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Yuan G, Shi J, Zeng C, Shi H, Yang Y, Zhang C, Ma T, Wu M, Jia Z, Du J, Zou C, Ma L, Pan G, Shen Y. Integrated analysis of transcriptomics and defense-related phytohormones to discover hub genes conferring maize Gibberella ear rot caused by Fusarium Graminearum. BMC Genomics 2024; 25:733. [PMID: 39080512 PMCID: PMC11288080 DOI: 10.1186/s12864-024-10656-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 07/23/2024] [Indexed: 08/03/2024] Open
Abstract
BACKGROUND Gibberella ear rot (GER) is one of the most devastating diseases in maize growing areas, which directly reduces grain yield and quality. However, the underlying defense response of maize to pathogens infection is largely unknown. RESULTS To gain a comprehensive understanding of the defense response in GER resistance, two contrasting inbred lines 'Nov-82' and 'H10' were used to explore transcriptomic profiles and defense-related phytohormonal alterations during Fusarium graminearum infection. Transcriptomic analysis revealed 4,417 and 4,313 differentially expressed genes (DEGs) from the Nov-82 and H10, respectively, and 647 common DEGs between the two lines. More DEGs were obviously enriched in phenylpropanoid biosynthesis, secondary metabolites biosynthesis, metabolic process and defense-related pathways. In addition, the concentration of the defense-related phytohormones, jasmonates (JAs) and salicylates (SAs), was greatly induced after the pathogen infection. The level of JAs in H10 was more higher than in Nov-82, whereas an opposite pattern for the SA between the both lines. Integrated analysis of the DEGs and the phytohormones revealed five vital modules based on co-expression network analysis according to their correlation. A total of 12 hub genes encoding fatty acid desaturase, subtilisin-like protease, ethylene-responsive transcription factor, 1-aminocyclopropane-1-carboxylate oxidase, and sugar transport protein were captured from the key modules, indicating that these genes might play unique roles in response to pathogen infection, CONCLUSIONS: Overall, our results indicate that large number DEGs related to plant disease resistance and different alteration of defensive phytohormones were activated during F. graminearum infection, providing new insight into the defense response against pathogen invasion, in addition to the identified hub genes that can be further investigated for enhancing maize GER resistance.
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Affiliation(s)
- Guangsheng Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jiahao Shi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cheng Zeng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haoya Shi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yong Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chuntian Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tieli Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengyang Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zheyi Jia
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Juan Du
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
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Zhang X, Zheng S, Yu M, Xu C, Li Y, Sun L, Hu G, Yang J, Qiu X. Evaluation of Resistance Resources and Analysis of Resistance Mechanisms of Maize to Stalk Rot Caused by Fusarium graminearum. PLANT DISEASE 2024; 108:348-358. [PMID: 37443398 DOI: 10.1094/pdis-04-23-0825-re] [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] [Indexed: 07/15/2023]
Abstract
Stalk rot is one of the most destructive and widely distributed diseases in maize plants worldwide. Research on the performance and resistance mechanisms of maize against stem rot is constantly improving. In this study, among 120 inbred maize lines infected by Fusarium graminearum using the injection method, 4 lines (3.33%) were highly resistant to stalk rot, 28 lines (23.33%) were resistant, 57 lines (47.50%) were susceptible, and 31 lines (25.84%) were highly susceptible. The inbred lines 18N10118 and 18N10370 were the most resistant and susceptible with disease indices of 7.5 and 75.6, respectively. Treatment of resistant and susceptible maize inbred seedlings with F. graminearum showed that root hair growth of the susceptible inbred lines was significantly inhibited, and a large number of hyphae attached and adsorbed multiple conidia near the root system. However, the resistant inbred lines were delayed and inconspicuous, with only a few hyphae and spores appearing near the root system. Compared with susceptible inbred lines, resistant maize inbred line seedlings treated with F. graminearum exhibited elevated activities of catalase, phenylalanine ammonia-lyase, polyphenol oxidase, and superoxide dismutase. We identified 153 genes related to disease resistance by transcriptome analysis. The mitogen-activated protein kinase signaling and peroxisome pathways mainly regulated the resistance mechanism of maize inbred lines to F. graminearum infection. These two pathways might play an important role in the disease resistance mechanism, and the function of genes in the two pathways must be further studied, which might provide a theoretical basis for further understanding the molecular resistance mechanism of stalk rot and resistance gene mining.
