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Wang H, Qin L, Feng C, Wu M, Zhong H, Liu J, Wu Q, Que Y. Pathogen resistance was negatively regulated by the NAC transcription factor ScATAF1 in sugarcane. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108828. [PMID: 38896914 DOI: 10.1016/j.plaphy.2024.108828] [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: 05/15/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
The NAC (NAM, ATAF, and CUC) is one of the largest transcription factor gene families in plants. In this study, 180, 141, and 131 NAC family members were identified from Saccharum complex, including S. officinarum, S. spontaneum, and Erianthus rufipilus. The Ka/Ks ratio of ATAF subfamily was all less than 1. Besides, 52 ATAF members from 12 representative plants were divided into three clades and there was only a significant expansion in maize. Surprisingly, ABA and JA cis-elements were abundant in hormonal response factor, followed by transcriptional regulator and abiotic stressor. The ATAF subfamily was differentially expressed in various tissues, under low temperature and smut pathogen treatments. Further, the ScATAF1 gene, with high expression in leaves, stem epidermis, and buds, was isolated. The encoded protein, lack of self-activation activity, was situated in the cell nucleus. Moreover, SA and JA stresses down-regulated the expression of this gene, while ABA, NaCl, and 4°C treatments led to its up-regulation. Interestingly, its expression in the smut susceptible sugarcane cultivars was much higher than the smut resistant ones. Notably, the colors presented slight brown in tobacco transiently overexpressing ScATAF1 at 1 d after DAB staining, while the symptoms were more obvious at 3 d after inoculation with Ralstonia solanacearum, with ROS, JA, and SA signaling pathway genes significantly up-regulated. We thus speculated ScATAF1 gene could negatively mediate hypersensitive reactions and produce ROS by JA and SA signaling pathways. These findings lay the groundwork for in-depth investigation on the biological roles of ATAF subfamily in sugarcane.
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Affiliation(s)
- Hengbo Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Instrumental Analysis Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, Haikou, 572024/571101, Hainan, China
| | - Liqian Qin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Instrumental Analysis Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chunyan Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Instrumental Analysis Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Mingxing Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Instrumental Analysis Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hui Zhong
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Instrumental Analysis Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Junhong Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Instrumental Analysis Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, Haikou, 572024/571101, Hainan, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Instrumental Analysis Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, Haikou, 572024/571101, Hainan, China.
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2
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Kumaravel N, Ebinezer LB, Ashwin NMR, Franchin C, Battisti I, Carletti P, Ramesh Sundar A, Masi A, Malathi P, Viswanathan R, Arrigoni G. Comparative proteomics of sugarcane smut fungus - Sporisorium scitamineum unravels dynamic proteomic alterations during the dimorphic transition. J Proteomics 2024; 304:105230. [PMID: 38901800 DOI: 10.1016/j.jprot.2024.105230] [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: 12/11/2023] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
Life cycle of the dimorphic sugarcane smut fungi, Sporisorium scitamineum, involves recognition and mating of compatible saprophytic yeast-like haploid sporidia (MAT-1 and MAT-2) that upon fusion, develop into infective dikaryotic mycelia. Although the dimorphic transition is intrinsically linked with the pathogenicity and virulence of S. scitamineum, it has never been studied using a proteomic approach. In the present study, an iTRAQ-based comparative proteomic analysis of three distinct stages was carried out. The stages were: the dimorphic transition period - haploid sporidial stage (MAT-1 and MAT-2); the transition phase (24 h post co-culturing (hpc)) and the dikaryotic mycelial stage (48 hpc). Functional categorization of differentially abundant proteins showed that the most altered biological processes were energy production, primary metabolism, especially, carbohydrate, amino acid, fatty acid, followed by translation, post-translation and protein turnover. Several differentially abundant proteins (DAPs), especially in the dikaryotic mycelial stage were predicted as effectors. Taken together, key molecular mechanisms underpinning the dimorphic transition in S. scitamineum at the proteome level were highlighted. The catalogue of stage-specific and dimorphic transition-associated-proteins and potential effectors identified herein represents a list of potential candidates for defective mutant screening to elucidate their functional role in the dimorphic transition and pathogenicity in S. scitamineum. BIOLOGICAL SIGNIFICANCE: Being the first comparative proteomics analysis of S. scitamineum, this study comprehensively examined three pivotal life cycle stages of the pathogen: the non-pathogenic haploid phase, the transition phase, and the pathogenic dikaryotic mycelial stage. While previous studies have reported the sugarcane and S. scitamineum interactions, this study endeavored to specifically identify the proteins responsible for pathogenicity. By analyzing the proteomic alterations between the haploid and dikaryotic mycelial phases, the study revealed significant changes in metabolic pathway-associated proteins linked to energy production, notably oxidative phosphorylation, and the citrate cycle. Furthermore, this study successfully identified key metabolic pathways that undergo reprogramming during the transition from the non-pathogenic to the pathogenic stage. The study also deciphered the underlying mechanisms driving the morphological and physiological alterations crucial for the S. scitamineum virulence. By studying its life cycle stages, identifying the key metabolic pathways and stage-specific proteins, it provides unprecedented insights into the pathogenicity and potential avenues for intervention. As proteomics continues to advance, such studies pave the way for a deeper understanding of plant-pathogen interactions and the development of innovative strategies to mitigate the impact of devastating pathogens like S. scitamineum.
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Affiliation(s)
- Nalayeni Kumaravel
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - N M R Ashwin
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; Biochemical Sciences Division, Council of Scientific and Industrial Research - National Chemical Laboratory, Pune 411008, Maharashtra, India.
| | - Cinzia Franchin
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
| | - Ilaria Battisti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Amalraj Ramesh Sundar
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Palaniyandi Malathi
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Rasappa Viswanathan
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; Indian Council of Agricultural Research - Indian Institute of Sugarcane Research, Lucknow, Uttar Pradesh 226002, India.
| | - Giorgio Arrigoni
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
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3
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Rajput MA, Iqbal O, Syed RN, Elsalahy HH, Rajput NA, Ahmad S, Khan R, Khanzada MA, Younas MU, Qasim M, Rizwana H, Almaary KS, Iqbal R, Lodhi AM. Screening of sugarcane germplasm against Sporisorium scitamineum and its effects on setts germination and tillering. Sci Rep 2024; 14:14653. [PMID: 38918529 PMCID: PMC11199591 DOI: 10.1038/s41598-024-64810-1] [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: 04/05/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Sugarcane smut is the most damaging disease that is present almost across the globe, causing mild to severe yield losses depending upon the cultivar types, pathogen races and climatic conditions. Cultivation of smut-resistant cultivars is the most feasible and economical option to mitigate its damages. Previous investigations revealed that there is a scarcity of information on early detection and effective strategies to suppress etiological agents of smut disease due to the characteristics overlapping within species complexes. In this study, 104 sugarcane cultivars were screened by artificial inoculation with homogenate of all possible pathogen races of Sporisorium scitamineum during two consecutive growing seasons. The logistic smut growth pattern and the disease intrinsic rate were recorded by disease growth curve. Variable levels of disease incidence i.e., ranging from 0 to 54.10% were observed among these sugarcane cultivars. Besides, pathogen DNA in plant shoots of all the cultivars was successfully amplified by PCR method using smut-specific primers except 26 cultivars which showed an immune reaction in the field trial. Furthermore, the plant germination and tillering of susceptible sugarcane cultivars were greatly influenced by pathogen inoculation. In susceptible cultivars, S. scitamineum caused a significant reduction in setts germination, coupled with profuse tillering, resulting in fewer millable canes. Correlation analysis demonstrated that there was a positive relationship between reduction in setts germination and increase in the number of tillers. The present study would be helpful for the evaluation of smut resistance in a wide range of sugarcane germplasm, especially from the aspects of setts germination and tillers formation, and it also screened out several excellent germplasm for potential application in sugarcane breeding.
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Affiliation(s)
- Muhammad Aslam Rajput
- CDRI, Pakistan Agricultural Research Council, University of Karachi, Karachi, 75270, Pakistan
- Department of Plant Protection, Faculty of Crop Protection, Sindh Agriculture University, Tandojam, 70060, Pakistan
| | - Owais Iqbal
- Department of Plant Protection, Faculty of Crop Protection, Sindh Agriculture University, Tandojam, 70060, Pakistan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Rehana Naz Syed
- Department of Plant Protection, Faculty of Crop Protection, Sindh Agriculture University, Tandojam, 70060, Pakistan
| | - Heba H Elsalahy
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374, Müncheberg, Germany.
| | - Nasir Ahmed Rajput
- Department of Plant Pathology, University of Agriculture, Faisalabad, 38000, Pakistan.
| | - Sagheer Ahmad
- Plant Sciences Division, Pakistan Agricultural Research Council, Sector G-5/1, Islamabad, Pakistan
| | - Rizwan Khan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Muhammad Ali Khanzada
- Department of Plant Protection, Faculty of Crop Protection, Sindh Agriculture University, Tandojam, 70060, Pakistan
| | - Muhammad Usama Younas
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Muhammad Qasim
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Humaira Rizwana
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, 11451, Riyadh, Saudi Arabia
| | - Khalid S Almaary
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, 11451, Riyadh, Saudi Arabia
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Abdul Mubeen Lodhi
- Department of Plant Protection, Faculty of Crop Protection, Sindh Agriculture University, Tandojam, 70060, Pakistan.
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4
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Zhang C, Li Z, Sun T, Zang S, Wang D, Su Y, Wu Q, Que Y. Sugarcane ScCAX4 is a Negative Regulator of Resistance to Pathogen Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13205-13216. [PMID: 38809782 DOI: 10.1021/acs.jafc.4c00805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Calcium (Ca2+) is a second messenger in various physiological processes within plants. The significance of the Ca2+/H+ exchanger (CAX) has been established in facilitating Ca2+ transport in plants; however, disease resistance functions of the CAX gene remain elusive. In this study, we conducted sequence characterization and expression analysis for a sugarcane CAX gene, ScCAX4 (GenBank Accession Number: MW206380). In order to further investigate the disease resistance functions, this gene was then transiently overexpressed in Nicotiana benthamiana leaves, which were subsequently inoculated with Fusarium solani var. coeruleum. Results showed that ScCAX4 overexpression increased the susceptibility of N. benthamiana to pathogen infection by regulating the expression of genes related to salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) pathways, suggesting its negative role in disease resistance. Furthermore, we genetically transformed the ScCAX4 gene into N. benthamiana and obtained three positive T2 generation lines. Interestingly, the symptomatology of transgenic plants was consistent with that of transient overexpression after pathogen inoculation. Notably, the JA content in transgenic overexpression lines was significantly higher than that in the wild-type. RNA-seq revealed that ScCAX4 could mediate multiple signaling pathways, and the JA signaling pathway played a key role in modulating disease resistance. Finally, a regulatory model was depicted for the increased susceptibility to pathogen infection conferred by the ScCAX4 gene. This study provides genetic resources for sugarcane molecular breeding and the research direction for plant CAX genes.
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Affiliation(s)
- Chang Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenxiang Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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5
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Wu Q, Zhang C, Xu F, Zang S, Wang D, Sun T, Su Y, Yang S, Ding Y, Que Y. Transcriptional Regulation of SugarCane Response to Sporisorium scitamineum: Insights from Time-Course Gene Coexpression and Ca 2+ Signaling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10506-10520. [PMID: 38651833 PMCID: PMC11082935 DOI: 10.1021/acs.jafc.4c02123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Sugarcane response to Sporisorium scitamineum is determined by multiple major genes and numerous microeffector genes. Here, time-ordered gene coexpression networks were applied to explore the interaction between sugarcane and S. scitamineum. Totally, 2459 differentially expressed genes were identified and divided into 10 levels, and several stress-related subnetworks were established. Interestingly, the Ca2+ signaling pathway was activated to establish the response to sugarcane smut disease. Accordingly, two CAX genes (ScCAX2 and ScCAX3) were cloned and characterized from sugarcane. They were significantly upregulated under ABA stress but inhibited by MeJA treatment. Furthermore, overexpression of ScCAX2 and ScCAX3 enhanced the susceptibility of transgenic plants to the pathogen infection, suggesting its negative role in disease resistance. A regulatory model for ScCAX genes in disease response was thus depicted. This work helps to clarify the transcriptional regulation of sugarcane response to S. scitamineum stress and the function of the CAX gene in disease response.
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Affiliation(s)
- Qibin Wu
- National
Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience
and Biotechnology, Chinese Academy of Tropical
Agricultural Sciences, Sanya 572024, Haikou 571101, Hainan, China
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang Zhang
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Fu Xu
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongjiao Wang
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Tingting Sun
- National
Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience
and Biotechnology, Chinese Academy of Tropical
Agricultural Sciences, Sanya 572024, Haikou 571101, Hainan, China
| | - Yachun Su
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Shaolin Yang
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
- Yunnan
Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research
Institute, Yunnan Academy of Agricultural
Sciences, Kaiyuan 661600, China
| | - Yinghong Ding
- College
of Landscape Architecture and Art, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
| | - Youxiong Que
- National
Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience
and Biotechnology, Chinese Academy of Tropical
Agricultural Sciences, Sanya 572024, Haikou 571101, Hainan, China
- Key
Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of
Agriculture and Rural Affairs, National Engineering Research Center
for Sugarcane, College of Agriculture, Fujian
Agriculture and Forestry University, Fuzhou 350002, China
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6
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Hu X, Luo Z, Xu C, Wu Z, Wu C, Ebid MHM, Zan F, Zhao L, Liu X, Liu J. A Comprehensive Analysis of Transcriptomics and Metabolomics Revealed Key Pathways Involved in Saccharum spontaneum Defense against Sporisorium scitamineum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4476-4492. [PMID: 38373255 DOI: 10.1021/acs.jafc.3c07768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Sugarcane smut, caused by Sporisorium scitamineum, poses a severe threat to sugarcane production. The genetic basis of sugarcane resistance to S. scitamineum remains elusive. A comparative transcriptomic and metabolomic study was conducted on two wild Saccharum species of S. spontaneum with contrast smut resistance. Following infection, the resistant line exhibited greater down-regulation of genes and metabolites compared to the susceptible line, indicating distinct biological processes. Lignan and lignin biosynthesis and SA signal transduction were activated in the resistant line, while flavonoid biosynthesis and auxin signal transduction were enhanced in the susceptible line. TGA2.2 and ARF14 were identified as playing positive and negative roles, respectively, in plant defense. Exogenous auxin application significantly increased the susceptibility of S. spontaneum to S. scitaminum. This study established the significant switching of defense signaling pathways in contrast-resistant S. spontaneum following S. scitamineum infection, offering a hypothetical model and candidate genes for further research into sugarcane smut disease.
