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Wang Z, Peng Z, Khan S, Qayyum A, Rehman A, Du X. Unveiling the power of MYB transcription factors: Master regulators of multi-stress responses and development in cotton. Int J Biol Macromol 2024; 276:133885. [PMID: 39019359 DOI: 10.1016/j.ijbiomac.2024.133885] [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: 02/03/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
Plants, being immobile, are subject to environmental stresses more than other creatures, necessitating highly effective stress tolerance systems. Transcription factors (TFs) play a crucial role in the adaptation mechanism as they can be activated by diverse signals and ultimately control the expression of stress-responsive genes. One of the most prominent plant TFs family is MYB (myeloblastosis), which is involved in secondary metabolites, developmental mechanisms, biological processes, cellular architecture, metabolic pathways, and stress responses. Extensive research has been conducted on the involvement of MYB TFs in crops, while their role in cotton remains largely unexplored. We also utilized genome-wide data to discover potential 440 MYB genes and investigated their plausible roles in abiotic and biotic stress conditions, as well as in different tissues across diverse transcriptome databases. This review primarily summarized the structure and classification of MYB TFs biotic and abiotic stress tolerance and their role in secondary metabolism in different crops, especially in cotton. However, it intends to identify gaps in current knowledge and emphasize the need for further research to enhance our understanding of MYB roles in plants.
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Affiliation(s)
- Zhenzhen Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan 455000, China; Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Zhen Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan 455000, China
| | - Sana Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38040, Pakistan
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan 455000, China.
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan 455000, China.
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Shan S, Tang P, Wang R, Ren Y, Wu B, Yan N, Zhang G, Niu N, Song Y. The characteristic analysis of TaTDF1 reveals its function related to male sterility in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:746. [PMID: 39098914 PMCID: PMC11299293 DOI: 10.1186/s12870-024-05456-z] [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: 11/04/2023] [Accepted: 07/26/2024] [Indexed: 08/06/2024]
Abstract
BACKGROUND The male sterile lines are an important foundation for heterosis utilization in wheat (Triticum aestivum L.). Thereinto, pollen development is one of the indispensable processes of wheat reproductive development, and its fertility plays an important role in wheat heterosis utilization, and are usually influencing by genes. However, these key genes and their regulatory networks during pollen abortion are poorly understood in wheat. RESULTS DEFECTIVE IN TAPETAL DEVELOPMENT AND FUNCTION 1 (TDF1) is a member of the R2R3-MYB family and has been shown to be essential for early tapetal layer development and pollen grain fertility in rice (Oryza sativa L.) and Arabidopsis thaliana. In order to clarify the function of TDF1 in wheat anthers development, we used OsTDF1 gene as a reference sequence and homologous cloned wheat TaTDF1 gene. TaTDF1 is localized in the nucleus. The average bolting time of Arabidopsis thaliana overexpressed strain (TaTDF1-OE) was 33 d, and its anther could be colored normally by Alexander staining solution, showing red. The dominant Mosaic suppression silence-line (TaTDF1-EAR) was blue-green in color, and the anthers were shrimpy and thin. The TaTDF1 interacting protein (TaMAP65) was confirmed using Yeast Two-Hybrid Assay (Y2H) and Bimolecular-Fluorescence Complementation (BiFC) experiments. The results showed that downregulated expression of TaTDF1 and TaMAP65 could cause anthers to be smaller and shrunken, leading to pollen abortion in TaTDF1 wheat plants induced by virus-induced gene-silencing technology. The expression pattern of TaTDF1 was influenced by TaMAP65. CONCLUSIONS Thus, systematically revealing the regulatory mechanism of wheat TaTDF1 during anther and pollen grain development may provide new information on the molecular mechanism of pollen abortion in wheat.
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Affiliation(s)
- Sicong Shan
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- National Yangling Agricultural Biotechnology & Breeding Center/Yangling Branch of State Wheat Improvement Center/Wheat Breeding Engineering Research Center, Ministry of Education/Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Peng Tang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- National Yangling Agricultural Biotechnology & Breeding Center/Yangling Branch of State Wheat Improvement Center/Wheat Breeding Engineering Research Center, Ministry of Education/Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Rui Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- National Yangling Agricultural Biotechnology & Breeding Center/Yangling Branch of State Wheat Improvement Center/Wheat Breeding Engineering Research Center, Ministry of Education/Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Yihang Ren
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- National Yangling Agricultural Biotechnology & Breeding Center/Yangling Branch of State Wheat Improvement Center/Wheat Breeding Engineering Research Center, Ministry of Education/Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Baolin Wu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- National Yangling Agricultural Biotechnology & Breeding Center/Yangling Branch of State Wheat Improvement Center/Wheat Breeding Engineering Research Center, Ministry of Education/Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Nuo Yan
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- National Yangling Agricultural Biotechnology & Breeding Center/Yangling Branch of State Wheat Improvement Center/Wheat Breeding Engineering Research Center, Ministry of Education/Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Gaisheng Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- National Yangling Agricultural Biotechnology & Breeding Center/Yangling Branch of State Wheat Improvement Center/Wheat Breeding Engineering Research Center, Ministry of Education/Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Na Niu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.