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Affiliation(s)
- Xue Zhang
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Suli Zheng
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Miao Yu
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Chuzhen Xu
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Yonggang Li
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Lei Sun
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin 150086, China
| | - Guanghi Hu
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Jianfei Yang
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Xiaojing Qiu
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
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Quiroz-Figueroa FR, Cruz-Mendívil A, Ibarra-Laclette E, García-Pérez LM, Gómez-Peraza RL, Hanako-Rosas G, Ruíz-May E, Santamaría-Miranda A, Singh RK, Campos-Rivero G, García-Ramírez E, Narváez-Zapata JA. Cell wall-related genes and lignin accumulation contribute to the root resistance in different maize ( Zea mays L.) genotypes to Fusarium verticillioides (Sacc.) Nirenberg infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1195794. [PMID: 37441182 PMCID: PMC10335812 DOI: 10.3389/fpls.2023.1195794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 07/15/2023]
Abstract
Introduction The fungal pathogen Fusarium verticillioides (Sacc.) Nirenberg (Fv) causes considerable agricultural and economic losses and is harmful to animal and human health. Fv can infect maize throughout its long agricultural cycle, and root infection drastically affects maize growth and yield. Methods The root cell wall is the first physical and defensive barrier against soilborne pathogens such as Fv. This study compares two contrasting genotypes of maize (Zea mays L.) roots that are resistant (RES) or susceptible (SUS) to Fv infection by using transcriptomics, fluorescence, scanning electron microscopy analyses, and ddPCR. Results Seeds were infected with a highly virulent local Fv isolate. Although Fv infected both the RES and SUS genotypes, infection occurred faster in SUS, notably showing a difference of three to four days. In addition, root infections in RES were less severe in comparison to SUS infections. Comparative transcriptomics (rate +Fv/control) were performed seven days after inoculation (DAI). The analysis of differentially expressed genes (DEGs) in each rate revealed 733 and 559 unique transcripts that were significantly (P ≤0.05) up and downregulated in RES (+Fv/C) and SUS (+Fv/C), respectively. KEGG pathway enrichment analysis identified coumarin and furanocoumarin biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction pathways as being highly enriched with specific genes involved in cell wall modifications in the RES genotype, whereas the SUS genotype mainly displayed a repressed plant-pathogen interaction pathway and did not show any enriched cell wall genes. In particular, cell wall-related gene expression showed a higher level in RES than in SUS under Fv infection. Analysis of DEG abundance made it possible to identify transcripts involved in response to abiotic and biotic stresses, biosynthetic and catabolic processes, pectin biosynthesis, phenylpropanoid metabolism, and cell wall biosynthesis and organization. Root histological analysis in RES showed an increase in lignified cells in the sclerenchymatous hypodermis zone during Fv infection. Discussion These differences in the cell wall and lignification could be related to an enhanced degradation of the root hairs and the epidermis cell wall in SUS, as was visualized by SEM. These findings reveal that components of the root cell wall are important against Fv infection and possibly other soilborne phytopathogens.