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Affiliation(s)
- Xin Hu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Zhengying Luo
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Chaohua Xu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Zhuandi Wu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Caiwen Wu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Mahmoud H M Ebid
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Fengang Zan
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Liping Zhao
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Xinlong Liu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
| | - Jiayong Liu
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China
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7
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Zhu P, Li H, Lu T, Liang R, Wan B. Combined analysis of mRNA and miRNA transcriptomes reveals the regulatory mechanism of Xanthomonas arboricola pv pruni resistance in Prunus persica. BMC Genomics 2024; 25:214. [PMID: 38413907 PMCID: PMC10898114 DOI: 10.1186/s12864-024-10113-8] [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: 08/10/2023] [Accepted: 02/11/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Peach bacterial shot hole, caused by Xanthomonas arboricola pv pruni (Xap), is a global bacterial disease that poses a threat to the yield and quality of cultivated peach trees (Prunus persica). RESULTS This study compared the mRNA and miRNA profiles of two peach varieties, 'Yanbao' (resistant) and 'Yingzui' (susceptible), after inoculation with Xap to identify miRNAs and target genes associated with peach tree resistance. mRNA sequencing results revealed that in the S0-vs-S3 comparison group, 1574 genes were upregulated and 3975 genes were downregulated. In the R0-vs-R3 comparison group, 1575 genes were upregulated and 3726 genes were downregulated. Through miRNA sequencing, a total of 112 known miRNAs belonging to 70 miRNA families and 111 new miRNAs were identified. Notably, some miRNAs were exclusively expressed in either resistant or susceptible varieties. Additionally, 59 miRNAs were downregulated and 69 miRNAs were upregulated in the R0-vs-R3 comparison group, while 46 miRNAs were downregulated and 52 miRNAs were upregulated in the S0-vs-S3 comparison group. Joint analysis of mRNA and miRNA identified 79 relationship pairs in the S0-vs-S3 comparison group, consisting of 48 miRNAs and 51 target genes. In the R0-vs-R3 comparison group, there were 58 relationship pairs, comprising 28 miRNAs and 20 target genes. Several target genes related to resistance, such as SPL6, TIFY6B, and Prupe.4G041800_v2.0.a1 (PPO), were identified through literature reports and GO/KEGG enrichment analysis. CONCLUSION In conclusion, this study discovered several candidate genes involved in peach tree resistance by analyzing differential expression of mRNA and miRNA. These findings provide valuable insights into the mechanisms underlying resistance to Xap in peach trees.
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Affiliation(s)
- Pengxiang Zhu
- Guangxi Academy of Specialty Crops, Guilin, 541004, China
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China
| | - Haiyan Li
- Guangxi Academy of Specialty Crops, Guilin, 541004, China
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China
| | - Tailiang Lu
- Guangxi Academy of Specialty Crops, Guilin, 541004, China
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China
| | - Ruizheng Liang
- Guangxi Academy of Specialty Crops, Guilin, 541004, China.
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China.
| | - Baoxiong Wan
- Guangxi Academy of Specialty Crops, Guilin, 541004, China.
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China.
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8
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Zhou S, Lin Y, Cai Y, Li L, Yao X, Sun K, Song Q, Zhang Q. The response of rhubarb to smut infection is revealed through a comparative transcriptome and metabolome study. PLANTA 2023; 259:27. [PMID: 38112830 DOI: 10.1007/s00425-023-04306-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
MAIN CONCLUSION Integrated transcriptome and metabolome analysis have unveiled the physiological and molecular responses of rhubarb to infection by smut fungi. Rhubarb is an important medicinal plant that is easily infected by smut fungi during its growth. Thus far, no research on the influence of smut fungi on the growth of rhubarb and its secondary metabolism has been conducted. In this study, petioles of Chinese rhubarb (Rheum officinale) [healthy or infected with smut fungus (Thecaphora schwarzmaniana)] were characterized. Microscopic structure, global gene expression profiling, global metabolic profiling, and key enzyme activity and metabolite levels in infected plants were analyzed. Infection by smut fungi resulted in numerous holes inside the petiole tissue and led to visible tumors on the external surface of the petiole. Through metabolic changes, T. schwarzmaniana induced the production of specific sugars, lipids, and amino acids, and inhibited the metabolism of phenolics and flavonoids in R. officinale. The concentrations of key medicinal compounds (anthraquinones) were decreased because of smut fungus infection. In terms of gene expression, the presence of T. schwarzmaniana led to upregulation of the genes associated with nutrient (sugar, amino acid, etc.) transport and metabolism. The gene expression profiling showed a stimulated cell division activity (the basis of tumor formation). Although plant antioxidative response was enhanced, the plant defense response against pathogen was suppressed by T. schwarzmaniana, as indicated by the expression profiling of genes involved in biotic and abiotic stress-related hormone signaling and the synthesis of plant disease resistance proteins. This study demonstrated physiological and molecular changes in R. officinale under T. schwarzmaniana infection, reflecting the survival tactics employed by smut fungus for parasitizing rhubarb.
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Affiliation(s)
- Shuangshuang Zhou
- Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Chongqing Nanchuan Institute of Traditional Chinese Medicinal Plants, Chongqing, 408407, China
| | - Ya Lin
- Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Chongqing Nanchuan Institute of Traditional Chinese Medicinal Plants, Chongqing, 408407, China
| | - Yu Cai
- Chongqing Nanchuan Institute of Traditional Chinese Medicinal Plants, Chongqing, 408407, China
| | - Linfang Li
- Teaching and research group of biology, Kunming No.8 High School, Kunming, China
| | - Xiaohui Yao
- Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Teaching and research group of biology, Hohhot 35th Middle School, Hohhot, China
| | - Kuan Sun
- Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qin Song
- Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qingwei Zhang
- Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China.
- Chongqing Nanchuan Institute of Traditional Chinese Medicinal Plants, Chongqing, 408407, China.
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9
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Bini AP, Rossi GD, Poeschl Y, Serra MCD, Camargo LEA, Monteiro-Vitorello CB, van Sluys MA, van Dam NM, Uthe H, Creste S. Molecular, biochemical and metabolomics analyses reveal constitutive and pathogen-induced defense responses of two sugarcane contrasting genotypes against leaf scald disease. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108033. [PMID: 37757720 DOI: 10.1016/j.plaphy.2023.108033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 08/26/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023]
Abstract
Leaf scald caused by the bacteria Xanthomonas albilineans is one of the major concerns to sugarcane production. To breed for resistance, mechanisms underlying plant-pathogen interaction need deeper investigations. Herein, we evaluated sugarcane defense responses against X. albilineans using molecular and biochemical approaches to assess pathogen-triggered ROS, phytohormones and metabolomics in two contrasting sugarcane genotypes from 0.5 to 144 h post-inoculation (hpi). In addition, the infection process was monitored using TaqMan-based quantification of X. albilineans and the disease symptoms were evaluated in both genotypes after 15 d post-inoculation (dpi). The susceptible genotype presented a response to the infection at 0.5 hpi, accumulating defense-related metabolites such as phenolics and flavonoids with no significant defense responses thereafter, resulting in typical symptoms of leaf scald at 15 dpi. The resistant genotype did not respond to the infection at 0.5 hpi but constitutively presented higher levels of salicylic acid and of the same metabolites induced by the infection in the susceptible genotype. Moreover, two subsequent pathogen-induced metabolic responses at 12 and 144 hpi were observed only in the resistant genotype in terms of amino acids, quinic acids, coumarins, polyamines, flavonoids, phenolics and phenylpropanoids together with an increase of hydrogen peroxide, ROS-related genes expression, indole-3-acetic-acid and salicylic acid. Multilevel approaches revealed that constitutive chemical composition and metabolic reprogramming hampers the development of leaf scald at 48 and 72 hpi, reducing the disease symptoms in the resistant genotype at 15 dpi. Phenylpropanoid pathway is suggested as a strong candidate marker for breeding sugarcane resistant to leaf scald.
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Affiliation(s)
- Andressa Peres Bini
- Instituto Agronômico (IAC), Centro de Cana, Rodovia Antônio Duarte Nogueira KM 321, 14032-800, Ribeirão Preto, São Paulo, Brazil
| | - Guilherme Duarte Rossi
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Via de Acesso Professor Paulo Donato Castellane S/N, 14884-900, Jaboticabal, SP, Brazil
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Marina Carnaz Duarte Serra
- Instituto Agronômico (IAC), Centro de Cana, Rodovia Antônio Duarte Nogueira KM 321, 14032-800, Ribeirão Preto, São Paulo, Brazil
| | - Luis Eduardo Aranha Camargo
- Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Av. Pádua Dias 11, 13418-900, Piracicaba, SP, Brazil
| | | | - Marie-Anne van Sluys
- Universidade de São Paulo, Departamento de Botânica - Instituto de Biociências, Rua do Matão 277, 05508-090, São Paulo, SP, Brazil
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Henriette Uthe
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.
| | - Silvana Creste
- Instituto Agronômico (IAC), Centro de Cana, Rodovia Antônio Duarte Nogueira KM 321, 14032-800, Ribeirão Preto, São Paulo, Brazil.
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10
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Chen S, Chen Z, Lin X, Zhou X, Yang S, Tan H. Why different sugarcane cultivars show different resistant abilities to smut? : Comparisons of endophytic microbial compositions and metabolic functions in stems of sugarcane cultivars with different abilities to resist smut. BMC PLANT BIOLOGY 2023; 23:427. [PMID: 37710150 PMCID: PMC10500793 DOI: 10.1186/s12870-023-04446-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
To elucidate the mechanisms underlying the resistance to smut of different sugarcane cultivars, endophytic bacterial and fungal compositions, functions and metabolites in the stems of the sugarcane cultivars were analyzed using high-throughput sequencing techniques and nontargeted metabolomics. The results showed that the levels of ethylene, salicylic acid and jasmonic acid in sugarcane varieties that were not sensitive to smut were all higher than those in sensitive sugarcane varieties. Moreover, endophytic fungi, such as Ramichloridium, Alternaria, Sarocladium, Epicoccum, and Exophiala species, could be considered antagonistic to sugarcane smut. Additionally, the highly active arginine and proline metabolism, pentose phosphate pathway, phenylpropanoid biosynthesis, and tyrosine metabolism in sugarcane varieties that were not sensitive to smut indicated that these pathways contribute to resistance to smut. All of the above results suggested that the relatively highly abundant antagonistic microbes and highly active metabolic functions of endophytes in non-smut-sensitive sugarcane cultivars were important for their relatively high resistance to smut.
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Affiliation(s)
- Siyu Chen
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, 100 University Road, Nanning, Guangxi, 530004, P.R. China
| | - Zhongliang Chen
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, 530007, Guangxi, P.R. China
| | - Xinru Lin
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, 100 University Road, Nanning, Guangxi, 530004, P.R. China
| | - Xinyan Zhou
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, 100 University Road, Nanning, Guangxi, 530004, P.R. China
| | - Shangdong Yang
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, 100 University Road, Nanning, Guangxi, 530004, P.R. China.
| | - Hongwei Tan
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, 530007, Guangxi, P.R. China.
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11
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Wu Q, Li Z, Yang J, Xu F, Fu X, Xu L, You C, Wang D, Su Y, Que Y. Deciphering the Atlas of Post-Translational Modification in Sugarcane. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37339007 DOI: 10.1021/acs.jafc.3c01886] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
In plants, lysine acetylation (Kac), 2-hydroxyisobutyrylation (Khib), and lysine lactylation (Kla), the three new types of post-translational modification (PTM), play very important roles in growth, development, and resistance to adverse environmental stresses. Herein, we report the first global acetylome, 2-hydroxyisobutyrylome, and lactylome in sugarcane. A total of 8573 Kac, 4637 Khib, and 215 Kla sites across 3903, 1507, and 139 modified proteins were identified. Besides, homology analyses revealed the Kac, Khib, and Kla sites on histones were conserved between sugarcane and rice or poplar. Functional annotations demonstrated that the Kac, Khib, and Kla proteins were mainly involved in energy metabolism. In addition, a number of modified transcription factors and stress-related proteins, which were constitutively expressed in different tissues of sugarcane and induced by drought, cold or Sporisorium scitamineum stress, were identified. Finally, a proposed working mode on how PTM functions in sugarcane was depicted. We thus concluded that PTM should play a role in sugarcane growth, development, and response to biotic and abiotic stresses, but the mechanisms require further investigation. The present study provided the all-new comprehensive profile of proteins Kac, Khib, and Kla and a new perspective to understand the molecular mechanisms of protein PTMs in sugarcane.
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Affiliation(s)
- Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenxiang Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingtao Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xueqin Fu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National Key Laboratory for Tropical Crop Breeding, Kaiyuan, Yunnan 661699, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National Key Laboratory for Tropical Crop Breeding, Kaiyuan, Yunnan 661699, China
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12
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Li AM, Liao F, Wang M, Chen ZL, Qin CX, Huang RQ, Verma KK, Li YR, Que YX, Pan YQ, Huang DL. Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors. Int J Mol Sci 2023; 24:ijms24108913. [PMID: 37240257 DOI: 10.3390/ijms24108913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Sugarcane, a C4 plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.