- National Yangling Agricultural Biotechnology & Breeding Center/Yangling Branch of State Wheat Improvement Center/Wheat Breeding Engineering Research Center, Ministry of Education/Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China.
| | - Yulong Song
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, P.R. China.
- National Yangling Agricultural Biotechnology & Breeding Center/Yangling Branch of State Wheat Improvement Center/Wheat Breeding Engineering Research Center, Ministry of Education/Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China.
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Yuan Y, Huang C, Pan K, Yao W, Xia R, Zhang M. Small RNA and Degradome Deep Sequencing Reveal Regulatory Roles of MicroRNAs in Response to Sugarcane Mosaic Virus Infection on Two Contrasting Sugarcane Cultivars. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:583-593. [PMID: 38598845 DOI: 10.1094/mpmi-12-23-0220-r] [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: 04/12/2024]
Abstract
MicroRNAs (miRNAs) play an essential regulatory role in plant-virus interaction. However, few studies have focused on the roles of miRNAs and their targets after sugarcane mosaic virus (SCMV) infection in sugarcane. To address this issue, we conducted small RNA (sRNA) and degradome sequencing on two contrasting sugarcanes (SCMV-resistant 'Fuoguo1' [FG1] and susceptible 'Badila') infected by SCMV at five time points. A total of 1,578 miRNAs were profiled from 30 sRNA libraries, comprising 660 known miRNAs and 380 novel miRNAs. Differential expression analysis of miRNAs revealed that most were highly expressed during the SCMV exponential phase in Badila at 18 h postinfection, with expression profiles positively correlated with virus replication dynamics as observed through clustering. Analysis of degradome data indicated a higher number of differential miRNA targets in Badila compared to FG1 at 18 h postinfection. Gene ontology (GO) enrichment analysis significantly enriched the stimulus-response pathway, suggesting negative regulatory roles to SCMV resistance. Specifically, miR160 upregulated expression patterns and validated in Badila through quantitative real-time PCR (qRT-PCR) in the early stages of SCMV multiplication. Our research provides new insights into the dynamic response of plant miRNA and virus replication and contributes valuable information on the intricate interplay between miRNAs and SCMV infection dynamics. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Agro-Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530005, China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 570105, China
| | - Cuilin Huang
- State Key Laboratory for Conservation and Utilization of Agro-Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Kaiyuan Pan
- State Key Laboratory for Conservation and Utilization of Agro-Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Agro-Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Agro-Bioresources, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530005, China
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Zhou SL, Zhang JX, Jiang S, Lu Y, Huang YS, Dong XM, Hu Q, Yao W, Zhang MQ, Xiao SH. Genome-wide identification of JAZ gene family in sugarcane and function analysis of ScJAZ1/2 in drought stress response and flowering regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108577. [PMID: 38579542 DOI: 10.1016/j.plaphy.2024.108577] [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: 11/02/2023] [Revised: 03/06/2024] [Accepted: 03/28/2024] [Indexed: 04/07/2024]
Abstract
The JASMONATE ZIM DOMAIN (JAZ) proteins are a key inhibitors of the jasmonic acid (JA) signaling pathway that play an important role in the regulation of plant growth and development and environmental stress responses. However, there is no systematic identification and functional analysis of JAZ gene family members in sugarcane. In this study, a total of 49 SsJAZ genes were identified from the wild sugarcane species Saccharum spontaneum genome that were unevenly distributed on 13 chromosomes. Phylogenetic analysis showed that all SsJAZ members can be divided into six groups, and most of the SsJAZ genes contained photoreactive and ABA-responsive elements. RNA-seq analysis revealed that SsJAZ1-1/2/3/4 and SsJAZ7-1 were significantly upregulated under drought stress. The transcript level of ScJAZ1 which is the homologous gene of SsJAZ1 in modern sugarcane cultivars was upregulated by JA, PEG, and abscisic acid (ABA). Moreover, ScJAZ1 can interact with three other JAZ proteins to form heterodimers. The spatial and temporal expression analysis showed that SsJAZ2-1/2/3/4 were highly expressed in different tissues and growth stages and during the day-night rhythm between 10:00 and 18:00. Overexpression of ScJAZ2 in Arabidopsis accelerated flowering through activating the expression of AtSOC1, AtFT, and AtLFY. Moreover, the transcription level of ScJAZ2 was about 30-fold in the early-flowering sugarcane variety than that of the non-flowering variety, indicating ScJAZ2 positively regulated flowering. This first systematic analysis of the JAZ gene family and function analysis of ScJAZ1/2 in sugarcane provide key candidate genes and lay the foundation for sugarcane breeding.