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Affiliation(s)
- Francisco Roberto Quiroz-Figueroa
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Abraham Cruz-Mendívil
- Consejo Nacional de Ciencia y Tecnología (CONACYT)-Instituto Politécnico Nacional, (CIIDIR) Unidad Sinaloa, Guasave, Mexico
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Cluster BioMimic®, Xalapa, Mexico
| | - Luz María García-Pérez
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Rosa Luz Gómez-Peraza
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Greta Hanako-Rosas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Cluster BioMimic®, Xalapa, Mexico
| | - Eliel Ruíz-May
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Cluster BioMimic®, Xalapa, Mexico
| | - Apolinar Santamaría-Miranda
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Rupesh Kumar Singh
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Gerardo Campos-Rivero
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Elpidio García-Ramírez
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Liu P, Jiang L, Long P, Li Q, Hou F, Yuan G, Chen Z, Zhang M, Zou C, Pan G, Ma L, Shen Y. A genome-wide co-expression network analysis revealed ZmNRAMP6-mediated regulatory pathway involved in maize tolerance to lead stress. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:122. [PMID: 37142873 DOI: 10.1007/s00122-023-04371-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE A metal transporter ZmNRAMP6 was identified by using a trait-associated co-expression network analysis at a genome-wide level. ZmNRAMP6 confers maize sensitivity to Pb by accumulating it to maize shoots. ZmNRAMP6 knockout detains Pb in roots, activates antioxidant enzymes, and improves Pb tolerance. Lead (Pb) is one of the most toxic heavy metal pollutants, which can penetrate plant cells via root absorption and thus cause irreversible damages to the human body through the food chain. To identify the key gene responsible for Pb tolerance in maize, we performed a trait-associated co-expression network analysis at a genome-wide level, using two maize lines with contrasting Pb tolerances. Finally, ZmNRAMP6 that encodes a metal transporter was identified as the key gene among the Pb tolerance-associated co-expression module. Heterologous expression of ZmNRAMP6 in yeast verified its role in Pb transport. Combined Arabidopsis overexpression and maize mutant analysis suggested that ZmNRAMP6 conferred plant sensitivity to Pb stress by mediating Pb distribution across the roots and shoots. Knockout of ZmNRAMP6 caused Pb retention in the roots and activation of the antioxidant enzyme system, resulting in an increased Pb tolerance in maize. ZmNRAMP6 was likely to transport Pb from the roots to shoots and environment. An integration of yeast one-hybrid and dual-luciferase reporter assay uncovered that ZmNRAMP6 was negatively regulated by a known Pb tolerance-related transcript factor ZmbZIP54. Collectively, knockout of ZmNRAMP6 will aid in the bioremediation of contaminated soil and food safety guarantee of forage and grain corn.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ping Long
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinglin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fengxia Hou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangsheng Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minyan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Fu J, Wang L, Pei W, Yan J, He L, Ma B, Wang C, Zhu C, Chen G, Shen Q, Wang Q. ZmEREB92 interacts with ZmMYC2 to activate maize terpenoid phytoalexin biosynthesis upon Fusarium graminearum infection through jasmonic acid/ethylene signaling. THE NEW PHYTOLOGIST 2023; 237:1302-1319. [PMID: 36319608 DOI: 10.1111/nph.18590] [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: 08/19/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Maize (Zea mays) terpenoid phytoalexins (MTPs) induced by multiple fungi display extensive antimicrobial activities, yet how maize precisely regulates MTP accumulation upon pathogen infection remains elusive. In this study, pretreatment with jasmonic acid (JA)/ethylene (ET)-related inhibitors significantly reduced Fusarium graminearum-induced MTP accumulation and resulted in enhanced susceptibility to F. graminearum, indicating the involvement of JA/ET in MTP regulatory network. ZmEREB92 positively regulated MTP biosynthetic gene (MBG) expression by correlation analysis. Knockout of ZmEREB92 significantly compromised maize resistance to F. graminearum with delayed induction of MBGs and attenuated MTP accumulation. The activation of ZmEREB92 on MBGs is dependent on the interaction with ZmMYC2, which directly binds to MBG promoters. ZmJAZ14 interacts both with ZmEREB92 and with ZmMYC2 in a competitive manner to negatively regulate MBG expression. Altogether, our findings illustrate the regulatory mechanism for JA/ET-mediated MTP accumulation upon F. graminearum infection with the involvement of ZmEREB92, ZmMYC2, and ZmJAZ14, which provides new insights into maize disease responses.
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Affiliation(s)
- Jingye Fu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenzheng Pei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jie Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linqian He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ben Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chenying Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gang Chen
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8510, Japan
| | - Qinqin Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
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Wang Y, Li T, Sun Z, Huang X, Yu N, Tai H, Yang Q. Comparative transcriptome meta-analysis reveals a set of genes involved in the responses to multiple pathogens in maize. FRONTIERS IN PLANT SCIENCE 2022; 13:971371. [PMID: 36186003 PMCID: PMC9521429 DOI: 10.3389/fpls.2022.971371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Maize production is constantly threatened by the presence of different fungal pathogens worldwide. Genetic resistance is the most favorable approach to reducing yield losses resulted from fungal diseases. The molecular mechanism underlying disease resistance in maize remains largely unknown. The objective of this study was to identify key genes/pathways that are consistently associated with multiple fungal pathogen infections in maize. Here, we conducted a meta-analysis of gene expression profiles from seven publicly available RNA-seq datasets of different fungal pathogen infections in maize. We identified 267 common differentially expressed genes (co-DEGs) in the four maize leaf infection experiments and 115 co-DEGs in all the seven experiments. Functional enrichment analysis showed that the co-DEGs were mainly involved in the biosynthesis of diterpenoid and phenylpropanoid. Further investigation revealed a set of genes associated with terpenoid phytoalexin and lignin biosynthesis, as well as potential pattern recognition receptors and nutrient transporter genes, which were consistently up-regulated after inoculation with different pathogens. In addition, we constructed a weighted gene co-expression network and identified several hub genes encoding transcription factors and protein kinases. Our results provide valuable insights into the pathways and genes influenced by different fungal pathogens, which might facilitate mining multiple disease resistance genes in maize.