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Affiliation(s)
- Ao-Mei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Fen Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Miao Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Zhong-Liang Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Cui-Xian Qin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Ruo-Qi Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Krishan K Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - You-Xiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - You-Qiang Pan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Dong-Liang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
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13
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Zhao Z, Zhang R, Wang D, Zhang J, Zang S, Zou W, Feng A, You C, Su Y, Wu Q, Que Y. Dissecting the features of TGA gene family in Saccharum and the functions of ScTGA1 under biotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107760. [PMID: 37207494 DOI: 10.1016/j.plaphy.2023.107760] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/22/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023]
Abstract
Sugarcane is an important sugar and energy crop and smut disease caused by Sporisorium scitamineum is a major fungal disease which can seriously reduce the yield and quality of sugarcane. In plants, TGACG motif binding (TGA) transcription factors are involved in the regulation of salicylic acid (SA) and methyl jasmonate (MeJA) signaling pathways, as well as in response to various biotic and abiotic stresses. However, no TGA-related transcription factor has been reported in Saccharum. In the present study, 44 SsTGA genes were identified from Saccharum spontaneum, and were assorted into three clades (I, II, III). Cis-regulatory elements (CREs) analysis revealed that SsTGA genes may be involved in hormone and stress response. RNA-seq data and RT-qPCR analysis indicated that SsTGAs were constitutively expressed in different tissues and induced by S. scitamineum stress. In addition, a ScTGA1 gene (GenBank accession number ON416997) was cloned from the sugarcane cultivar ROC22, which was homologous to SsTGA1e in S. spontaneum and encoded a nucleus protein. It was constitutively expressed in sugarcane tissues and up-regulated by SA, MeJA and S. scitamineum stresses. Furthermore, transient overexpression of ScTGA1 in Nicotiana benthamiana could enhance its resistance to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum, by regulating the expression of immune genes related to hypersensitive response (HR), ethylene (ET), SA and jasmonic acid (JA) pathways. This study should contribute to our understanding on the evolution and function of the SsTGA gene family in Saccharum, and provide a basis for the functional identification of ScTGA1 under biotic stresses.
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Affiliation(s)
- Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Renren Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Aoyin Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chuihuai You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China.
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14
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Wang D, Qin L, Wu M, Zou W, Zang S, Zhao Z, Lin P, Guo J, Wang H, Que Y. Identification and characterization of WAK gene family in Saccharum and the negative roles of ScWAK1 under the pathogen stress. Int J Biol Macromol 2022; 224:1-19. [PMID: 36481328 DOI: 10.1016/j.ijbiomac.2022.11.300] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Wall-associated kinase (WAK) is widely involved in signal transduction, reproductive growth, responses to pathogen infection and metal ion stress in plants. In this study, 19, 12, and 37 SsWAK genes were identified in Saccharum spontaneum, Saccharum hybrid and Sorghum bicolor, respectively. Phylogenetic tree showed that they could be divided into three groups. These WAK genes contained multiple cis-acting elements related to stress, growth and hormone response. RNA-seq analysis demonstrated that SsWAK genes were constitutively expressed in different sugarcane tissues and involved in response to smut pathogen (Sporisorium scitamineum) stress. Additionally, ScWAK1 (GenBank Accession No. OP479864), was then isolated from sugarcane cultivar ROC22. It was highly expressed in leaves and roots and its expression could be induced under SA and MeJA stress. Besides, ScWAK1 was significantly downregulated in both smut-resistant and susceptible sugarcane cultivars in response to S. scitamineum infection. ScWAK1 was a membrane protein without self-activating activity. Furthermore, transient expression of ScWAK1 in Nicotiana benthamiana enhanced the susceptibility of tobacco to the inoculation of Ralstonia solanacearum and Fusarium solani var. coeruleum, suggesting its negative role in disease resistance. The present study reveals the origin, distribution and evolution of WAK gene family and provides potential gene resources for sugarcane molecular breeding.
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Affiliation(s)
- Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Liqian Qin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Mingxing Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hengbo Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
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Genome-Wide Identification of Auxin-Responsive GH3 Gene Family in Saccharum and the Expression of ScGH3-1 in Stress Response. Int J Mol Sci 2022; 23:ijms232112750. [PMID: 36361540 PMCID: PMC9654502 DOI: 10.3390/ijms232112750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Gretchen Hagen3 (GH3), one of the three major auxin-responsive gene families, is involved in hormone homeostasis in vivo by amino acid splicing with the free forms of salicylic acid (SA), jasmonic acid (JA) or indole-3-acetic acid (IAA). Until now, the functions of sugarcane GH3 (SsGH3) family genes in response to biotic stresses have been largely unknown. In this study, we performed a systematic identification of the SsGH3 gene family at the genome level and identified 41 members on 19 chromosomes in the wild sugarcane species, Saccharum spontaneum. Many of these genes were segmentally duplicated and polyploidization was the main contributor to the increased number of SsGH3 members. SsGH3 proteins can be divided into three major categories (SsGH3-I, SsGH3-II, and SsGH3-III) and most SsGH3 genes have relatively conserved exon-intron arrangements and motif compositions. Diverse cis-elements in the promoters of SsGH3 genes were predicted to be essential players in regulating SsGH3 expression patterns. Multiple transcriptome datasets demonstrated that many SsGH3 genes were responsive to biotic and abiotic stresses and possibly had important functions in the stress response. RNA sequencing and RT-qPCR analysis revealed that SsGH3 genes were differentially expressed in sugarcane tissues and under Sporisorium scitamineum stress. In addition, the SsGH3 homolog ScGH3-1 gene (GenBank accession number: OP429459) was cloned from the sugarcane cultivar (Saccharum hybrid) ROC22 and verified to encode a nuclear- and membrane-localization protein. ScGH3-1 was constitutively expressed in all tissues of sugarcane and the highest amount was observed in the stem pith. Interestingly, it was down-regulated after smut pathogen infection but up-regulated after MeJA and SA treatments. Furthermore, transiently overexpressed Nicotiana benthamiana, transduced with the ScGH3-1 gene, showed negative regulation in response to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum. Finally, a potential model for ScGH3-1-mediated regulation of resistance to pathogen infection in transgenic N. benthamiana plants was proposed. This study lays the foundation for a comprehensive understanding of the sequence characteristics, structural properties, evolutionary relationships, and expression of the GH3 gene family and thus provides a potential genetic resource for sugarcane disease-resistance breeding.
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Agisha V, Ashwin N, Vinodhini R, Nalayeni K, Ramesh Sundar A, Malathi P, Viswanathan R. Transcriptome analysis of sugarcane reveals differential switching of major defense signaling pathways in response to Sporisorium scitamineum isolates with varying virulent attributes. FRONTIERS IN PLANT SCIENCE 2022; 13:969826. [PMID: 36325538 PMCID: PMC9619058 DOI: 10.3389/fpls.2022.969826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022]
Abstract
Sugarcane smut caused by the basidiomycetous fungus Sporisorium scitamineum is one of the most devastating diseases that affect sugarcane production, globally. At present, the most practical and effective management strategy for the disease is the cultivation of resistant cultivars. In this connection, a detailed understanding of the host’s defense mechanism in response to smut isolates with varying degrees of virulence at the molecular level would facilitate the development of reliable and durable smut-resistant sugarcane varieties. Hence, in this study, a comparative whole transcriptome analysis was performed employing Illumina RNA-seq in the smut susceptible cultivar Co 97009 inoculated with two distinct S. scitamineum isolates, Ss97009 (high-virulent) and SsV89101 (low-virulent) during the early phases of infection (2 dpi and 5 dpi) and at the phase of sporogenesis (whip emergence) (60 dpi). Though the differential gene expression profiling identified significant transcriptional changes during the early phase of infection in response to both the isolates, the number of differentially expressed genes (DEGs) were more abundant at 60 dpi during interaction with the high virulent isolate Ss97009, as compared to the low virulent isolate SsV89101. Functional analysis of these DEGs revealed that a majority of them were associated with hormone signaling and the synthesis of defense-related metabolites, suggesting a complex network of defense mechanisms is being operated in response to specific isolates of the smut pathogen. For instance, up-regulation of hormone-related genes, transcription factors, and flavonoid biosynthesis pathway genes was observed in response to both the isolates in the early phase of interaction. In comparison to early phases of infection, only a few pathogenesis-related proteins were up-regulated at 60 dpi in response to Ss97009, which might have rendered the host susceptible to infection. Strikingly, few other carbohydrate metabolism-associated genes like invertases were up-regulated in Ss97009 inoculated plants during the whip emergence stage, representing a shift from sucrose storage to smut symptoms. Altogether, this study established the major switching of defense signaling pathways in response to S. scitamineum isolates with different virulence attributes and provided novel insights into the molecular mechanisms of sugarcane-smut interaction.
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Wu Q, Su Y, Pan YB, Xu F, Zou W, Que B, Lin P, Sun T, Grisham MP, Xu L, Que Y. Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq. FRONTIERS IN PLANT SCIENCE 2022; 13:1035266. [PMID: 36311133 PMCID: PMC9608552 DOI: 10.3389/fpls.2022.1035266] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/27/2022] [Indexed: 06/01/2023]
Abstract
Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases worldwide. In this study, a cross was made between a smut-resistant variety YT93-159 and a smut-susceptible variety ROC22, and 312 progenies were obtained. Two bulks of progenies were then constructed, one consisted of 27 highly smut resistant progenies and the other 24 smut susceptible progenies. Total RNAs of the progenies of each bulk, were pooled and subject to bulked segregant RNA-sequence analysis (BSR-Seq). A total of 164.44 Gb clean data containing 2,341,449 SNPs and 64,999 genes were obtained, 7,295 of which were differentially expressed genes (DEGs). These DEGs were mainly enriched in stress-related metabolic pathways, including carbon metabolism, phenylalanine metabolism, plant hormone signal transduction, glutathione metabolism, and plant-pathogen interactions. Besides, 45,946 high-quality, credible SNPs, a 1.27 Mb region at Saccharum spontaneum chromosome Chr5B (68,904,827 to 70,172,982), and 129 candidate genes were identified to be associated with smut resistance. Among them, twenty-four genes, either encoding key enzymes involved in signaling pathways or being transcription factors, were found to be very closely associated with stress resistance. RT-qPCR analysis demonstrated that they played a positive role in smut resistance. Finally, a potential molecular mechanism of sugarcane and S. scitamineum interaction is depicted that activations of MAPK cascade signaling, ROS signaling, Ca2+ signaling, and PAL metabolic pathway and initiation of the glyoxalase system jointly promote the resistance to S. scitamineum in sugarcane. This study provides potential SNP markers and candidate gene resources for smut resistance breeding in sugarcane.
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Affiliation(s)
- Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yong-Bao Pan
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Beibei Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- International College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Michael P. Grisham
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
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Zhang J, Cui T, Su Y, Zang S, Zhao Z, Zhang C, Zou W, Chen Y, Cao Y, Chen Y, Que Y, Chen N, Luo J. Genome-Wide Identification, Characterization, and Expression Analysis of Glutamate Receptor-like Gene (GLR) Family in Sugarcane. PLANTS 2022; 11:plants11182440. [PMID: 36145840 PMCID: PMC9506223 DOI: 10.3390/plants11182440] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022]
Abstract
The plant glutamate receptor-like gene (GLR) plays a vital role in development, signaling pathways, and in its response to environmental stress. However, the GLR gene family has not been comprehensively and systematically studied in sugarcane. In this work, 43 GLR genes, including 34 in Saccharum spontaneum and 9 in the Saccharum hybrid cultivar R570, were identified and characterized, which could be divided into three clades (clade I, II, and III). They had different evolutionary mechanisms, the former was mainly on the WGD/segmental duplication, while the latter mainly on the proximal duplication. Those sugarcane GLR proteins in the same clade had a similar gene structure and motif distribution. For example, 79% of the sugarcane GLR proteins contained all the motifs, which proved the evolutionary stability of the sugarcane GLR gene family. The diverse cis-acting regulatory elements indicated that the sugarcane GLRs may play a role in the growth and development, or under the phytohormonal, biotic, and abiotic stresses. In addition, GO and KEGG analyses predicted their transmembrane transport function. Based on the transcriptome data, the expression of the clade III genes was significantly higher than that of the clade I and clade II. Furthermore, qRT-PCR analysis demonstrated that the expression of the SsGLRs was induced by salicylic acid (SA) treatment, methyl jasmonic acid (MeJA) treatment, and abscisic acid (ABA) treatment, suggesting their involvement in the hormone synthesis and signaling pathway. Taken together, the present study should provide useful information on comparative genomics to improve our understanding of the GLR genes and facilitate further research on their functions.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianzhen Cui
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanling Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yue Cao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yao Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Niandong Chen
- New Huadu Business School, Minjiang University, Fuzhou 350108, China
- Correspondence: (N.C.); (J.L.); Tel.: +86-591-8385-2547 (N.C. & J.L.)
| | - Jun Luo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (N.C.); (J.L.); Tel.: +86-591-8385-2547 (N.C. & J.L.)
