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Zhang A, Pi W, Wang Y, Li Y, Wang J, Liu S, Cui X, Liu H, Yao D, Zhao R. Update on functional analysis of long non-coding RNAs in common crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1389154. [PMID: 38872885 PMCID: PMC11169716 DOI: 10.3389/fpls.2024.1389154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024]
Abstract
With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.
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Affiliation(s)
- Aijing Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Wenxuan Pi
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yashuo Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yuxin Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jiaxin Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Shuying Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiyan Cui
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Huijing Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Rengui Zhao
- College of Agronomy, Jilin Agricultural University, Changchun, China
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Li X, Zhang L, Wei X, Datta T, Wei F, Xie Z. Polyploidization: A Biological Force That Enhances Stress Resistance. Int J Mol Sci 2024; 25:1957. [PMID: 38396636 PMCID: PMC10888447 DOI: 10.3390/ijms25041957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.
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Affiliation(s)
- Xiaoying Li
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Luyue Zhang
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Tanusree Datta
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Fang Wei
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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Jiang S, Zhang JX, Shen WL, Lu Y, Zhou SL, Dong XM, Liao MJ, Bi ZF, Hu Q, Yao W, Zhang MQ, Gao SJ, Xiao SH. Genome-wide identification of GTE family proteins in sugarcane (Saccharum spontaneum) reveals that SsGTEL3a confers drought tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108169. [PMID: 37977028 DOI: 10.1016/j.plaphy.2023.108169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/29/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
The bromodomain is a highly conserved protein domain that specifically binds to acetylated lysine residues in histones, thereby activating transcription of target genes. Although some progress in Global Transcription Factor Group E (GTE) has been achieved in numerous animals and a few plant species, no systematic analysis of GTE gene families has been reported yet in sugarcane. In our study, 37 GTE and GTE-Like (GTEL) genes were characterized in the Saccharum spontaneum. All SsGTE/SsGTEL members were heterogeneously located on all chromosomes of the sugarcane genome and divided into five groups. Transcriptome data showed that SsGTEL3a was expressed at significantly higher levels under drought stress in drought-resistant varieties than in drought-sensitive varieties. Moreover, the overexpression of SsGTEL3a significantly improved the drought tolerance in Arabidopsis through improving the scavenging ability of reactive oxygen species. Additionally, an interaction between ScFAR1 and SsGTEL3a was identified, with ScFAR1 showing a positive response to drought stress in bacterium. In summary, this systematic analysis of GTE gene family in sugarcane and functional research of SsGTEL3a broadened deeper insight into their evolutionary dynamics and functional properties and provided new candidate genes for drought-resistant molecular breeding of sugarcane.
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Affiliation(s)
- Shuo Jiang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Jin-Xu Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Wen-Long Shen
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Yan Lu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Shao-Li Zhou
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Xian-Man Dong
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Ming-Jing Liao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Zhao-Fu Bi
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Qin Hu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Mu-Qing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Sheng-Hua Xiao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China.
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Li H, Gui Y, Zhu K, Wei J, Zhang R, Yang R, Tang L, Zhou H, Liu X. Comparative transcriptomic analyses of two sugarcane Saccharum L. cultivars differing in drought tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1243664. [PMID: 37885666 PMCID: PMC10598656 DOI: 10.3389/fpls.2023.1243664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, beta-alanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future.
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Affiliation(s)
- Haibi Li
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Yiyun Gui
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kai Zhu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jinju Wei
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ronghua Zhang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rongzhong Yang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Liqiu Tang
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Hui Zhou
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xihui Liu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
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