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Affiliation(s)
- 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, 530005, 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, 530005, China
| | - 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, 530005, 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, 530005, China
| | - Yong-Shuang Huang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, 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, 530005, 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, 530005, 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, 530005, 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, 530005, 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, 530005, China; Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530005, China.
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Fang J, Chai Z, Huang C, Huang R, Chen B, Yao W, Zhang M. Functional characterization of sugarcane ScFTIP1 reveals its role in Arabidopsis flowering. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108629. [PMID: 38626657 DOI: 10.1016/j.plaphy.2024.108629] [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: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 04/18/2024]
Abstract
The timing of floral transition is essential for reproductive success in flowering plants. In sugarcane, flowering time affects the production of sugar and biomass. Although the function of the crucial floral pathway integrators, FLOWERING LOCUS T (FT), in sugarcane, has been uncovered, the proteins responsible for FT export and the underlying mechanism remain unexplored. In this study, we identified a member of the multiple C2 domain and transmembrane region proteins (MCTPs) family in sugarcane, FT-interacting protein 1 (ScFTIP1), which was localized to the endoplasmic reticulum. Ectopic expression of ScFTIP1 in the Arabidopsis mutant ftip1-1 rescued the late-flowering phenotype. ScFTIP1 interacted with AtFT in vitro and in vivo assays. Additionally, ScFTIP1 interacted with ScFT1 and the floral inducer ScFT3. Furthermore, we found that the NAC member, ScNAC23, could directly bind to the ScFTIP1 promoter and negatively regulate its transcription. Overall, our findings revealed the function of ScFTIP1 and proposed a potential mechanism underlying flowering regulation in sugarcane.
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Affiliation(s)
- Jinlan Fang
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zhe Chai
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cuilin Huang
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Run Huang
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Wei Yao
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
| | - Muqing Zhang
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
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Wu X, Cui Z, Li X, Yu Z, Lin P, Xue L, Khan A, Ou C, Deng Z, Zhang M, Yao W, Yu F. Identification and characterization of PAL genes involved in the regulation of stem development in Saccharum spontaneum L. BMC Genom Data 2024; 25:38. [PMID: 38689211 PMCID: PMC11061975 DOI: 10.1186/s12863-024-01219-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/12/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Saccharum spontaneum L. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane. RESULTS In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage. CONCLUSIONS The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving.
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Affiliation(s)
- Xiaoqing Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Zetian Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Xinyi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Zehuai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Pingping Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Li Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Abdullah Khan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Cailan Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Zuhu Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China.
| | - Fan Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China.
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Liu X, Yan W, Liu S, Wu J, Leng P, Hu Z. LiNAC100 contributes to linalool biosynthesis by directly regulating LiLiS in Lilium 'Siberia'. PLANTA 2024; 259:73. [PMID: 38393405 DOI: 10.1007/s00425-024-04340-2] [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: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/25/2024]
Abstract
MAIN CONCLUSION The transcription factor LiNAC100 has a novel function of regulating floral fragrance by directly regulating linalool synthase gene LiLiS. Lilium 'Siberia', an Oriental hybrid, is renowned as both a cut flower and garden plant, prized for its color and fragrance. The fragrance comprises volatile organic compounds (VOCs), primarily monoterpenes found in the plant. While the primary terpene synthases in Lilium 'Siberia' were identified, the transcriptional regulation of these terpene synthase (TPS) genes remains unclear. Thus, understanding the regulatory mechanisms of monoterpene biosynthesis is crucial for breeding flower fragrance, thereby improving ornamental and commercial values. In this study, we isolated a nuclear-localized LiNAC100 transcription factor from Lilium 'Siberia'. The virus-induced gene silencing (VIGS) of LiNAC100 was found to down-regulate the expression of linalool synthase gene (LiLiS) and significantly inhibit linalool synthesis. Conversely, transient overexpression of LiNAC100 produced opposite effects. Additionally, yeast one-hybrid and dual-luciferase assays confirmed that LiNAC100 directly activates LiLiS expression. Our findings reveal that LiNAC100 plays a key role in monoterpene biosynthesis in Lilium 'Siberia', promoting linalool synthesis through the activation of LiLiS expression. These results offer insights into the molecular mechanisms of terpene biosynthesis in Lilium 'Siberia' and open avenues for biotechnological enhancement of floral scent.