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Zhang R, Li H, Gui Y, Wei J, Zhu K, Zhou H, Lakshmanan P, Mao L, Lu M, Liu J, Que Y, Li S, Liu X. Comparative Transcriptome Analysis of Two Sugarcane Cultivars in Response to Paclobutrazol Treatment. PLANTS (BASEL, SWITZERLAND) 2022; 11:2417. [PMID: 36145817 PMCID: PMC9502373 DOI: 10.3390/plants11182417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Sugarcane is an important crop across the globe, and the rapid multiplication of excellent cultivars is an important object of the sugarcane industry. As one of the plant growth regulators, paclobutrazol (PBZ) has been frequently used in the tissue culture of sugarcane seedlings. However, little is known about the molecular mechanisms of response to PBZ in this crop. Here, we performed a comparative transcriptome analysis between sensitive (LC05-136) and non-sensitive (GGZ001) sugarcane cultivars treated by PBZ at three time points (0 d, 10 d, and 30 d) using RNA sequencing (RNA-Seq). The results showed that approximately 70.36 Mb of clean data for each sample were generated and assembled into 239,212 unigenes. A total of 6108 and 4404 differentially expressed genes (DEGs) were identified within the sensitive and non-sensitive sugarcane cultivars, respectively. Among them, DEGs in LC05-136 were most significantly enriched in the photosynthesis and valine, leucine and isoleucine degradation pathways, while in GGZ001, DEGs associated with ion channels and plant-pathogen interaction were mainly observed. Notably, many interesting genes, including those encoding putative regulators, key components of photosynthesis, amino acids degradation and glutamatergic synapse, were identified, revealing their importance in the response of sugarcane to PBZ. Furthermore, the expressions of sixteen selected DEGs were tested by quantitative reverse transcription PCR (RT-qPCR), confirming the reliability of the RNA-seq data used in this study. These results provide valuable information regarding the transcriptome changes in sugarcane treated by PBZ and provide an insight into understanding the molecular mechanisms underlying the resistance to PBZ in sugarcane.
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Affiliation(s)
- Ronghua Zhang
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Haibi Li
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Longzhou 532415, China
| | - Yiyun Gui
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Jinju Wei
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Kai Zhu
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Hui Zhou
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Prakash Lakshmanan
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Lianying Mao
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Manman Lu
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Junxian Liu
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Youxiong Que
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Song Li
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xihui Liu
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning 530007, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
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WGCNA Identifies a Comprehensive and Dynamic Gene Co-Expression Network That Associates with Smut Resistance in Sugarcane. Int J Mol Sci 2022; 23:ijms231810770. [PMID: 36142681 PMCID: PMC9506403 DOI: 10.3390/ijms231810770] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data analysis revealed 20,273 (12,659 up-regulated and 7614 down-regulated) and 11,897 (7806 up-regulated and 4091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weighted gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. The GO and KEGG enrichment analyses indicated that the DEGs involving in these four modules could be enriched in stress-related metabolic pathways, such as MAPK and hormone signal transduction, plant-pathogen interaction, amino acid metabolism, glutathione metabolism, and flavonoid, and phenylpropanoid biosynthesis. In total, 38 hub genes, including six from the Skyblue module, four from the Salmon module, 12 from the Darkorange module, and 16 from the Grey60 module, were screened as candidate hub genes by calculating gene connectivity in the corresponding network. Only 30 hub genes were amplifiable with RT-qPCR, of which 27 were up-regulated upon S. scitamineum infection. The results were consistent with the trend of gene expression in RNA-Seq, suggesting their positive roles in smut resistance. Interestingly, the expression levels of AOX, Cyb5, and LAC were higher in ROC22 than in YT93-159, indicating these three genes may act as negative regulators in response to S. scitamineum infection. This study revealed the transcriptome dynamics in sugarcane challenged by S. scitamineum infection and provided gene targets for smut resistance breeding in sugarcane.
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21
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Identification of Gene Modules and Hub Genes Associated with Sporisorium scitamineum Infection Using Weighted Gene Co-Expression Network Analysis. J Fungi (Basel) 2022; 8:jof8080852. [PMID: 36012840 PMCID: PMC9409688 DOI: 10.3390/jof8080852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
Sporisorium scitamineum is a biotrophic fungus responsible for sugarcane smut disease. To investigate the key genes involved in S. scitamineum infection, we conducted RNA sequencing of sugarcane sprouts inoculated with S. scitamineum teliospores. A weighted gene co-expression network analysis (WGCNA) showed that two co-expressed gene modules, MEdarkturquoise and MEpurple—containing 66 and 208 genes, respectively—were associated with S. scitamineum infection. The genes in these two modules were further studied using Gene Ontology (GO) enrichment analysis, pathogen-host interaction (PHI) database BLASTp, and small secreted cysteine-rich proteins (SCRPs) prediction. The top ten hub genes in each module were identified using the Cytohubba plugin. The GO enrichment analysis found that endoplasmic reticulum-related and catabolism-related genes were expressed during S. scitamineum infection. A total of 83 genes had homologs in the PHI database, 62 of which correlated with pathogen virulence. A total of 21 proteins had the characteristics of small secreted cysteine-rich proteins (SCRPs), a common source of fungal effectors. The top ten hub genes in each module were identified, and seven were annotated as Mig1-Mig1 protein, glycosyl hydrolase, beta-N-acetylglucosaminidase, secreted chorismate mutase, collagen, mRNA export factor, and pleckstrin homology domain protein, while the remaining three were unknown. Two SCRPs—SPSC_06609 and SPSC_04676—and three proteins—SPSC_01958, SPSC_02155, and SPSC_00940—identified in the PHI database were also among the top ten hub genes in the MEdarkturquoise and MEpurple modules, suggesting that they may play important roles in S. scitamineum infection. A S. scitamineum infection model was postulated based on current findings. These findings help to deepen the current understanding of early events in S. scitamineum infection.
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Poloni A, Garde R, Dittiger LD, Heidrich T, Müller C, Drechsler F, Zhao Y, Mazumdar T, Schirawski J. Transcriptome Analysis Reveals Contrasting Plant Responses of Sorghum bicolor upon Colonization by Two Formae Speciales of Sporisorium reilianum. Int J Mol Sci 2022; 23:ijms23168864. [PMID: 36012130 PMCID: PMC9407964 DOI: 10.3390/ijms23168864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 12/05/2022] Open
Abstract
The biotrophic fungus Sporisorium reilianum exists in two host-adapted formae speciales that cause head smut in maize (S. reilianum f. sp. zeae; SRZ) and sorghum (S. reilianum f. sp. reilianum; SRS). In sorghum, the spread of SRZ is limited to the leaves. To understand the plant responses to each forma specialis, we determined the transcriptome of sorghum leaves inoculated either with SRS or SRZ. Fungal inoculation led to gene expression rather than suppression in sorghum. SRZ induced a much greater number of genes than SRS. Each forma specialis induced a distinct set of plant genes. The SRZ-induced genes were involved in plant defense mainly at the plasma membrane and were associated with the Molecular Function Gene Ontology terms chitin binding, abscisic acid binding, protein phosphatase inhibitor activity, terpene synthase activity, chitinase activity, transmembrane transporter activity and signaling receptor activity. Specifically, we found an upregulation of the genes involved in phospholipid degradation and sphingolipid biosynthesis, suggesting that the lipid content of the plant plasma membrane may contribute to preventing the systemic spread of SRZ. In contrast, the colonization of sorghum with SRS increased the expression of the genes involved in the detoxification of cellular oxidants and in the unfolded protein response at the endoplasmic reticulum, as well as of the genes modifying the cuticle wax and lipid composition through the generation of alkanes and phytosterols. These results identified plant compartments that may have a function in resistance against SRZ (plasma membrane) and susceptibility towards SRS (endoplasmic reticulum) that need more attention in the future.
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Affiliation(s)
- Alana Poloni
- Department for Molecular Biology of Plant-Microbe Interaction, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
- Department of Microbial Genetics, Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ravindra Garde
- Department of Genetics, Matthias-Schleiden-Institute, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743 Jena, Germany
| | - Lukas Dorian Dittiger
- Department of Genetics, Matthias-Schleiden-Institute, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743 Jena, Germany
| | - Theresa Heidrich
- Department for Molecular Biology of Plant-Microbe Interaction, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
- Department of Microbial Genetics, Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Christian Müller
- Department of Microbial Genetics, Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Department of Genetics, Matthias-Schleiden-Institute, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743 Jena, Germany
| | - Frank Drechsler
- Department of Microbial Genetics, Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Yulei Zhao
- Department for Molecular Biology of Plant-Microbe Interaction, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
- Department of Microbial Genetics, Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Tilottama Mazumdar
- Department of Genetics, Matthias-Schleiden-Institute, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743 Jena, Germany
| | - Jan Schirawski
- Department for Molecular Biology of Plant-Microbe Interaction, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
- Department of Microbial Genetics, Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Department of Genetics, Matthias-Schleiden-Institute, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743 Jena, Germany
- Correspondence: ; Tel.: +49-3641-949555
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Song X, Mo F, Yan M, Zhang X, Zhang B, Huang X, Huang D, Pan Y, Verma KK, Li YR. Effect of Smut Infection on the Photosynthetic Physiological Characteristics and Related Defense Enzymes of Sugarcane. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081201. [PMID: 36013380 PMCID: PMC9410379 DOI: 10.3390/life12081201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 11/23/2022]
Abstract
Pathogen infection seriously affects plant development and crop productivity, sometimes causing total crop failure. In this study, artificial stab inoculation was used to inoculate sugarcane smut. The changes in leaf gas exchange, chlorophyll fluorescence variables, and related defense enzyme activities were measured in sugarcane cultivar ROC22 after pathogen infection. The results showed that the net photosynthetic rate (Pn), stomatal conductance (gs), and transpiration rate (Tr) downregulated in the first three days after smut infection and upregulated on the fourth day; intercellular CO2 concentration (Ci) increased in the first three days of smut infection and reduced on the fourth day. The chlorophyll fluorescence parameters, i.e., Fo, Fm, Fv/Fm, Fs, and Fv′/Fm′ decreased at the initial stage of pathogen infection but increased rapidly up to 3 days after smut infection. It can be seen that sugarcane seedlings showed a positive response to pathogen infection. The correlation coefficient relationship between Pn, gs, and Tr reached above 0.800, showing a significant correlation; Ci was positively correlated with Fv′/Fm′ and ΦPSII, reaching above 0.800 and showing a significant correlation; Fo positively correlated with Fv/Fm, Fs, and ETR; Fv /Fm was positively correlated with Fv′/Fm′; Fs significantly correlated with Fv′/Fm′; and Fv′/Fm′ positively correlated with ΦPSII. After inoculation with smut, the related defense enzymes, i.e., POD, SOD, PPO, and PAL, were increased and upregulated; photosynthetic parameters can be associated with an increase in enzymatic activities. The results of this study will help to further study of the response mechanism to smut in the sugarcane growing period and provide a theoretical reference for sugarcane resistance to smut breeding.
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Affiliation(s)
- Xiupeng Song
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
| | - Fenglian Mo
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Meixin Yan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
| | - Xiaoqiu Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
| | - Baoqing Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
| | - Xing Huang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
| | - Dongmei Huang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
| | - Yangfei Pan
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Krishan K. Verma
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- Correspondence: (K.K.V.); (Y.-R.L.)
| | - Yang-Rui Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning 530007, China
- College of Agriculture, Guangxi University, Nanning 530004, China
- Correspondence: (K.K.V.); (Y.-R.L.)
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Zang S, Qin L, Zhao Z, Zhang J, Zou W, Wang D, Feng A, Yang S, Que Y, Su Y. Characterization and Functional Implications of the Nonexpressor of Pathogenesis-Related Genes 1 (NPR1) in Saccharum. Int J Mol Sci 2022; 23:ijms23147984. [PMID: 35887330 PMCID: PMC9317693 DOI: 10.3390/ijms23147984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
Sugarcane (Saccharum spp.) is an important sugar and energy crop worldwide. As a core regulator of the salicylic acid (SA) signaling pathway, nonexpressor of pathogenesis-related genes 1 (NPR1) plays a significant role in the response of the plant to biotic and abiotic stresses. However, there is currently no report on the NPR1-like gene family in sugarcane. In this study, a total of 18 NPR1-like genes were identified in Saccharum spontaneum and classified into three clades (clade I, II, and III). The cis-elements predicted in the promotors revealed that the sugarcane NPR1-like genes may be involved in various phytohormones and stress responses. RNA sequencing and quantitative real-time PCR analysis demonstrated that NPR1-like genes were differentially expressed in sugarcane tissues and under Sporisorium scitamineum stress. In addition, a novel ShNPR1 gene from Saccharum spp. hybrid ROC22 was isolated by homologous cloning and validated to be a nuclear-localized clade II member. The ShNPR1 gene was constitutively expressed in all the sugarcane tissues, with the highest expression level in the leaf and the lowest in the bud. The expression level of ShNPR1 was decreased by the plant hormones salicylic acid (SA) and abscisic acid (ABA). Additionally, the transient expression showed that the ShNPR1 gene plays a positive role in Nicotiana benthamiana plants’ defense response to Ralstonia solanacearum and Fusarium solani var. coeruleum. This study provided comprehensive information for the NPR1-like family in sugarcane, which should be helpful for functional characterization of sugarcane NPR1-like genes in the future.
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Affiliation(s)
- Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
| | - Liqian Qin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
| | - Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
| | - Jing Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
| | - Aoyin Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
| | - Shaolin Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan 661600, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Y.Q.); (Y.S.); Tel.: +86-591-8385-2547 (Y.Q. & Y.S.)
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Z.); (L.Q.); (Z.Z.); (J.Z.); (W.Z.); (D.W.); (A.F.); (S.Y.)
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Y.Q.); (Y.S.); Tel.: +86-591-8385-2547 (Y.Q. & Y.S.)