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Affiliation(s)
- Yapeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Ting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Zedan Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Xiaojian Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Naibing Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Huanhuan Tai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Qin Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
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Tang B, Zhang Z, Zhao X, Xu Y, Wang L, Chen XL, Wang W. Multi-Omics Analysis Reveals a Regulatory Network of ZmCCT During Maize Resistance to Gibberella Stalk Rot at the Early Stage. FRONTIERS IN PLANT SCIENCE 2022; 13:917493. [PMID: 35812937 PMCID: PMC9260664 DOI: 10.3389/fpls.2022.917493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the most devastating diseases in maize; however, the regulatory mechanism of resistance to GSR remains largely unknown. We performed a comparative multi-omics analysis to reveal the early-stage resistance of maize to GSR. We inoculated F. graminearum to the roots of susceptible (Y331) and resistant (Y331-ΔTE) near-isogenic lines containing GSR-resistant gene ZmCCT for multi-omics analysis. Transcriptome detected a rapid reaction that confers resistance at 1-3 hpi as pattern-triggered immunity (PTI) response to GSR. Many key properties were involved in GSR resistance, including genes in photoperiod and hormone pathways of salicylic acid and auxin. The activation of programmed cell death-related genes and a number of metabolic pathways at 6 hpi might be important to prevent further colonization. This is consistent with an integrative analysis of transcriptomics and proteomics that resistant-mediated gene expression reprogramming exhibited a dynamic pattern from 3 to 6 hpi. Further metabolomics analysis revealed that the amount of many chemical compounds was altered in pathways associated with the phenylpropanoid biosynthesis and the phenylalanine metabolism, which may play key roles to confer the GSR resistance. Taken together, we generated a valuable resource to interpret the defense mechanism during early GSR resistance.
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Affiliation(s)
- Bozeng Tang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Zhaoheng Zhang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xinyu Zhao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yang Xu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Li Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xiao-Lin Chen
- State Key Laboratory of Agricultural Microbiology and Provincial Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weixiang Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
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Yang T, Liu J, Li X, Amanullah S, Lu X, Zhang M, Zhang Y, Luan F, Liu H, Wang X. Transcriptomic Analysis of Fusarium oxysporum Stress-Induced Pathosystem and Screening of Fom-2 Interaction Factors in Contrasted Melon Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:961586. [PMID: 35937314 PMCID: PMC9354789 DOI: 10.3389/fpls.2022.961586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/22/2022] [Indexed: 05/03/2023]
Abstract
Fusarium wilt is one of the most destructive and less controllable diseases in melon, which is usually caused by fusarium oxysporum. In this study, transcriptome sequencing and Yeast Two-Hybrid (Y2H) methods were used for quantification of differentially expressed genes (DEGs) involved in fusarium oxysporum (f. sp. melonis race 1) stress-induced mechanisms in contrasted melon varieties (M4-45 "susceptible" and MR-1 "resistant"). The interaction factors of Fom-2 resistance genes were also explored in response to the plant-pathogen infection mechanism. Transcriptomic analysis exhibited total 1,904 new genes; however, candidate DEGs analysis revealed a total of 144 specific genes (50 upregulated and 94 downregulated) for M4-45 variety and 104 specific genes (71 upregulated and 33 downregulated) for MR-1 variety, respectively. The analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway depicted some candidate DEGs, including Phenylalanine metabolism, phenylpropane biosynthesis, plants-pathogen interaction, and signal transduction of plant hormones, which were mainly involved in disease resistance metabolic pathways. The weighted gene co-expression network analysis (WGCNA) analysis revealed a strong correlation module and exhibited the disease resistance-related genes encoding course proteins, transcription factors, protein kinase, benzene propane biosynthesis path, plants-pathogen interaction pathway, and glutathione S-transferase. Meanwhile, the resistance-related specific genes expression was relatively abundant in MR-1 compared to the M4-45, and cell wall-associated receptor kinases (MELO3C008452 and MELO3C008453), heat shock protein (Cucumis_melo_newGene_172), defensin-like protein (Cucumis_melo_newGene_5490), and disease resistance response protein (MELO3C016325), activator response protein (MELO3C021623), leucine-rich repeat receptor protein kinase (MELO3C024412), lactyl glutathione ligase (Cucumis_melo_newGene_36), and unknown protein (MELO3C007588) were persisted by exhibiting the upregulated expressions. At the transcription level, the interaction factors between the candidate genes in response to the fusarium oxysporum induced stress, and Y2H screening signified the main contribution of MYB transcription factors (MELO3C009678 and MELO3C014597), BZIP (MELO3C011839 and MELO3C019349), unknown proteins, and key enzymes in the ubiquitination process (4XM334FK014). The candidate genes were further verified in exogenously treated melon plants with f. oxysporum (Fom-2, Race 1), Abscisic acid (ABA), Methyl Jasmonite (MeJA), and Salicylic acid (SA), using the fluorescence quantitative polymerase chain reaction (qRT-PCR) analysis. The overall expression results indicated that the SA signal pathway is involved in effective regulation of the Fom-2 gene activity.