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Affiliation(s)
- Xuping Liu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Engineering Research Center of Rural Landscape Planning and Design, Beijing, 102206, China
| | - Wenxin Yan
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Engineering Research Center of Rural Landscape Planning and Design, Beijing, 102206, China
| | - Sijia Liu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Engineering Research Center of Rural Landscape Planning and Design, Beijing, 102206, China
| | - Jing Wu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Engineering Research Center of Rural Landscape Planning and Design, Beijing, 102206, China
| | - Pingsheng Leng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Engineering Research Center of Rural Landscape Planning and Design, Beijing, 102206, China.
| | - Zenghui Hu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Engineering Research Center of Rural Landscape Planning and Design, Beijing, 102206, China.
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Ding H, Feng X, Yuan Y, Wang B, Wang Y, Zhang J. Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum. BMC Genomics 2024; 25:165. [PMID: 38336615 PMCID: PMC10854099 DOI: 10.1186/s12864-024-10073-z] [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: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes. RESULTS Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases. CONCLUSIONS This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.
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Affiliation(s)
- Hongyan Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Xiaoxi Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuhao Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
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9
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Huang Z, Wang C, Li H, Zhou Y, Duan Z, Bao Y, Hu Q, Powell CA, Chen B, Zhang J, Zhang M, Yao W. Small secreted effector protein from Fusarium sacchari suppresses host immune response by inhibiting ScPi21-induced cell death. MOLECULAR PLANT PATHOLOGY 2024; 25:e13414. [PMID: 38279852 PMCID: PMC10782473 DOI: 10.1111/mpp.13414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 01/29/2024]
Abstract
Fusarium sacchari is one of the primary pathogens causing pokkah boeng disease, which impairs the yield and quality of sugarcane around the world. Understanding the molecular mechanisms of the F. sacchari effectors that regulate plant immunity is of great importance for the development of novel strategies for the persistent control of pokkah boeng disease. In a previous study, Fs00367 was identified to inhibit BAX-induced cell death. In this study, Fs00367nsp (without signal peptide) was found to suppress BAX-induced cell death, reactive oxygen species bursts and callose accumulation. The amino acid region 113-142 of Fs00367nsp is the functional region. Gene mutagenesis indicated that Fs00367 is important for the full virulence of F. sacchari. A yeast two-hybrid assay revealed an interaction between Fs00367nsp and sugarcane ScPi21 in yeast that was further confirmed using bimolecular fluorescence complementation, pull-down assay and co-immunoprecipitation. ScPi21 can induce plant immunity, but this effect could be blunted by Fs00367nsp. These results suggest that Fs00367 is a core pathogenicity factor that suppresses plant immunity through inhibiting ScPi21-induced cell death. The findings of this study provide new insights into the molecular mechanisms of effectors in regulating plant immunity.
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Affiliation(s)
- Zhen Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
| | - Caixia Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
| | - Huixue Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
| | - Yuming Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
| | - Zhenzhen Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
| | - Yixue Bao
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
| | - Qin Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
| | | | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
- IRREC‐IFASUniversity of FloridaFort PierceFloridaUSA
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agri‐Biological Resources, Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
- IRREC‐IFASUniversity of FloridaFort PierceFloridaUSA
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10
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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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11
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Rao X, Qian Z, Xie L, Wu H, Luo Q, Zhang Q, He L, Li F. Genome-Wide Identification and Expression Pattern of MYB Family Transcription Factors in Erianthus fulvus. Genes (Basel) 2023; 14:2128. [PMID: 38136950 PMCID: PMC10743048 DOI: 10.3390/genes14122128] [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: 10/24/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
MYB family genes have many functions and are widely involved in plant abiotic-stress responses. Erianthus fulvus is an important donor material for stress-resistance genes in sugarcane breeding. However, the MYB family genes in E. fulvus have not been systematically investigated. In this study, 133 EfMYB genes, including 48 Ef1R-MYB, 84 EfR2R3-MYB and 1 Ef3R-MYB genes, were identified in the E. fulvus genome. Among them, the EfR2R3-MYB genes were classified into 20 subgroups. In addition, these EfMYB genes were unevenly distributed across 10 chromosomes. A total of 4 pairs of tandemly duplicated EfMYB genes and 21 pairs of segmentally duplicated EfMYB genes were identified in the E. fulvus genome. Protein-interaction analysis predicted that 24 EfMYB proteins had potential interactions with 14 other family proteins. The EfMYB promoter mainly contains cis-acting elements related to the hormone response, stress response, and light response. Expression analysis showed that EfMYB39, EfMYB84, and EfMYB124 could be significantly induced using low-temperature stress. EfMYB30, EfMYB70, EfMYB81, and EfMYB101 responded positively to drought stress. ABA treatment significantly induced EfMYB1, EfMYB30, EfMYB39, EfMYB84, and EfMYB130. All nine genes were induced using MeJA treatment. These results provide comprehensive information on EfMYB genes and can serve as a reference for further studies of gene function.