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Su Y, Peng Q, Ling H, You C, Wu Q, Xu L, Que Y. Systematic identification of miRNA-regulatory networks unveils their potential roles in sugarcane response to Sorghum mosaic virus infection. BMC PLANT BIOLOGY 2022; 22:247. [PMID: 35585486 PMCID: PMC9118776 DOI: 10.1186/s12870-022-03641-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/06/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Sugarcane mosaic disease (SMD) is a major viral disease of sugarcane (Saccharum spp.) worldwide. Sorghum mosaic virus (SrMV) is the dominant pathogen of SMD in the sugarcane planting areas of China. There is no report on miRNAs and their regulatory networks in sugarcane response to SrMV infection. RESULTS In this study, small RNA sequencing (sRNA-seq) of samples from the leaves of SMD-susceptible variety ROC22 and -resistant variety FN39 infected by SrMV was performed. A total of 132 mature miRNAs (55 known miRNAs and 77 novel miRNAs) corresponding to 1,037 target genes were identified. After the SrMV attack, there were 30 differentially expressed miRNAs (17 up-regulated and 13 down-regulated) in FN39 and 19 in ROC22 (16 up-regulated and 3 down-regulated). Besides, there were 18 and 7 variety-specific differentially expressed miRNAs for FN39 and ROC22, respectively. KEGG enrichment analysis showed that the differentially expressed miRNAs targeted genes involved in several disease resistance-related pathways, such as mRNA surveillance, plant pathway interaction, sulfur metabolism, and regulation of autophagy. The reliability of sequencing data, and the expression patterns / regulation relationships between the selected differentially expressed miRNAs and their target genes in ROC22 and FN39 were confirmed by quantitative real-time PCR. A regulatory network diagram of differentially expressed miRNAs and their predicted target genes in sugarcane response to SrMV infection was sketched. In addition, precursor sequences of three candidate differentially expressed novel miRNAs (nov_3741, nov_22650 and nov_40875) were cloned from the ROC22 leaf infected by SrMV. Transient overexpression demonstrated that they could induce the accumulation of hydrogen peroxide and the expression level of hypersensitive response marker genes, salicylic acid-responsive genes and ethylene synthesis-depended genes in Nicotiana benthamiana. It is thus speculated that these three miRNAs may be involved in regulating the early immune response of sugarcane plants following SrMV infection. CONCLUSIONS This study lays a foundation for revealing the miRNA regulation mechanism in the interaction of sugarcane and SrMV, and also provides a resource for miRNAs and their predicted target genes for SrMV resistance improvement in sugarcane.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Qiong Peng
- Fuzhou Institute of Agricultural Sciences, Fuzhou, 350018 Fujian China
| | - Hui Ling
- College of Agriculture, Yulin Normal University, Yulin, 537000 Guangxi, China
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
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Cen G, Sun T, Chen Y, Wang W, Feng A, Liu A, Que Y, Gao S, Su Y, You C. Characterization of silicon transporter gene family in Saccharum and functional analysis of the ShLsi6 gene in biotic stress. Gene X 2022; 822:146331. [PMID: 35183686 DOI: 10.1016/j.gene.2022.146331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/19/2022] [Accepted: 02/11/2022] [Indexed: 11/04/2022] Open
Abstract
Silicon, one of the most prevalent elements in the soil, is beneficial for plant growth and defense against different stresses. The silicon transporter gene (Lsi) plays an important role in the uptake and transport of silicon in higher plants. In this study, a total of 32 Lsi genes, including 20 SsLsi in sugarcane wild species Saccharum spontaneum, 5 ShLsi in Saccharum hybrid cultivar R570 and 7 SbLsi in sugarcane related species Sorghum bicolor, were identified and classified into three groups. Bioinformatics analysis showed that instability, hydrophobicity, localization of cell membranes and vacuoles were the main features of the Lsi proteins. Whole genome and segmental duplication contributed to the main expansion of Lsi gene family. Collinearity analysis of the Lsi genes showed that S. spontanum and R570 had a collinear relationship with monocotyledonous plants S. bicolor and Oryza sativa, but not with dicotyledonous plants Arabidopsis thaliana and Vitis vinifera. The replicated Lsi genes were mainly subjected to strong selection pressure for purification. The diverse cis-regulatory elements in the promoter of SsLsi, ShLsi and SbLsi genes suggested that they were widely involved in the response of plants to various stresses and the regulation of the growth and development. Transcriptome data and real time quantitative PCR analysis showed that the Lsi genes exhibited different expression profiles in sugarcane tissues and under Sporisorium scitamineum, drought and cold stresses. In addition, the cDNA and genomic DNA sequences of ShLsi6 that was homologous to SsLsi1b gene was cloned from Saccharum hybrid cultivar ROC22. Transient expression analysis showed that, compared with the control, Nicotiana benthamiana leaves which overexpressed the ShLsi6 gene showed a high sensitivity after inoculation with tobacco pathogens Ralstonia solanacearum and Fusarium solani var. coeruleum. This study provides important information for further functional analysis of Lsi genes and resistant breeding in sugarcane.
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Affiliation(s)
- Guangli Cen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province (Fujian Agriculture and Forestry University), Fuzhou, Fujian 350002, China
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yanling Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Wenju Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Aoyin Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Anyu Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shiwu Gao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province (Fujian Agriculture and Forestry University), Fuzhou, Fujian 350002, China.
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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Sun T, Meng Y, Cen G, Feng A, Su W, Chen Y, You C, Que Y, Su Y. Genome-wide identification and expression analysis of the coronatine-insensitive 1 (COI1) gene family in response to biotic and abiotic stresses in Saccharum. BMC Genomics 2022; 23:38. [PMID: 34998383 PMCID: PMC8742417 DOI: 10.1186/s12864-021-08255-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
Background The coronatine insensitive 1 (COI1) gene is the core member of jasmonate signaling pathway, which is closely related to plant biotic and abiotic resistance. However, there have been no reports on COI1 in sugarcane (Sacharum spp.). Hence, systematically investigating the characteristics of the COI1 multigene family in sugarcane can provide a means to study and manipulate the jasmonic acid signaling pathway. Results A total of 156 COI1 proteins were obtained from the genomes of 19 land plants, while none were obtained from five algae species. A phylogenetic tree demonstrated that these COI1 proteins were classified into four groups, while 31 proteins of SsCOI1 from Saccharum spontaneum, SbCOI1 from Sorghum bicolor, and ShCOI1 from Saccharum spp. hybrid cultivar R570 clustered into three groups. Synteny analysis and duplication patterns revealed that COI1 genes expanded through various genome replication events and could have experienced strong purifying selective pressure during evolution in S. spontaneum, S. bicolor, and R570. An investigation of cis-acting elements suggests that COI1 genes may be involved in plant growth and development and response to various stresses. Expression analysis implied that 21 SsCOI1 genes were constitutively expressed, and had positive responses to drought, cold, and Sporisorium scitamineum stresses with different expression patterns. Among them, seven SsCOI1 haplotype genes may play different roles in response to methyl jasmonate. Furthermore, the ShCOI1–4, ShCOI1–5, and ShCOI1–6 genes were cloned from Saccharum spp. hybrid cultivar ROC22. Real-time quantitative PCR (RT-qPCR) analysis demonstrated that these three ShCOI1 genes had divergent expression profiles in response to salicylic acid, abscisic acid, polyethylene glycol, cold, and S. scitamineum. Conclusions These results suggest that COI1 genes may act in sugarcane growth, development, and response to various stresses via different regulatory mechanisms, which laying a foundation for the functional identification of the sugarcane COI1 gene. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08255-0.
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Affiliation(s)
- Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yintian Meng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Guangli Cen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Aoyin Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yanling Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Ling H, Fu X, Huang N, Zhong Z, Su W, Lin W, Cui H, Que Y. A sugarcane smut fungus effector simulates the host endogenous elicitor peptide to suppress plant immunity. THE NEW PHYTOLOGIST 2022; 233:919-933. [PMID: 34716592 PMCID: PMC9298926 DOI: 10.1111/nph.17835] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/22/2021] [Indexed: 05/03/2023]
Abstract
The smut fungus Sporisorium scitamineum causes the most prevalent disease on sugarcane. The mechanism of its pathogenesis, especially the functions and host targets of its effector proteins, are unknown. In order to identify putative effectors involving in S. scitamineum infection, a weighted gene co-expression network analysis was conducted based on the transcriptome profiles of both smut fungus and sugarcane using a customized microarray. A smut effector gene, termed SsPele1, showed strong co-expression with sugarcane PLANT ELICITOR PEPTIDE RECEPTOR1 (ScPEPR1), which encodes a receptor like kinase for perception of plant elicitor peptide1 (ScPep1). The relationship between SsPele1 and ScPEPR1, and the biological function of SsPele1 were characterized in this study. The SsPele1 C-terminus contains a plant elicitor peptide-like motif, by which SsPele1 interacts strongly with ScPEPR1. Strikingly, the perception of ScPep1 on ScPEPR1 is competed by SsPele1 association, leading to the suppression of ScPEPR1-mediated immune responses. Moreover, the Ustilago maydis effector UmPele1, an ortholog of SsPele1, promotes fungal virulence using the same strategy. This study reveals a novel strategy by which a fungal effector can mimic the plant elicitor peptide to complete its perception and attenuate receptor-activated immunity.
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Affiliation(s)
- Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
- College of AgricultureYulin Normal UniversityYulin537000China
| | - Xueqin Fu
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Ning Huang
- College of AgricultureYulin Normal UniversityYulin537000China
| | - Zaofa Zhong
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Wenxiong Lin
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Haitao Cui
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
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Bhuiyan SA, Magarey RC, McNeil MD, Aitken KS. Sugarcane Smut, Caused by Sporisorium scitamineum, a Major Disease of Sugarcane: A Contemporary Review. PHYTOPATHOLOGY 2021; 111:1905-1917. [PMID: 34241540 DOI: 10.1094/phyto-05-21-0221-rvw] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sugarcane smut caused by the fungus Sporisorium scitamineum is one of the major diseases of sugarcane worldwide, causing significant losses in productivity and profitability of this perennial crop. Teliospores of this fungus are airborne, can travel long distances, and remain viable in hot and dry conditions for >6 months. The disease is easily recognized by its long whiplike sorus produced on the apex or side shoots of sugarcane stalks. Each sorus can release ≤100 million teliospores in a day; the spores are small (≤7.5 µ) and light and can survive in harsh environmental conditions. The airborne teliospores are the primary mode of smut spread around the world and across cane-growing regions. The most effective method of managing this disease is via resistant varieties. Because of the complex genomic makeup of sugarcane, selection for resistant traits is difficult in sugarcane breeding programs. In recent times, the application of molecular markers as a rapid tool of discarding susceptible genotypes early in the selection program has been investigated. Large effect resistance loci have been identified and have the potential to be used for marker-assisted selection to increase the frequency of resistant breeding lines in breeding programs. Recent developments in omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have contributed to our understanding and provided insights into the mechanism of resistance and susceptibility. This knowledge will further our understanding of smut and its interactions with sugarcane genotypes and aid in the development of durable resistant varieties.
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Affiliation(s)
- Shamsul A Bhuiyan
- Sugar Research Australia, Woodford, QLD 4514, Australia, and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | | | - Meredith D McNeil
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia
| | - Karen S Aitken
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia
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Genome-Wide Identification of LRR-RLK Family in Saccharum and Expression Analysis in Response to Biotic and Abiotic Stress. Curr Issues Mol Biol 2021; 43:1632-1651. [PMID: 34698114 PMCID: PMC8929030 DOI: 10.3390/cimb43030116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/17/2022] Open
Abstract
The leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family is the largest family of the receptor-like protein kinases (RLKs) superfamily in higher plants, which is involved in regulating the plant growth and development, stress responses, signal transduction and so on. However, no comprehensive analyses of LRR-RLKs have been reported in sugarcane. Here, we performed a comprehensive analysis of the LRR-RLK gene family in sugarcane ancestor species Saccharum spontaneum. A total of 437 LRR-RLK genes were identified and categorized into 14 groups based on a maximum likelihood phylogenetic tree. The chromosome location showed an uneven distribution on all 32 chromosomes in sugarcane. Subsequently, the exon-intron organization structure and conserved motif arrangement were relatively conserved among the same groups or subgroups and between Arabidopsis and S. spontaneum genomes. Furthermore, the promoter sequences analyses showed that sugarcane LRR-RLK genes (SsLRR-RLKs) were strongly regulated by various environmental stimuli, phytohormonal factors and transcription factors (TFs). Eventually, the expression profiles of SsLRR-RLK genes at different stresses were analyzed based on RNA-seq data, suggesting their potential roles in the regulation of sugarcane responses to diverse abiotic and biotic stress. Overall, the findings provide insight into the potential functional roles and lay the foundation for further functional study.
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Su W, Zhang C, Wang D, Ren Y, Sun T, Feng J, Su Y, Xu L, Shi M, Que Y. The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stress. BMC Genomics 2021; 22:549. [PMID: 34275454 PMCID: PMC8286586 DOI: 10.1186/s12864-021-07828-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In plants, Calcium (Ca2+) acts as a universal messenger in various signal transduction pathways, including responses to biotic and abiotic stresses and regulation of cellular and developmental processes. The Ca2+/cation antiporter (CaCA) superfamily proteins play vital roles in the transport of Ca2+ and/or other cations. However, the characteristics of these superfamily members in Saccharum and their evolutionary and functional implications have remained unclear. RESULTS A total of 34 CaCA genes in Saccharum spontaneum, 5 CaCA genes in Saccharum spp. R570, and 14 CaCA genes in Sorghum bicolor were identified and characterized. These genes consisted of the H+/cation exchanger (CAX), cation/Ca2+ exchanger (CCX), EF-hand / CAX (EFCAX), and Mg2+/H+ exchanger (MHX) families, among which the CCX and EFCAX could be classified into three groups while the CAX could be divided into two groups. The exon/intron structures and motif compositions suggested that the members in the same group were highly conserved. Synteny analysis of CaCAs established their orthologous and paralogous relationships among the superfamily in S. spontaneum, R570, and S. bicolor. The results of protein-protein interactions indicated that these CaCA proteins had direct or indirect interactions. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis demonstrated that most members of Saccharum CaCA genes exhibited a similar expression pattern in response to hormonal (abscisic acid, ABA) treatment but played various roles in response to biotic (Sporisorium scitamineum) and abiotic (cold) stresses. Furthermore, ScCAX4, a gene encoding a cytoplasm, plasma membrane and nucleus positioning protein, was isolated from sugarcane. This gene was constitutively expressed in different sugarcane tissues and its expression was only induced at 3 and 6 h time points after ABA treatment, however was inhibited and indued in the whole process under cold and S. scitamineum stresses, respectively. CONCLUSIONS This study systematically conducted comparative analyses of CaCA superfamily genes among S. spontaneum, R570, and S. bicolor, delineating their sequence and structure characteristics, classification, evolutionary history, and putative functions. These results not only provided rich gene resources for exploring the molecular mechanism of the CaCA superfamily genes but also offered guidance and reference for research on other gene families in Saccharum.