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Affiliation(s)
- Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Jiajun Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xiaomei Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xueyan Lu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Mingchong Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Yanhang Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- *Correspondence: Hongyu Liu,
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- Xuezheng Wang,
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9
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Ding Y, Gardiner DM, Powell JJ, Colgrave ML, Park RF, Kazan K. Adaptive defence and sensing responses of host plant roots to fungal pathogen attack revealed by transcriptome and metabolome analyses. PLANT, CELL & ENVIRONMENT 2021; 44:3526-3544. [PMID: 34591319 DOI: 10.1111/pce.14195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Plant root-produced constitutive and inducible defences inhibit pathogenic microorganisms within roots and in the rhizosphere. However, regulatory mechanisms underlying host responses during root-pathogen interactions are largely unexplored. Using the model species Brachypodium distachyon (Bd), we studied transcriptional and metabolic responses altered in Bd roots following challenge with Fusarium graminearum (Fg), a fungal pathogen that causes diseases in diverse organs of cereal crops. Shared gene expression patterns were found between Bd roots and spikes during Fg infection associated with the mycotoxin deoxynivalenol (DON). Overexpression of BdMYB78, an up-regulated transcription factor, significantly increased root resistance during Fg infection. We show that Bd roots recognize encroaching Fg prior to physical contact by altering transcription of genes associated with multiple cellular processes such as reactive oxygen species and cell development. These changes coincide with altered levels of secreted host metabolites detected by an untargeted metabolomic approach. The secretion of Bd metabolites was suppressed by Fg as enhanced levels of defence-associated metabolites were found in roots during pre-contact with a Fg mutant defective in host perception and the ability to cause disease. Our results help to understand root defence strategies employed by plants, with potential implications for improving the resistance of cereal crops to soil pathogens.
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Affiliation(s)
- Yi Ding
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- The Plant Breeding Institute, School of Life & Environmental Sciences, Faculty of Science, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Donald M Gardiner
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Jonathan J Powell
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Michelle L Colgrave
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Australian Research Council, Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Robert F Park
- The Plant Breeding Institute, School of Life & Environmental Sciences, Faculty of Science, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Kemal Kazan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
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10
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He W, Zhu Y, Leng Y, Yang L, Zhang B, Yang J, Zhang X, Lan H, Tang H, Chen J, Gao S, Tan J, Kang J, Deng L, Li Y, He Y, Rong T, Cao M. Transcriptomic Analysis Reveals Candidate Genes Responding Maize Gray Leaf Spot Caused by Cercospora zeina. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112257. [PMID: 34834621 PMCID: PMC8625984 DOI: 10.3390/plants10112257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 05/27/2023]
Abstract
Gray leaf spot (GLS), caused by the fungal pathogen Cercospora zeina (C. zeina), is one of the most destructive soil-borne diseases in maize (Zea mays L.), and severely reduces maize production in Southwest China. However, the mechanism of resistance to GLS is not clear and few resistant alleles have been identified. Two maize inbred lines, which were shown to be resistant (R6) and susceptible (S8) to GLS, were injected by C. zeina spore suspensions. Transcriptome analysis was carried out with leaf tissue at 0, 6, 24, 144, and 240 h after inoculation. Compared with 0 h of inoculation, a total of 667 and 419 stable common differentially expressed genes (DEGs) were found in the resistant and susceptible lines across the four timepoints, respectively. The DEGs were usually enriched in 'response to stimulus' and 'response to stress' in GO term analysis, and 'plant-pathogen interaction', 'MAPK signaling pathways', and 'plant hormone signal transduction' pathways, which were related to maize's response to GLS, were enriched in KEGG analysis. Weighted-Genes Co-expression Network Analysis (WGCNA) identified two modules, while twenty hub genes identified from these indicated that plant hormone signaling, calcium signaling pathways, and transcription factors played a central role in GLS sensing and response. Combing DEGs and QTL mapping, five genes were identified as the consensus genes for the resistance of GLS. Two genes, were both putative Leucine-rich repeat protein kinase family proteins, specifically expressed in R6. In summary, our results can provide resources for gene mining and exploring the mechanism of resistance to GLS in maize.