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Affiliation(s)
- Xibing Rao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Zhenfeng Qian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Linyan Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Huaying Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Quan Luo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Qiyue Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Lilian He
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Fusheng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
- The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Kunming 650201, China
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming 650201, China
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12
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Qin S, Wei F, Liang Y, Tang D, Lin Q, Miao J, Wei K. Genome-wide analysis of the R2R3-MYB gene family in Spatholobus suberectus and identification of its function in flavonoid biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1219019. [PMID: 37670861 PMCID: PMC10476624 DOI: 10.3389/fpls.2023.1219019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
Spatholobus suberectus Dunn (S. suberectus), a plant species within the Leguminosae family, has a long history of use in traditional medicines. The dried stem of S. suberectus exhibits various pharmacological activities because it contains various flavonoids. Diverse functions in plants are associated with the R2R3-MYB gene family, including the biosynthesis of flavonoids. Nonetheless, its role remains unelucidated in S. suberectus. Therefore, the newly sequenced S. suberectus genome was utilized to conduct a systematic genome-wide analysis of the R2R3-MYB gene family. The resulting data identified 181 R2R3-SsMYB genes in total, which were then categorized by phylogenetic analysis into 35 subgroups. Among the R2R3-SsMYB genes, 174 were mapped to 9 different chromosomes, and 7 genes were not located on any chromosome. Moreover, similarity in terms of exon-intron structures and motifs was exhibited by most genes in the same subgroup. The expansion of the gene family was primarily driven by segmental duplication events, as demonstrated by collinearity analysis. Notably, most of the duplicated genes underwent purifying selection, which was depicted through the Ka/Ks analysis. In this study, 22 R2R3-SsMYB genes were shown to strongly influence the level of flavonoids. The elevated expression level of these genes was depicted in the tissues with flavonoid accumulation in contrast with other tissues through qRT-PCR data. The resulting data elucidate the structural and functional elements of R2R3-SsMYB genes and present genes that could potentially be utilized for enhancing flavonoid biosynthesis in S. suberectus.
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Affiliation(s)
- Shuangshuang Qin
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Fan Wei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ying Liang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Danfeng Tang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Quan Lin
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jianhua Miao
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Kunhua Wei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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13
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Li Z, Wang J, Wang J. Identification of a Comprehensive Gene Co-Expression Network Associated with Autotetraploid Potato ( Solanum tuberosum L.) Development Using WGCNA Analysis. Genes (Basel) 2023; 14:1162. [PMID: 37372342 DOI: 10.3390/genes14061162] [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: 04/06/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
The formation and development of potato tissues and organs is a complex process regulated by a variety of genes and environmental factors. The regulatory mechanisms underlying the growth and development are still unclear. In this work, we aimed to explore the changes in gene expression patterns and genetic characteristics of potato tissues throughout different developmental stages. To achieve this, we used autotetraploid potato JC14 as an experimental subject to analyze the transcriptome of the root, stem, and leaf at the seedling, tuber formation, and tuber expansion stages. The results revealed thousands of differentially expressed genes, predominantly involved in defense response and carbohydrate metabolism according to KEGG pathway enrichment analysis. Weighted gene co-expression network analysis (WGCNA) revealed a total of 12 co-expressed gene modules, with 4 modules showing the highest correlation with potato stem development. By calculating the connectivity of genes within the module, hub genes were identified, and functional annotations were subsequently performed. A total of 40 hub genes from the four modules were identified, and their functions were found to be related to carbohydrate metabolism, defense response, and transcription factors. These findings provide important insights for further understanding of the molecular regulation and genetic mechanisms involved in potato tissue development.