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Affiliation(s)
- Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Chang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Yongjuan Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Jingfang Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Mutian Shi
- College of Horticulture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian Province China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
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Umeda M, Sakaigaichi T, Tanaka M, Tarumoto Y, Adachi K, Hattori T, Hayano M, Takahashi H, Tamura Y, Kimura T, Mori M. Detection of a major QTL related to smut disease resistance inherited from a Japanese wild sugarcane using GRAS-Di technology. BREEDING SCIENCE 2021; 71:365-374. [PMID: 34776743 PMCID: PMC8573549 DOI: 10.1270/jsbbs.20137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/23/2021] [Indexed: 06/13/2023]
Abstract
Smut disease of sugarcane causes considerable yield losses and the use of resistant varieties is the best control practice. Our group identified a Japanese wild sugarcane with highly smut disease resistance named 'Iriomote8'. In this study, we conducted QTL analysis for smut disease resistance using a mapping population derived from a resistant variety 'Yaenoushie', in which resistance is inherited from 'Iriomote8'. We identified 4813 non-redundant markers using GRAS-Di technology and developed a linkage map of mapping parents. We evaluated smut disease resistance of the mapping population by the inoculation test. Consequently, a large number of clones did not show the disease symptoms and the distribution of smut disease incidence tended to be "L shaped". Composite interval mapping detected an identical QTL for indices of smut disease incidence with a markedly high LOD score (26.6~45.6) at the end of linkage group 8 of 'Yaenoushie'. This QTL explained approximately 50% of the cases of smut disease incidence. In the mapping population, there were no correlations between the indices of smut disease incidence and other agronomic traits. In conclusion, this QTL could be used for marker-assisted selection to significantly improve smut disease resistance without negative effects on other agronomic traits.
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Affiliation(s)
- Makoto Umeda
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Takeo Sakaigaichi
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Kyushu Okinawa Agricultural Research Center, Miyakonojo Research Station, 6651-2 Yokoichi-cho, Miyakonojo, Miyazaki 885-0091, Japan
| | - Minoru Tanaka
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Central Region Agricultural Research Center, Tsukuba Headquarters, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Yusuke Tarumoto
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Katsuki Adachi
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- Kubota Corporation, Agri-Solution Department, 1-2-47 Shikitsuhigashi, Naniwa-ku, Osaka 556-8601, Japan
| | - Taiichiro Hattori
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Kyushu Okinawa Agricultural Research Center, Headquarters, 2421 Suya, Koshi, Kumamoto 861-1192, Japan
| | - Michiko Hayano
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Institute for Agro-Environmental Science, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Hiroyuki Takahashi
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Yasuaki Tamura
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Tatsuro Kimura
- Toyota Motor Corporation, Agriculture & Biotechnology Business Division, 1 Toyota-cho, Toyota, Aichi 471-8571, Japan
| | - Masaaki Mori
- Toyota Motor Corporation, Environmental Affairs Division, 1-4-18 Koraku, Bunkyo-ku, Tokyo 112-8701, Japan
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Li C, Wang Z, Nong Q, Lin L, Xie J, Mo Z, Huang X, Song X, Malviya MK, Solanki MK, Li Y. Physiological changes and transcriptome profiling in Saccharum spontaneum L. leaf under water stress and re-watering conditions. Sci Rep 2021; 11:5525. [PMID: 33750876 PMCID: PMC7943799 DOI: 10.1038/s41598-021-85072-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
As the polyploidy progenitor of modern sugarcane, Saccharum spontaneum is considered to be a valuable resistance source to various biotic and abiotic stresses. However, little has been reported on the mechanism of drought tolerance in S. spontaneum. Herein, the physiological changes of S. spontaneum GXS87-16 at three water-deficit levels (mild, moderate, and severe) and after re-watering during the elongation stage were investigated. RNA sequencing was utilized for global transcriptome profiling of GXS87-16 under severe drought and re-watered conditions. There were significant alterations in the physiological parameters of GXS87-16 in response to drought stress and then recovered differently after re-watering. A total of 1569 differentially expressed genes (DEGs) associated with water stress and re-watering were identified. Notably, the majority of the DEGs were induced by stress. GO functional annotations and KEGG pathway analysis assigned the DEGs to 47 GO categories and 93 pathway categories. The pathway categories were involved in various processes, such as RNA transport, mRNA surveillance, plant hormone signal transduction, and plant-pathogen interaction. The reliability of the RNA-seq results was confirmed by qRT-PCR. This study shed light on the regulatory processes of drought tolerance in S. spontaneum and identifies useful genes for genetic improvement of drought tolerance in sugarcane.
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Affiliation(s)
- Changning Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Zhen Wang
- College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China
| | - Qian Nong
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Li Lin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Jinlan Xie
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Zhanghong Mo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Xing Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Xiupeng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Manoj Kumar Solanki
- Department of Food Quality and Safety, The Volcani Center, Institute for Post-Harvest and Food Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Yangrui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China.
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A transcriptomic analysis of sugarcane response to Leifsonia xyli subsp. xyli infection. PLoS One 2021; 16:e0245613. [PMID: 33529190 PMCID: PMC7853508 DOI: 10.1371/journal.pone.0245613] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Abstract
Sugarcane ratoon stunting disease (RSD) caused by Leifsonia xyli subsp. xyli (Lxx) is a common destructive disease that occurs around the world. Lxx is an obligate pathogen of sugarcane, and previous studies have reported some physiological responses of RSD-affected sugarcane. However, the molecular understanding of sugarcane response to Lxx infection remains unclear. In the present study, transcriptomes of healthy and Lxx-infected sugarcane stalks and leaves were studied to gain more insights into the gene activity in sugarcane in response to Lxx infection. RNA-Seq analysis of healthy and diseased plants transcriptomes identified 107,750 unigenes. Analysis of these unigenes showed a large number of differentially expressed genes (DEGs) occurring mostly in leaves of infected plants. Sugarcane responds to Lxx infection mainly via alteration of metabolic pathways such as photosynthesis, phytohormone biosynthesis, phytohormone action-mediated regulation, and plant-pathogen interactions. It was also found that cell wall defense pathways and protein phosphorylation/dephosphorylation pathways may play important roles in Lxx pathogeneis. In Lxx-infected plants, significant inhibition in photosynthetic processes through large number of differentially expressed genes involved in energy capture, energy metabolism and chloroplast structure. Also, Lxx infection caused down-regulation of gibberellin response through an increased activity of DELLA and down-regulation of GID1 proteins. This alteration in gibberellic acid response combined with the inhibition of photosynthetic processes may account for the majority of growth retardation occurring in RSD-affected plants. A number of genes associated with plant-pathogen interactions were also differentially expressed in Lxx-infected plants. These include those involved in secondary metabolite biosynthesis, protein phosphorylation/dephosphorylation, cell wall biosynthesis, and phagosomes, implicating an active defense response to Lxx infection. Considering the fact that RSD occurs worldwide and a significant cause of sugarcane productivity, a better understanding of Lxx resistance-related processes may help develop tools and technologies for producing RSD-resistant sugarcane varieties through conventional and/or molecular breeding.
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Physiological Basis of Smut Infectivity in the Early Stages of Sugar Cane Colonization. J Fungi (Basel) 2021; 7:jof7010044. [PMID: 33445484 PMCID: PMC7827540 DOI: 10.3390/jof7010044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 12/11/2022] Open
Abstract
Sugar cane smut (Sporisorium scitamineum) interactions have been traditionally considered from the plant’s point of view: How can resistant sugar cane plants defend themselves against smut disease? Resistant plants induce several defensive mechanisms that oppose fungal attacks. Herein, an overall view of Sporisorium scitamineum’s mechanisms of infection and the defense mechanisms of plants are presented. Quorum sensing effects and a continuous reorganization of cytoskeletal components, where actin, myosin, and microtubules are required to work together, seem to be some of the keys to a successful attack.
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Su W, Ren Y, Wang D, Huang L, Fu X, Ling H, Su Y, Huang N, Tang H, Xu L, Que Y. New insights into the evolution and functional divergence of the CIPK gene family in Saccharum. BMC Genomics 2020; 21:868. [PMID: 33287700 PMCID: PMC7720545 DOI: 10.1186/s12864-020-07264-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 11/22/2020] [Indexed: 11/20/2022] Open
Abstract
Background Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. Results In this study, 48 CIPK genes (SsCIPKs) were identified from the genome of Saccharum spontaneum. Phylogenetic reconstruction suggested that the SsCIPK gene family may have undergone six gene duplication events from the last common ancestor (LCA) of SsCIPKs. Whole-genome duplications (WGDs) served as the driving force for the amplification of SsCIPKs. The Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that the duplicated genes were possibly under strong purifying selection pressure. The divergence time of these duplicated genes had an average duplication time of approximately 35.66 Mya, suggesting that these duplication events occurred after the divergence of the monocots and eudicots (165 Mya). The evolution of gene structure analysis showed that the SsCIPK family genes may involve intron losses. Ten ScCIPK genes were amplified from sugarcane (Saccharum spp. hybrids). The results of real-time quantitative polymerase chain reaction (qRT-PCR) demonstrated that these ten ScCIPK genes had different expression patterns under abscisic acid (ABA), polyethylene glycol (PEG), and sodium chloride (NaCl) stresses. Prokaryotic expression implied that the recombinant proteins of ScCIPK3, − 15 and − 17 could only slightly enhance growth under salinity stress conditions, but the ScCIPK21 did not. Transient N. benthamiana plants overexpressing ScCIPKs demonstrated that the ScCIPK genes were involved in responding to external stressors through the ethylene synthesis pathway as well as to bacterial infections. Conclusions In generally, a comprehensive genome-wide analysis of evolutionary relationship, gene structure, motif composition, and gene duplications of SsCIPK family genes were performed in S. spontaneum. The functional study of expression patterns in sugarcane and allogenic expressions in E. coli and N. benthamiana showed that ScCIPKs played various roles in response to different stresses. Thus, these results improve our understanding of the evolution of the CIPK gene family in sugarcane as well as provide a basis for in-depth functional studies of CIPK genes in sugarcane. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07264-9.
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Affiliation(s)
- Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongjuan Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Long Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueqin Fu
- Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hanchen Tang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Transcriptional reprogramming of major defense-signaling pathways during defense priming and sugarcane-Colletotrichum falcatum interaction. Mol Biol Rep 2020; 47:8911-8923. [PMID: 33161528 DOI: 10.1007/s11033-020-05944-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/22/2020] [Indexed: 02/08/2023]
Abstract
Red rot caused by Colletotrichum falcatum poses a serious threat to sugarcane cultivation in many tropical and sub-tropical countries. Deciphering the molecular network of major defense-signaling pathways in sugarcane cultivars with varying red rot resistance is essential to elucidate the phenomenon of defense priming exerted by resistance inducers. Therefore, in this study, expression pattern of transcripts coding for major defense-signaling pathway regulatory genes was profiled during compatible and incompatible interactions and in response to defense priming using qRT-PCR. Candidate genes that were profiled are involved in or related to hypersensitive response and reactive oxygen species production (HR/ROS), salicylic acid (SA), and jasmonic acid/ethylene (JA/ET) pathways. For compatible and incompatible interactions, susceptible (CoC 671), field tolerant (Co 86032) and resistant (Co 93009) sugarcane cultivars were used, whereas for defense priming, benzothiadiazole (BTH) and the pathogen-associated molecular patterns (PAMPs) of C. falcatum viz., CfEPL1 (eliciting plant response-like) and CfPDIP1 (plant defense inducing protein) were used in CoC 671 cultivar. Results indicated that the master regulator of defense pathways, nonexpressor of pathogenesis-related genes 1 (NPR1) was highly upregulated in incompatible interactions (in both Co 86032 and Co 93009) than the compatible interaction along with SA pathway-associated genes. Similarly, in response to defense priming with BTH, CfEPL1 and CfPDIP1, only the SA pathway-associated genes showed considerable upregulation at 0 h post inoculation (hpi) and other intermittent time points. Overall, this study showed that SA-mediated defense pathway is the most predominant pathway reprogrammed during priming with BTH, CfEPL1 and CfPDIP1 and substantiated the earlier findings that these agents indeed induce systemic resistance against red rot of sugarcane.