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Affiliation(s)
- Wenzhu He
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Yonghui Zhu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Yifeng Leng
- College of Agricultural Sciences, Xichang University, Xichang 615000, China;
| | - Lin Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Biao Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Junpin Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Haitao Tang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Jie Chen
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Jun Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Jiwei Kang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Luchang Deng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Yan Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Yuanyuan He
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Moju Cao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
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11
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Manes N, Brauer EK, Hepworth S, Subramaniam R. MAMP and DAMP signaling contributes resistance to Fusarium graminearum in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6628-6639. [PMID: 34405877 DOI: 10.1093/jxb/erab285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 08/06/2021] [Indexed: 05/19/2023]
Abstract
Plants perceive externally produced microbe-associated molecular patterns (MAMPs) and endogenously produced danger-associated molecular patterns (DAMPs) to activate inducible immunity. While several inducible immune responses have been observed during Fusarium graminearum infection, the identity of the signaling pathways involved is only partly known. We screened 227 receptor kinase and innate immune response genes in Arabidopsis to identify nine genes with a role in F. graminearum resistance. Resistance-promoting genes included the chitin receptors LYK5 and CERK1, and the reactive oxygen species (ROS)-producing NADPH oxidase RbohF, which were required for full inducible immune responses during infection. Two of the genes identified in our screen, APEX and the PAMP-induced peptide 1 (PIP1) DAMP receptor RLK7, repressed F. graminearum resistance. Both RbohF and RLK7 were required for full chitin-induced immune responses and PIP1 precursor expression was induced by chitin and F. graminearum infection. Together, this indicates that F. graminearum resistance is mediated by MAMP and DAMP signaling pathways and that chitin-induced signaling is enhanced by PIP1 perception and ROS production.
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Affiliation(s)
- Nimrat Manes
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Carleton University, Department of Biology, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Elizabeth K Brauer
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Shelley Hepworth
- Carleton University, Department of Biology, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Carleton University, Department of Biology, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
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12
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Prasanna BM, Cairns JE, Zaidi PH, Beyene Y, Makumbi D, Gowda M, Magorokosho C, Zaman-Allah M, Olsen M, Das A, Worku M, Gethi J, Vivek BS, Nair SK, Rashid Z, Vinayan MT, Issa AB, San Vicente F, Dhliwayo T, Zhang X. Beat the stress: breeding for climate resilience in maize for the tropical rainfed environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1729-1752. [PMID: 33594449 PMCID: PMC7885763 DOI: 10.1007/s00122-021-03773-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/09/2021] [Indexed: 05/03/2023]
Abstract
Intensive public sector breeding efforts and public-private partnerships have led to the increase in genetic gains, and deployment of elite climate-resilient maize cultivars for the stress-prone environments in the tropics. Maize (Zea mays L.) plays a critical role in ensuring food and nutritional security, and livelihoods of millions of resource-constrained smallholders. However, maize yields in the tropical rainfed environments are now increasingly vulnerable to various climate-induced stresses, especially drought, heat, waterlogging, salinity, cold, diseases, and insect pests, which often come in combinations to severely impact maize crops. The International Maize and Wheat Improvement Center (CIMMYT), in partnership with several public and private sector institutions, has been intensively engaged over the last four decades in breeding elite tropical maize germplasm with tolerance to key abiotic and biotic stresses, using an extensive managed stress screening network and on-farm testing system. This has led to the successful development and deployment of an array of elite stress-tolerant maize cultivars across sub-Saharan Africa, Asia, and Latin America. Further increasing genetic gains in the tropical maize breeding programs demands judicious integration of doubled haploidy, high-throughput and precise phenotyping, genomics-assisted breeding, breeding data management, and more effective decision support tools. Multi-institutional efforts, especially public-private alliances, are key to ensure that the improved maize varieties effectively reach the climate-vulnerable farming communities in the tropics, including accelerated replacement of old/obsolete varieties.