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Affiliation(s)
- Zhimin Li
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Juan Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jiayin Wang
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
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14
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Viswanath KK, Kuo SY, Tu CW, Hsu YH, Huang YW, Hu CC. The Role of Plant Transcription Factors in the Fight against Plant Viruses. Int J Mol Sci 2023; 24:ijms24098433. [PMID: 37176135 PMCID: PMC10179606 DOI: 10.3390/ijms24098433] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Plants are vulnerable to the challenges of unstable environments and pathogen infections due to their immobility. Among various stress conditions, viral infection is a major threat that causes significant crop loss. In response to viral infection, plants undergo complex molecular and physiological changes, which trigger defense and morphogenic pathways. Transcription factors (TFs), and their interactions with cofactors and cis-regulatory genomic elements, are essential for plant defense mechanisms. The transcriptional regulation by TFs is crucial in establishing plant defense and associated activities during viral infections. Therefore, identifying and characterizing the critical genes involved in the responses of plants against virus stress is essential for the development of transgenic plants that exhibit enhanced tolerance or resistance. This article reviews the current understanding of the transcriptional control of plant defenses, with a special focus on NAC, MYB, WRKY, bZIP, and AP2/ERF TFs. The review provides an update on the latest advances in understanding how plant TFs regulate defense genes expression during viral infection.
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Affiliation(s)
- Kotapati Kasi Viswanath
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Song-Yi Kuo
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chin-Wei Tu
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Centre, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Centre, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Centre, National Chung Hsing University, Taichung 40227, Taiwan
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15
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Zhang YS, Xu Y, Xing WT, Wu B, Huang DM, Ma FN, Zhan RL, Sun PG, Xu YY, Song S. Identification of the passion fruit ( Passiflora edulis Sims) MYB family in fruit development and abiotic stress, and functional analysis of PeMYB87 in abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1124351. [PMID: 37215287 PMCID: PMC10196401 DOI: 10.3389/fpls.2023.1124351] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/21/2023] [Indexed: 05/24/2023]
Abstract
Environmental stresses are ubiquitous in agricultural cultivation, and they affect the healthy growth and development of edible tissues in passion fruit. The study of resistance mechanisms is important in understanding the adaptation and resistance of plants to environmental stresses. In this work, two differently resistant passion fruit varieties were selected, using the expression characteristics of the transcription factor MYB, to explore the resistance mechanism of the MYB gene under various environmental stresses. A total of 174 MYB family members were identified using high-quality passion fruit genomes: 98 2R-MYB, 5 3R-MYB, and 71 1R-MYB (MYB-relate). Their family information was systematically analyzed, including subcellular localization, physicochemical properties, phylogeny at the genomic level, promoter function, encoded proteins, and reciprocal regulation. In this study, bioinformatics and transcriptome sequencing were used to identify members of the PeMYB genes in passion fruit whole-genome data, and biological techniques, such as qPCR, gene clone, and transient transformation of yeast, were used to determine the function of the passion fruit MYB genes in abiotic stress tolerance. Transcriptomic data were obtained for differential expression characteristics of two resistant and susceptible varieties, three expression patterns during pulp development, and four induced expression patterns under abiotic stress conditions. We further focused on the resistance mechanism of PeMYB87 in environmental stress, and we selected 10 representative PeMYB genes for quantitative expression verification. Most of the genes were differentially induced by four abiotic stresses, among which PeMYB87 responded significantly to high-temperature-induced expression and overexpression of the PeMYB87 gene in the yeast system. The transgenic PeMYB87 in yeast showed different degrees of stress resistance under exposure to cold, high temperatures, drought, and salt stresses. These findings lay the foundation for further analysis of the biological functions of PeMYBs involved in stress resistance in passion fruit.
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Affiliation(s)
- Yan-shu Zhang
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, Yunnan, China
| | - Yi Xu
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Wen-ting Xing
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Bin Wu
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Dong-mei Huang
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Fu-ning Ma
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Ru-lin Zhan
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Pei-guang Sun
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Yong-yan Xu
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, Yunnan, China
| | - Shun Song
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
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Tang M, Liu L, Hu X, Zheng H, Wang Z, Liu Y, Zhu Q, Cui L, Xie S. Genome-wide characterization of R2R3-MYB gene family in Santalum album and their expression analysis under cold stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1142562. [PMID: 36938022 PMCID: PMC10017448 DOI: 10.3389/fpls.2023.1142562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Sandalwood (Santalum album) is a high-value multifunctional tree species that is rich in aromatic substances and is used in medicine and global cosmetics. Due to the scarcity of land resources in tropical and subtropical regions, land in temperate regions is a potential resource for the development of S. album plantations in order to meet the needs of S. album production and medicine. The R2R3-MYB transcription factor family is one of the largest in plants and plays an important role in the response to various abiotic stresses. However, the R2R3-MYB gene family of S. album has not been studied. In this study, 144 R2R3-MYB genes were successfully identified in the assembly genome sequence, and their characteristics and expression patterns were investigated under various durations of low temperature stress. According to the findings, 31 of the 114 R2R3-MYB genes showed significant differences in expression after cold treatment. Combining transcriptome and weighted gene co-expression network analysis (WGCNA) revealed three key candidate genes (SaMYB098, SaMYB015, and SaMYB068) to be significantly involved in the regulation of cold resistance in S. album. The structural characteristics, evolution, and expression pattern of the R2R3-MYB gene in S. album were systematically examined at the whole genome level for the first time in this study. It will provide important information for future research into the function of the R2R3-MYB genes and the mechanism of cold stress response in S. album.