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38
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Zheng T, Zhang K, Sadeghnezhad E, Jiu S, Zhu X, Dong T, Liu Z, Guan L, Jia H, Fang J. Chitinase family genes in grape differentially expressed in a manner specific to fruit species in response to Botrytis cinerea. Mol Biol Rep 2020; 47:7349-7363. [PMID: 32914265 DOI: 10.1007/s11033-020-05791-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/28/2020] [Indexed: 01/03/2023]
Abstract
Chitinases (Chi), an important resistance-related protein, act against fungal pathogens by catalyzing the fungal cell wall, whereas are involved in different biological pathways in grape. In this study, we found 42 Chi family genes in Vitis vinifera L. (VvChis) and evaluated their expression levels after Botrytis infection, stress hormones like ethylene (ETH) and methyl-jasmonate (MeJA), and abiotic stresses like salinity and temperature changes in ripened fruits. VvChis were categorized into five groups including A, B, C, D, and E belonged to glycoside hydrolase family 18 and 19 (GH18 and GH19) according to genes structure, which expression analysis showed distinct temporal and spatial expression patterns changed in different tissues and various development stages. Different responsive elements to biotic and abiotic stresses were determined in the promoter regions of VvChis, specially elicitor-responsive element that was conserved among all VvChis genes. The expression levels of VvChis in groups A, B, and E increased after Botrytis cinerea infection in leaves and berries. Meanwhile, VvChis in glycoside hydrolase family 18 (GH18) were up-regulated under MeJA and ETH treatment, although the induction of VvChis by low temperature was more significant than high temperature. The expression of VvChis was also positively correlated with the concentration of NaCl treatment. Furthermore, differential gene-overexpression of VvChi5, VvChi17, VvChi22, VvChi26, and VvChi31 in strawberry and tomato fruits demonstrated the involvement of various isoforms in resistance to Botrytis infection through antioxidant system and lignin accumulation, which led to a reduction of damage. Among different isoforms of VvChis, we confirmed the interaction of Chi17 with Metallothionein (MTL) as oxidative stress protection, which suggests VvChis can modulate oxidative stress during postharvest storage in ripened fruits.
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Affiliation(s)
- Ting Zheng
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Kekun Zhang
- College of Enology, Northwest A&F University, Yangling, 712100, People's Republic of China
| | - Ehsan Sadeghnezhad
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Songtao Jiu
- Department of Plant Science, Shanghai Jiao Tong University, Shanghai City, 200030, Shanghai, People's Republic of China
| | - Xudong Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Tianyu Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Zhongjie Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Le Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Haifeng Jia
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China.
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China.
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39
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Su W, Ren Y, Wang D, Su Y, Feng J, Zhang C, Tang H, Xu L, Muhammad K, Que Y. The alcohol dehydrogenase gene family in sugarcane and its involvement in cold stress regulation. BMC Genomics 2020; 21:521. [PMID: 32727370 PMCID: PMC7392720 DOI: 10.1186/s12864-020-06929-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alcohol dehydrogenases (ADHs) in plants are encoded by a multigene family. ADHs participate in growth, development, and adaptation in many plant species, but the evolution and function of the ADH gene family in sugarcane is still unclear. RESULTS In the present study, 151 ADH genes from 17 species including 32 ADH genes in Saccharum spontaneum and 6 ADH genes in modern sugarcane cultivar R570 were identified. Phylogenetic analysis demonstrated two groups of ADH genes and suggested that these genes underwent duplication during angiosperm evolution. Whole-genome duplication (WGD)/segmental and dispersed duplications played critical roles in the expansion of ADH family in S. spontaneum and R570, respectively. ScADH3 was cloned and preferentially expressed in response to cold stress. ScADH3 conferred improved cold tolerance in E. coli cells. Ectopic expression showed that ScADH3 can also enhance cold tolerance in transgenic tobacco. The accumulation of reactive oxygen species (ROS) in leaves of transgenic tobacco was significantly lower than in wild-type tobacco. The transcript levels of ROS-related genes in transgenic tobacco increased significantly. ScADH3 seems to affect cold tolerance by regulating the ROS-related genes to maintain the ROS homeostasis. CONCLUSIONS This study depicted the size and composition of the ADH gene family in 17 species, and investigated their evolution pattern. Comparative genomics analysis among the ADH gene families of S. bicolor, R570 and S. spontaneum revealed their close evolutionary relationship. Functional analysis suggested that ScADH3, which maintained the steady state of ROS by regulating ROS-related genes, was related to cold tolerance. These findings will facilitate research on evolutionary and functional aspects of the ADH genes in sugarcane, especially for the understanding of ScADH3 under cold stress.
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Affiliation(s)
- Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongjuan Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jingfang Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hanchen Tang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Khushi Muhammad
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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40
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Correr FH, Hosaka GK, Gómez SGP, Cia MC, Vitorello CBM, Camargo LEA, Massola NS, Carneiro MS, Margarido GRA. Time-series expression profiling of sugarcane leaves infected with Puccinia kuehnii reveals an ineffective defense system leading to susceptibility. PLANT CELL REPORTS 2020; 39:873-889. [PMID: 32314046 DOI: 10.1007/s00299-020-02536-w] [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: 12/20/2019] [Accepted: 03/30/2020] [Indexed: 05/02/2023]
Abstract
Successful orange rust development on sugarcane can potentially be explained as suppression of the plant immune system by the pathogen or delayed plant signaling to trigger defense responses. Puccinia kuehnii is an obligate biotrophic fungus that infects sugarcane leaves causing a disease called orange rust. It spread out to other countries resulting in reduction of crop yield since its first outbreak. One of the knowledge gaps of that pathosystem is to understand the molecular mechanisms altered in susceptible plants by this biotic stress. Here, we investigated the changes in temporal expression of transcripts in pathways associated with the immune system. To achieve this purpose, we used RNA-Seq to analyze infected leaf samples collected at five time points after inoculation. Differential expression analyses of adjacent time points revealed substantial changes at 12, 48 h after inoculation and 12 days after inoculation, coinciding with the events of spore germination, haustoria post-penetration and post-sporulation, respectively. During the first 24 h, a lack of transcripts involved with resistance mechanisms was revealed by underrepresentation of hypersensitive and defense response related genes. However, two days after inoculation, upregulation of genes involved with immune response regulation provided evidence of some potential defense response. Events related to biotic stress responses were predominantly downregulated in the initial time points, but expression was later restored to basal levels. Genes involved in carbohydrate metabolism showed evidence of repression followed by upregulation, possibly to ensure the pathogen nutritional requirements were met. Our results support the hypothesis that P. kuehnii initially suppressed sugarcane genes involved in plant defense systems. Late overexpression of specific regulatory pathways also suggests the possibility of an inefficient recognition system by a susceptible sugarcane genotype.
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Affiliation(s)
- Fernando Henrique Correr
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Guilherme Kenichi Hosaka
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Sergio Gregorio Pérez Gómez
- Departamento de Fitopatologia, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Mariana Cicarelli Cia
- Departamento de Fitopatologia, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Claudia Barros Monteiro Vitorello
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Luis Eduardo Aranha Camargo
- Departamento de Fitopatologia, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Nelson Sidnei Massola
- Departamento de Fitopatologia, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Universidade Federal de São Carlos, Centro de Ciências Agrárias, Araras, São Paulo, Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil.
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Ntambo MS, Meng JY, Rott PC, Henry RJ, Zhang HL, Gao SJ. Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans. Int J Mol Sci 2019; 20:ijms20246138. [PMID: 31817492 PMCID: PMC6940782 DOI: 10.3390/ijms20246138] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
Sugarcane (Saccharum spp. hybrids) is a major source of sugar and renewable bioenergy crop worldwide and suffers serious yield losses due to many pathogen infections. Leaf scald caused by Xanthomonas albilineans is a major bacterial disease of sugarcane in most sugarcane-planting countries. The molecular mechanisms of resistance to leaf scald in this plant are, however, still unclear. We performed a comparative transcriptome analysis between resistant (LCP 85-384) and susceptible (ROC20) sugarcane cultivars infected by X. albilineans using the RNA-seq platform. 24 cDNA libraries were generated with RNA isolated at four time points (0, 24, 48, and 72 h post inoculation) from the two cultivars with three biological replicates. A total of 105,783 differentially expressed genes (DEGs) were identified in both cultivars and the most upregulated and downregulated DEGs were annotated for the processes of the metabolic and single-organism categories, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the 7612 DEGs showed that plant-pathogen interaction, spliceosome, glutathione metabolism, protein processing in endoplasmic reticulum, and plant hormone signal transduction contributed to sugarcane's response to X. albilineans infection. Subsequently, relative expression levels of ten DEGs determined by quantitative reverse transcription-PCR (qRT-PCR), in addition to RNA-Seq data, indicated that different plant hormone (auxin and ethylene) signal transduction pathways play essential roles in sugarcane infected by X. albilineans. In conclusion, our results provide, for the first time, valuable information regarding the transcriptome changes in sugarcane in response to infection by X. albilineans, which contribute to the understanding of the molecular mechanisms underlying the interactions between sugarcane and this pathogen and provide important clues for further characterization of leaf scald resistance in sugarcane.
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Affiliation(s)
- Mbuya Sylvain Ntambo
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.N.); (H.-L.Z.)
| | - Jian-Yu Meng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.N.); (H.-L.Z.)
| | - Philippe C. Rott
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France;
| | - Robert J. Henry
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia;
| | - Hui-Li Zhang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.N.); (H.-L.Z.)
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.N.); (H.-L.Z.)
- Correspondence:
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Diniz AL, Ferreira SS, Ten-Caten F, Margarido GRA, Dos Santos JM, Barbosa GVDS, Carneiro MS, Souza GM. Genomic resources for energy cane breeding in the post genomics era. Comput Struct Biotechnol J 2019; 17:1404-1414. [PMID: 31871586 PMCID: PMC6906722 DOI: 10.1016/j.csbj.2019.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023] Open
Abstract
Sugarcane is one of the most sustainable energy crops among cultivated crops presenting the highest tonnage of cultivated plants. Its high productivity of sugar, bioethanol and bioelectricity make it a promising green alternative to petroleum. Furthermore, the myriad of products that can be derived from sugarcane biomass has been driving breeding programs towards varieties with a higher yield of fiber and a more vigorous and sustainable performance: the energy cane. Here we provide an overview of the energy cane including plant description, breeding efforts, types, and end-uses. In addition, we describe recently published genomic resources for the development of this crop, discuss current knowledge of cell wall metabolism, bioinformatic tools and databases available for the community.
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Affiliation(s)
- Augusto L Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil
| | - Sávio S Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo 05508-090, SP, Brazil
| | - Felipe Ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil
| | - Gabriel R A Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba 13418-900, SP, Brazil
| | - João M Dos Santos
- Departamento de Fitotecnia e Fitossanidade, Centro de Ciências Agrárias, Universidade Federal de Alagoas, BR 104 Norte, km 85, Rio Largo 571000-000, AL, Brazil
| | - Geraldo V de S Barbosa
- Departamento de Fitotecnia e Fitossanidade, Centro de Ciências Agrárias, Universidade Federal de Alagoas, BR 104 Norte, km 85, Rio Largo 571000-000, AL, Brazil
| | - Monalisa S Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera km 174, Araras 13600-970, SP, Brazil
| | - Glaucia M Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil
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43
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Rody HVS, Bombardelli RGH, Creste S, Camargo LEA, Van Sluys MA, Monteiro-Vitorello CB. Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype. BMC Genomics 2019; 20:809. [PMID: 31694536 PMCID: PMC6836459 DOI: 10.1186/s12864-019-6207-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance Gene Analogs (RGAs) of modern sugarcane cultivars to its degrees of resistance to diseases such as smut. However, due to the highly polyploid and heterozygous nature of sugarcane genome, large scale RGA predictions is challenging. RESULTS We predicted, searched for orthologs, and investigated the genomic features of RGAs within a recently released sugarcane elite cultivar genome, alongside the genomes of sorghum, one sugarcane ancestor (Saccharum spontaneum), and a collection of de novo transcripts generated for six modern cultivars. In addition, transcriptomes from two sugarcane genotypes were obtained to investigate the roles of RGAs differentially expressed (RGADE) in their distinct degrees of resistance to smut. Sugarcane references lack RGAs from the TNL class (Toll-Interleukin receptor (TIR) domain associated to nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains) and harbor elevated content of membrane-associated RGAs. Up to 39% of RGAs were organized in clusters, and 40% of those clusters shared synteny. Basically, 79% of predicted NBS-encoding genes are located in a few chromosomes. S. spontaneum chromosome 5 harbors most RGADE orthologs responsive to smut in modern sugarcane. Resistant sugarcane had an increased number of RGAs differentially expressed from both classes of RLK (receptor-like kinase) and RLP (receptor-like protein) as compared to the smut-susceptible. Tandem duplications have largely contributed to the expansion of both RGA clusters and the predicted clades of RGADEs. CONCLUSIONS Most of smut-responsive RGAs in modern sugarcane were potentially originated in chromosome 5 of the ancestral S. spontaneum genotype. Smut resistant and susceptible genotypes of sugarcane have a distinct pattern of RGADE. TM-LRR (transmembrane domains followed by LRR) family was the most responsive to the early moment of pathogen infection in the resistant genotype, suggesting the relevance of an innate immune system. This work can help to outline strategies for further understanding of allele and paralog expression of RGAs in sugarcane, and the results should help to develop a more applied procedure for the selection of resistant plants in sugarcane.
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Affiliation(s)
- Hugo V S Rody
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Renato G H Bombardelli
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Silvana Creste
- Centro de Cana, IAC-Apta, Ribeirão Preto, Av. Pádua Dias n11, CEP 13418-900, Piracicaba, São Paulo, Brazil
| | - Luís E A Camargo
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânia, Universidade de São Paulo, Instituto de Biociências, São Paulo, Brazil
| | - Claudia B Monteiro-Vitorello
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil.
