (SBS), caused by the fungal pathogen Helminthosporium stenospilum, is one of the most serious threats to sugarcane production. However, its outbreaks and epidemics require suitable climatic conditions, resulting in the inefficient improvement of the SBS resistance by phenotype selection. The sugarcane F1 population of SBS-resistant YT93-159 × SBS-susceptible ROC22 was used for constructing the bulks. Bulked segregant RNA-seq (BSR-seq) was then performed on the parents YT93-159 (T01) and ROC22 (T02), and the opposite bulks of 30 SBS-susceptible individuals mixed bulk (T03) and 30 SBS-resistant individuals mixed bulk (T04) collected from 287 F1 individuals. A total of 170.00 Gb of clean data containing 297,921 SNPs and 70,426 genes were obtained. Differentially expressed genes (DEGs) analysis suggested that 7787 and 5911 DEGs were identified in the parents (T01 vs. T02) and two mixed bulks (T03 vs. T04), respectively. In addition, 25,363 high-quality and credible SNPs were obtained using the genome analysis toolkit GATK for SNP calling. Subsequently, six candidate regions with a total length of 8.72 Mb, which were located in the chromosomes 4B and 7C of sugarcane wild species Saccharum spontaneum, were identified, and 279 genes associated with SBS-resistance were annotated by ED algorithm and ΔSNP-index. Furthermore, the expression profiles of candidate genes were verified by quantitative real-time PCR (qRT-PCR) analysis, and the results showed that eight genes (LRR-RLK, DHAR1, WRKY7, RLK1, BLH4, AK3, CRK34, and NDA2) and seven genes (WRKY31, CIPK2, CKA1, CDPK6, PFK4, CBL2, and PR2) of the 20 tested genes were significantly up-regulated in YT93-159 and ROC22, respectively. Finally, a potential molecular mechanism of sugarcane response to H. stenospilum infection is illustrate that the activations of ROS signaling, MAPK cascade signaling, Ca2+ signaling, ABA signaling, and the ASA-GSH cycle jointly promote the SBS resistance in sugarcane. This study provides abundant gene resources for the SBS resistance breeding in sugarcane.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Youxiong Que
- Correspondence: (Y.Q.); (L.X.); Tel.: +86-591-8385-2547 (Y.Q.); +86-591-8377-2604 (L.X.)
| | - Liping Xu
- Correspondence: (Y.Q.); (L.X.); Tel.: +86-591-8385-2547 (Y.Q.); +86-591-8377-2604 (L.X.)
| |
Collapse
|
22
|
Genome-Wide Identification of Auxin-Responsive GH3 Gene Family in Saccharum and the Expression of ScGH3-1 in Stress Response. Int J Mol Sci 2022; 23:ijms232112750. [PMID: 36361540 PMCID: PMC9654502 DOI: 10.3390/ijms232112750] [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: 09/28/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Gretchen Hagen3 (GH3), one of the three major auxin-responsive gene families, is involved in hormone homeostasis in vivo by amino acid splicing with the free forms of salicylic acid (SA), jasmonic acid (JA) or indole-3-acetic acid (IAA). Until now, the functions of sugarcane GH3 (SsGH3) family genes in response to biotic stresses have been largely unknown. In this study, we performed a systematic identification of the SsGH3 gene family at the genome level and identified 41 members on 19 chromosomes in the wild sugarcane species, Saccharum spontaneum. Many of these genes were segmentally duplicated and polyploidization was the main contributor to the increased number of SsGH3 members. SsGH3 proteins can be divided into three major categories (SsGH3-I, SsGH3-II, and SsGH3-III) and most SsGH3 genes have relatively conserved exon-intron arrangements and motif compositions. Diverse cis-elements in the promoters of SsGH3 genes were predicted to be essential players in regulating SsGH3 expression patterns. Multiple transcriptome datasets demonstrated that many SsGH3 genes were responsive to biotic and abiotic stresses and possibly had important functions in the stress response. RNA sequencing and RT-qPCR analysis revealed that SsGH3 genes were differentially expressed in sugarcane tissues and under Sporisorium scitamineum stress. In addition, the SsGH3 homolog ScGH3-1 gene (GenBank accession number: OP429459) was cloned from the sugarcane cultivar (Saccharum hybrid) ROC22 and verified to encode a nuclear- and membrane-localization protein. ScGH3-1 was constitutively expressed in all tissues of sugarcane and the highest amount was observed in the stem pith. Interestingly, it was down-regulated after smut pathogen infection but up-regulated after MeJA and SA treatments. Furthermore, transiently overexpressed Nicotiana benthamiana, transduced with the ScGH3-1 gene, showed negative regulation in response to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum. Finally, a potential model for ScGH3-1-mediated regulation of resistance to pathogen infection in transgenic N. benthamiana plants was proposed. This study lays the foundation for a comprehensive understanding of the sequence characteristics, structural properties, evolutionary relationships, and expression of the GH3 gene family and thus provides a potential genetic resource for sugarcane disease-resistance breeding.
Collapse
|
23
|
Wu Q, Su Y, Pan YB, Xu F, Zou W, Que B, Lin P, Sun T, Grisham MP, Xu L, Que Y. Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq. FRONTIERS IN PLANT SCIENCE 2022; 13:1035266. [PMID: 36311133 PMCID: PMC9608552 DOI: 10.3389/fpls.2022.1035266] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/27/2022] [Indexed: 06/01/2023]
Abstract
Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases worldwide. In this study, a cross was made between a smut-resistant variety YT93-159 and a smut-susceptible variety ROC22, and 312 progenies were obtained. Two bulks of progenies were then constructed, one consisted of 27 highly smut resistant progenies and the other 24 smut susceptible progenies. Total RNAs of the progenies of each bulk, were pooled and subject to bulked segregant RNA-sequence analysis (BSR-Seq). A total of 164.44 Gb clean data containing 2,341,449 SNPs and 64,999 genes were obtained, 7,295 of which were differentially expressed genes (DEGs). These DEGs were mainly enriched in stress-related metabolic pathways, including carbon metabolism, phenylalanine metabolism, plant hormone signal transduction, glutathione metabolism, and plant-pathogen interactions. Besides, 45,946 high-quality, credible SNPs, a 1.27 Mb region at Saccharum spontaneum chromosome Chr5B (68,904,827 to 70,172,982), and 129 candidate genes were identified to be associated with smut resistance. Among them, twenty-four genes, either encoding key enzymes involved in signaling pathways or being transcription factors, were found to be very closely associated with stress resistance. RT-qPCR analysis demonstrated that they played a positive role in smut resistance. Finally, a potential molecular mechanism of sugarcane and S. scitamineum interaction is depicted that activations of MAPK cascade signaling, ROS signaling, Ca2+ signaling, and PAL metabolic pathway and initiation of the glyoxalase system jointly promote the resistance to S. scitamineum in sugarcane. This study provides potential SNP markers and candidate gene resources for smut resistance breeding in sugarcane.
Collapse
Affiliation(s)
- Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yong-Bao Pan
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Beibei Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- International College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Michael P. Grisham
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|