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Affiliation(s)
- Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Le Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Xu Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Haoyue Zheng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Zukai Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Yi Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Qing Zhu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Shangqian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
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17
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Genome-wide analysis of R2R3-MYB transcription factors reveals their differential responses to drought stress and ABA treatment in desert poplar (Populus euphratica). Gene 2023; 855:147124. [PMID: 36539045 DOI: 10.1016/j.gene.2022.147124] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The R2R3-MYB transcription factors are widely involved in the regulation of plant growth, biotic and abiotic stress responses. Meanwhile, seed germination, which is stimulated by internal and external environments, is a critical stage in the plant life cycle. However, the identification, characterization, and expression profiling of the Populus euphratica R2R3-MYB family in drought response during seed germination have been unknown. Our study attempted to identify and characterize the R2R3-MYB genes in P. euphratica (PeR2R3-MYBs) and explore how R2R3-MYBs trigger the drought and abscisic acid (ABA) response mechanism in its seedlings. Based on the analysis of comparative genomics, 174 PeR2R3-MYBs were identified and expanded driven by whole genome duplication or segment duplication events. The analysis of Ka/Ks ratios showed that, in contrast to most PeR2R3-MYBs, the other PeR2R3-MYBs were subjected to positive selection in P. euphratica. Further, the expression data of PeR2R3-MYBs under drought stress and ABA treatment, together with available functional data for Arabidopsis thaliana MYB genes, supported the hypothesis that PeR2R3-MYBs involved in response to drought are dependent or independent on ABA signaling pathway during seed germination, especially PeR2R3-MYBs with MYB binding sites (MBS) cis-element and/or tandem duplication. This study is the first report on the genome-wide analysis of PeR2R3-MYBs, as well as the other two Salicaceae species. The duplication events and differential expressions of PeR2R3-MYBs play important roles in enhancing the adaptation to drought desert environment. Our results provide a reference for prospective functional studies of R2R3-MYBs of poplars and lay the foundation for new breeding strategies to improve the drought tolerance of P. euphratica.
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18
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Ding Y, Yang Q, Waheed A, Zhao M, Liu X, Kahar G, Haxim Y, Wen X, Zhang D. Genome-wide characterization and functional identification of MYB genes in Malus sieversii infected by Valsa mali. FRONTIERS IN PLANT SCIENCE 2023; 14:1112681. [PMID: 37089647 PMCID: PMC10113540 DOI: 10.3389/fpls.2023.1112681] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Among the most important transcription factors in plants, the v-myb avian myeloblastosis viral oncogene homolog (MYB) regulates the expression network of response genes under stresses such as fungal infection. In China, the canker disease Valsa mali threatens the survival of Malus sieversii, an ancestor of cultivated apples. Using the M. sieversii genome, we identified 457 MsMYB and 128 R2R3-MsMYB genes that were randomly distributed across 17 chromosomes. Based on protein sequence and structure, the R2R3-MsMYB genes were phylogenetically divided into 29 categories, and 26 conserved motifs were identified. We further predicted cis-elements in the 2000-kb promoter region of R2R3-MsMYBs based on the genome. Transcriptome analysis of M. sieversii under V. mali infection showed that 27 R2R3-MsMYBs were significantly differentially expressed, indicating their key role in the response to V. mali infection. Using transient transformation, MsMYB14, MsMYB24, MsMYB39, MsMYB78, and MsMYB108, which were strongly induced by V. mali infection, were functionally identified. Among the five MsMYBs, MsMYB14 and MsMYB78 were both important in enhancing resistance to diseases, whereas MsMYB24 inhibited resistance. Based on the results of this study, we gained a better understanding of the MsMYB transcription factor family and laid the foundation for a future research program on disease prevention strategies in M. sieversii.