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Bedre R, Irigoyen S, Schaker PDC, Monteiro-Vitorello CB, Da Silva JA, Mandadi KK. Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen. Sci Rep 2019; 9:8876. [PMID: 31222001 PMCID: PMC6586842 DOI: 10.1038/s41598-019-45184-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/22/2019] [Indexed: 12/24/2022] Open
Abstract
Alternative splicing (AS) promotes transcriptome and proteome diversity during growth, development, and stress responses in eukaryotes. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to the absence of a high-quality sequenced reference genome, sugarcane's large, complex genome, and the variable chromosome numbers and polyploidy of sugarcane cultivars. Here, we analyzed changes in the sugarcane isoform-level transcriptome and AS landscape during infection with the smut fungus (Sporisorium scitamineum) using a hybrid approach involving Sorghum bicolor reference-based and Trinity de novo mapping tools. In total, this analysis detected 16,039 and 15,379 transcripts (≥2 FPKM) at 5 and 200 days after infection, respectively. A conservative estimate of isoform-level expression suggested that approximately 5,000 (14%) sugarcane genes undergo AS. Differential expression analysis of the alternatively spliced genes in healthy and smut-infected sugarcane revealed 896 AS events modulated at different stages of infection. Gene family and gene ontology functional enrichment analysis of the differentially spliced genes revealed overrepresentation of functional categories related to the cell wall, defense, and redox homeostasis pathways. Our study provides novel insight into the AS landscape of sugarcane during smut disease interactions.
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Affiliation(s)
- Renesh Bedre
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
| | - Sonia Irigoyen
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
| | - Patricia D C Schaker
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz," Piracicaba, São Paulo, Brazil
- Universidade Tecnológica Federal do Paraná, Toledo, Paraná, Brazil
| | - Claudia B Monteiro-Vitorello
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz," Piracicaba, São Paulo, Brazil
| | - Jorge A Da Silva
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA.
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA.
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Hua-Ying M, Wen-Ju W, Wei-Hua S, Ya-Chun S, Feng L, Cong-Na L, Ling W, Xu Z, Li-Ping X, You-Xiong Q. Genome-wide identification, phylogeny, and expression analysis of Sec14-like PITP gene family in sugarcane. PLANT CELL REPORTS 2019; 38:637-655. [PMID: 30747272 DOI: 10.1007/s00299-019-02394-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Six Sec14-like PITP genes from sugarcane were identified, two of them were cloned, and their biological functions were characterized indicating their involvement in plant defense against biotic and abiotic stresses. Sec14, a phosphatidylinositol transfer protein (PITP) is widely present in eukaryotes. In this study, the structure and expression patterns of six Sec14-like PITP genes (ScSEC14-1, ScSEC14p, ScSFH1, ScSFH2, ScPATL1, and ScPATL2) from sugarcane were analyzed, and two of them (ScSEC14-1 and ScSEC14p) were cloned and functionally verified. Phylogenetic analysis divided these genes into four groups, including group I (ScSFH1 and ScSFH2), group II (ScPATL1 and ScPATL2), Group III (ScSEC14p), and group V (ScSEC14-1). qRT-PCR analysis showed tissue-specific expression of these genes, primarily in the root, leaf, and bud tissues. They responded differently to SA, MeJA, and ABA stresses. ScSEC14-1, ScSEC14p, and ScSFH2 were upregulated by CuCl2 and CdCl2, while ScSEC14-1, ScSFH1, ScSFH2, and ScPATL1 were upregulated by PEG and NaCl. When infected by Sporisorium scitamineum, the transcripts of ScSFH1, ScSFH2, ScPATL1, and ScPATL2 were upregulated in the resistant genotype Yacheng 05-179, while those of ScSEC14-1 and ScSEC14p were upregulated in the susceptible genotype ROC22. Subcellular localization showed that ScSEC14-1 and ScSEC14p were mainly localized in the plasma membrane and cytoplasm. Enhanced growth of Escherichia coli BL21 cells expressing ScSEC14-1 and ScSEC14p showed high tolerance to NaCl and mannitol stresses. The transient overexpression of ScSEC14-1 and ScSEC14p in Nicotiana benthamiana leaves enhanced its resistance to the infection of tobacco pathogens Ralstonia solanacearum and Fusarium solani var. coeruleum. We can conclude the involvement of ScSEC14-1 and ScSEC14p in the defense against biotic and abiotic stresses, which should facilitate further research on Sec14-like PITP gene family, especially its regulatory mechanisms in sugarcane.
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Affiliation(s)
- Mao Hua-Ying
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wang Wen-Ju
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Su Wei-Hua
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Su Ya-Chun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liu Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li Cong-Na
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wang Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhang Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Li-Ping
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Que You-Xiong
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Singh P, Singh SN, Tiwari AK, Pathak SK, Singh AK, Srivastava S, Mohan N. Integration of sugarcane production technologies for enhanced cane and sugar productivity targeting to increase farmers' income: strategies and prospects. 3 Biotech 2019; 9:48. [PMID: 30729072 DOI: 10.1007/s13205-019-1568-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/03/2019] [Indexed: 10/27/2022] Open
Abstract
The idea of doubling the farmers' income in next 5 years has been slated by the Government of India. The specific target of increasing sugarcane farmers' income could be achieved by developing cost-effective technologies, transferring them from laboratory to land, educating the farmers and creating a linkage between all stakeholders. Consistent efforts shall be required to harness all possible sources for increasing farmer's income in and outside the agriculture sector with respect to improvement in sugarcane and sugar productivity, enhancement in resource use efficiency and adopting various other ways and means including intercropping, management of pests and diseases, use of biotechnological tools and minimizing post-harvest deterioration. The advances in sugarcane biotechnology could become remarkable in the coming years, both in terms of improving productivity as well as increasing the value and utility of this crop substantially. In future, genetically modified sugarcane varieties with increased resistance to different biotic and abiotic stresses would serve more towards sugarcane crop improvement. Any possibility of enhancement in the income of sugarcane farmers shall also be dependent upon the profitability and sustainability of the sugar industry. Integration of sugarcane production technologies for improvement in farm productivity, diversified sugarcane production system, reduced cost of cultivation along with increased processing plant efficiency and diversification to produce value added products shall ensure smooth and higher payment to the farmers. Development of low-cost technologies to convert "waste to resource" on a smaller scale shall also help the farmers to increase their income further. This paper focuses on possible measures to be taken up in each aspects of sugarcane cultivation including biotechnological approaches to achieve the goal of enhancing the income of sugarcane farmers substantially, particularly in the sub-tropical region of India.
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Proteomic Analysis of the Resistance Mechanisms in Sugarcane during Sporisorium scitamineum Infection. Int J Mol Sci 2019; 20:ijms20030569. [PMID: 30699953 PMCID: PMC6387155 DOI: 10.3390/ijms20030569] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/26/2019] [Accepted: 01/27/2019] [Indexed: 01/10/2023] Open
Abstract
Smut disease is caused by Sporisorium scitamineum, an important sugarcane fungal pathogen causing an extensive loss in yield and sugar quality. The available literature suggests that there are two types of smut resistance mechanisms: external resistance by physical or chemical barriers and intrinsic internal resistance mechanisms operating at host–pathogen interaction at cellular and molecular levels. The nature of smut resistance mechanisms, however, remains largely unknown. The present study investigated the changes in proteome occurring in two sugarcane varieties with contrasting susceptibility to smut—F134 and NCo310—at whip development stage after S. scitamineum infection. Total proteins from pathogen inoculated and uninoculated (control) leaves were separated by two-dimensional gel electrophoresis (2D-PAGE). Protein identification was performed using BLASTp and tBLASTn against NCBI nonredundant protein databases and EST databases, respectively. A total of thirty proteins spots representing differentially expressed proteins (DEPs), 16 from F134 and 14 from NCo310, were identified and analyzed by MALDI-TOF/TOF MS. In F134, 4 DEPs were upregulated and nine were downregulated, while, nine were upregulated and three were downregulated in NCo310. The DEPs were associated with DNA binding, metabolic processes, defense, stress response, photorespiration, protein refolding, chloroplast, nucleus and plasma membrane. Finally, the expression of CAT, SOD, and PAL with recognized roles in S. scitamineum infection in both sugarcane verities were analyzed by real-time quantitative PCR (RT-qPCR) technique. Identification of genes critical for smut resistance in sugarcane will increase our knowledge of S. scitamineum-sugarcane interaction and help to develop molecular and conventional breeding strategies for variety improvement.
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Su Y, Xiao X, Ling H, Huang N, Liu F, Su W, Zhang Y, Xu L, Muhammad K, Que Y. A dynamic degradome landscape on miRNAs and their predicted targets in sugarcane caused by Sporisorium scitamineum stress. BMC Genomics 2019; 20:57. [PMID: 30658590 PMCID: PMC6339412 DOI: 10.1186/s12864-018-5400-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. scitamineum is a complex network system. However, to date, there is no report on the identification of microRNA (miRNA) target genes of sugarcane in response to smut pathogen infection by degradome technology. RESULTS TaqMan qRT-PCR detection and enzyme activity determination showed that S. scitamineum rapidly proliferated and incurred significant enzyme activity changes in the reactive oxygen species metabolic pathway and phenylpropanoid metabolic pathway at 2 d and 5 d after inoculation, which was the best time points to study target gene degradation during sugarcane and S. scitamineum interaction. A total of 122.33 Mb of raw data was obtained from degradome sequencing analysis of YC05-179 (smut-resistant) and ROC22 (smut-susceptible) after inoculation. The Q30 of each sample was > 93%, and the sequence used for degradation site analysis exactly matched the sugarcane reference sequence. A total of 309 target genes were predicted in sugarcane, corresponding to 97 known miRNAs and 112 novel miRNAs, and 337 degradation sites, suggesting that miRNAs can efficiently direct cleavage at multiple sites in the predicted target mRNAs. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the predicted target genes were involved in various regulatory processes, such as signal transduction mechanisms, inorganic ion transport and metabolism, defense mechanisms, translation, posttranslational modifications, energy production and conversion, and glycerolipid metabolism. qRT-PCR analysis of the expression level of 13 predicted target genes and their corresponding miRNAs revealed that there was no obvious negative regulatory relationship between miRNAs and their target genes. In addition, a number of putative resistance-related target genes regulated by miRNA-mediated cleavage were accumulated in sugarcane during S. scitamineum infection, suggesting that feedback regulation of miRNAs may be involved in the response of sugarcane to S. scitamineum infection. CONCLUSIONS This study elucidates the underlying response of sugarcane to S. scitamineum infection, and also provides a resource for miRNAs and their predicted target genes for smut resistance improvement in sugarcane.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xinhuan Xiao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuye Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Khushi Muhammad
- Department of Genetics, Hazara University, Mansehra, 21300 Pakistan
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Wang L, Liu F, Zhang X, Wang W, Sun T, Chen Y, Dai M, Yu S, Xu L, Su Y, Que Y. Expression Characteristics and Functional Analysis of the ScWRKY3 Gene from Sugarcane. Int J Mol Sci 2018; 19:ijms19124059. [PMID: 30558233 PMCID: PMC6321069 DOI: 10.3390/ijms19124059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022] Open
Abstract
The plant-specific WRKY transcriptional regulatory factors have been proven to play vital roles in plant growth, development, and responses to biotic and abiotic stresses. However, there are few studies on the WRKY gene family in sugarcane (Saccharum spp.). In the present study, the characterization of a new subgroup, IIc WRKY protein ScWRKY3, from a Saccharum hybrid cultivar is reported. The ScWRKY3 protein was localized in the nucleus of Nicotiana benthamiana leaves and showed no transcriptional activation activity and no toxic effects on the yeast strain Y2HGold. An interaction between ScWRKY3 and a reported sugarcane protein ScWRKY4, was confirmed in the nucleus. The ScWRKY3 gene had the highest expression level in sugarcane stem pith. The transcript of ScWRKY3 was stable in the smut-resistant Saccharum hybrid cultivar Yacheng05-179, while it was down-regulated in the smut-susceptible Saccharum hybrid cultivar ROC22 during inoculation with the smut pathogen (Sporisorium scitamineum) at 0⁻72 h. ScWRKY3 was remarkably up-regulated by sodium chloride (NaCl), polyethylene glycol (PEG), and plant hormone abscisic acid (ABA), but it was down-regulated by salicylic acid (SA) and methyl jasmonate (MeJA). Moreover, transient overexpression of the ScWRKY3 gene in N. benthamiana indicated a negative regulation during challenges with the fungal pathogen Fusarium solani var. coeruleum or the bacterial pathogen Ralstonia solanacearum in N. benthamiana. The findings of the present study should accelerate future research on the identification and functional characterization of the WRKY family in sugarcane.
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Affiliation(s)
- Ling Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xu Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenju Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yufeng Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Mingjian Dai
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shengxiao Yu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Schmitz L, McCotter S, Kretschmer M, Kronstad JW, Heimel K. Transcripts and tumors: regulatory and metabolic programming during biotrophic phytopathogenesis. F1000Res 2018; 7. [PMID: 30519451 PMCID: PMC6248262 DOI: 10.12688/f1000research.16404.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/12/2018] [Indexed: 01/05/2023] Open
Abstract
Biotrophic fungal pathogens of plants must sense and adapt to the host environment to complete their life cycles. Recent transcriptome studies of the infection of maize by the biotrophic pathogen
Ustilago maydis are providing molecular insights into an ordered program of changes in gene expression and the deployment of effectors as well as key features of nutrient acquisition. In particular, the transcriptome data provide a deeper appreciation of the complexity of the transcription factor network that controls the biotrophic program of invasion, proliferation, and sporulation. Additionally, transcriptome analysis during tumor formation, a key late stage in the life cycle, revealed features of the remodeling of host and pathogen metabolism that may support the formation of tremendous numbers of spores. Transcriptome studies are also appearing for other smut species during interactions with their hosts, thereby providing opportunities for comparative approaches to understand biotrophic adaptation.
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Affiliation(s)
- Lara Schmitz
- Institute for Microbiology and Genetics, Department of Molecular Microbiology and Genetics, Georg-August-University-Göttingen, Göttingen, Lower Saxony, D-37077, Germany
| | - Sean McCotter
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - James W Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Kai Heimel
- Institute for Microbiology and Genetics, Department of Molecular Microbiology and Genetics, Georg-August-University-Göttingen, Göttingen, Lower Saxony, D-37077, Germany
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