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Affiliation(s)
- Yu Ding
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Qihang Yang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Abdul Waheed
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Mingqi Zhao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Xiaojie Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Gulnaz Kahar
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yakupjan Haxim
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Xuejing Wen
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
- *Correspondence: Daoyuan Zhang, ; Xuejing Wen,
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
- *Correspondence: Daoyuan Zhang, ; Xuejing Wen,
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Chai Z, Fang J, Yao W, Zhao Y, Cheng G, Akbar S, Khan MT, Chen B, Zhang M. ScGAIL, a sugarcane N-terminal truncated DELLA-like protein, participates in gibberellin signaling in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3462-3476. [PMID: 35172001 DOI: 10.1093/jxb/erac056] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
The hormone gibberellin (GA) is crucial for internode elongation in sugarcane. DELLA proteins are critical negative regulators of the GA signaling pathway. ScGAI encodes a DELLA protein that was previously implicated in the regulation of sugarcane culm development. Here, we characterized ScGAI-like (ScGAIL) in sugarcane, which lacked the N-terminal region but was otherwise homologous to ScGAI. ScGAIL differed from ScGAI in its chromosomal location, expression patterns, and cellular localization. Although transgenic Arabidopsis overexpressing ScGAIL were insensitive to GAs, GA synthesis was affected in these plants, suggesting that ScGAIL disrupted the GA signaling pathway. After GA treatment, the expression patterns of GA-associated genes differed between ScGAIL-overexpressing and wild-type Arabidopsis, and the degradation of AtDELLA proteins in transgenic lines was significantly inhibited compared with wild-type lines. A sugarcane GID1 gene (ScGID1) encoding a putative GA receptor was isolated and interacted with ScGAIL in a GA-independent manner. Five ScGAIL-interacting proteins were verified by yeast two-hybrid assays, and only one interacted with ScGAI. Therefore, ScGAIL may inhibit plant growth by modulating the GA signaling pathway.
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Affiliation(s)
- Zhe Chai
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Jinlan Fang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Yang Zhao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Guangyuan Cheng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sehrish Akbar
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | | | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
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20
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Pucker B. Automatic identification and annotation of MYB gene family members in plants. BMC Genomics 2022; 23:220. [PMID: 35305581 PMCID: PMC8933966 DOI: 10.1186/s12864-022-08452-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. This body of knowledge and characterized sequences provide the basis for the identification, classification, and functional annotation of candidate sequences in new genome and transcriptome assemblies. RESULTS A pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application. The analysis of one species takes only a few minutes depending on the number of predicted sequences and the size of the MYB gene family. This pipeline, the required bait sequences, and reference sequences for a classification are freely available on github: https://github.com/bpucker/MYB_annotator . CONCLUSIONS This automatic annotation of the MYB gene family in novel assemblies makes genome-wide investigations consistent and paves the way for comparative studies in the future. Candidate genes for in-depth analyses are presented based on their orthology to previously characterized sequences which allows the functional annotation of the newly identified MYBs with high confidence. The identification of orthologs can also be harnessed to detect duplication and deletion events.
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Affiliation(s)
- Boas Pucker
- Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Braunschweig, TU, Germany.
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21
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Anwar M, Chen L, Xiao Y, Wu J, Zeng L, Li H, Wu Q, Hu Z. Recent Advanced Metabolic and Genetic Engineering of Phenylpropanoid Biosynthetic Pathways. Int J Mol Sci 2021; 22:9544. [PMID: 34502463 PMCID: PMC8431357 DOI: 10.3390/ijms22179544] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/11/2022] Open
Abstract
The MYB transcription factors (TFs) are evolving as critical role in the regulation of the phenylpropanoid and tanshinones biosynthetic pathway. MYB TFs relate to a very important gene family, which are involved in the regulation of primary and secondary metabolisms, terpenoids, bioactive compounds, plant defense against various stresses and cell morphology. R2R3 MYB TFs contained a conserved N-terminal domain, but the domain at C-terminal sorts them different regarding their structures and functions. MYB TFs suppressors generally possess particular repressive motifs, such as pdLNLD/ELxiG/S and TLLLFR, which contribute to their suppression role through a diversity of complex regulatory mechanisms. A novel flower specific "NF/YWSV/MEDF/LW" conserved motif has a great potential to understand the mechanisms of flower development. In the current review, we summarize recent advanced progress of MYB TFs on transcription regulation, posttranscriptional, microRNA, conserved motif and propose directions to future prospective research. We further suggest there should be more focus on the investigation for the role of MYB TFs in microalgae, which has great potential for heterologous protein expression system for future perspectives.
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Affiliation(s)
- Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (M.A.); (L.C.); (Y.X.); (H.L.); (Q.W.)
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Liu Chen
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (M.A.); (L.C.); (Y.X.); (H.L.); (Q.W.)
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yibo Xiao
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (M.A.); (L.C.); (Y.X.); (H.L.); (Q.W.)
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jinsong Wu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China;
| | - Lihui Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Hui Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (M.A.); (L.C.); (Y.X.); (H.L.); (Q.W.)
| | - Qingyu Wu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (M.A.); (L.C.); (Y.X.); (H.L.); (Q.W.)
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China;
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (M.A.); (L.C.); (Y.X.); (H.L.); (Q.W.)
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China;
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