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Affiliation(s)
- Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, P.O.Box 1041-00621, Nairobi, Kenya.
| | | | - P H Zaidi
- CIMMYT, ICRISAT Campus, Patancheru, Greater Hyderabad, Telangana, India
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, P.O.Box 1041-00621, Nairobi, Kenya
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, P.O.Box 1041-00621, Nairobi, Kenya
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, P.O.Box 1041-00621, Nairobi, Kenya
| | | | | | - Mike Olsen
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, P.O.Box 1041-00621, Nairobi, Kenya
| | - Aparna Das
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, P.O.Box 1041-00621, Nairobi, Kenya
| | - Mosisa Worku
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, P.O.Box 1041-00621, Nairobi, Kenya
| | | | - B S Vivek
- CIMMYT, ICRISAT Campus, Patancheru, Greater Hyderabad, Telangana, India
| | - Sudha K Nair
- CIMMYT, ICRISAT Campus, Patancheru, Greater Hyderabad, Telangana, India
| | - Zerka Rashid
- CIMMYT, ICRISAT Campus, Patancheru, Greater Hyderabad, Telangana, India
| | - M T Vinayan
- CIMMYT, ICRISAT Campus, Patancheru, Greater Hyderabad, Telangana, India
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13
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Sun Y, Ruan X, Wang Q, Zhou Y, Wang F, Ma L, Wang Z, Gao X. Integrated Gene Co-expression Analysis and Metabolites Profiling Highlight the Important Role of ZmHIR3 in Maize Resistance to Gibberella Stalk Rot. FRONTIERS IN PLANT SCIENCE 2021; 12:664733. [PMID: 34046051 PMCID: PMC8144520 DOI: 10.3389/fpls.2021.664733] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/25/2021] [Indexed: 05/04/2023]
Abstract
Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the most devastating diseases causing significant yield loss of maize, and GSR resistance is a quantitative trait controlled by multiple genes. Although a few quantitative trait loci/resistance genes have been identified, the molecular mechanisms underlying GSR resistance remain largely unexplored. To identify potential resistance genes and to better understand the molecular mechanism of GSR resistance, a joint analysis using a comparative transcriptomic and metabolomic approaches was conducted using two inbred lines with contrasting GSR resistance, K09 (resistant) and A08 (susceptible), upon infection with F. graminearum. While a substantial number of differentially expressed genes associated with various defense-related signaling pathways were identified between two lines, multiple hub genes likely associated with GSR resistance were pinpointed using Weighted Gene Correlation Network Analysis and K-means clustering. Moreover, a core set of metabolites, including anthocyanins, associated with the hub genes was determined. Among the complex co-expression networks, ZmHIR3 showed strong correlation with multiple key genes, and genetic and histological studies showed that zmhir3 mutant is more susceptible to GSR, accompanied by enhanced cell death in the stem in response to infection with F. graminearum. Taken together, our study identified differentially expressed key genes and metabolites, as well as co-expression networks associated with distinct infection stages of F. graminearum. Moreover, ZmHIR3 likely plays a positive role in disease resistance to GSR, probably through the transcriptional regulation of key genes, functional metabolites, and the control of cell death.
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Affiliation(s)
- Yali Sun
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Xinsen Ruan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Qing Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yu Zhou
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Fang Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Liang Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Zhenhua Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xiquan Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
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14
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Li Y, Li Q, Chen S. Diazotroph Paenibacillus triticisoli BJ-18 Drives the Variation in Bacterial, Diazotrophic and Fungal Communities in the Rhizosphere and Root/Shoot Endosphere of Maize. Int J Mol Sci 2021; 22:1460. [PMID: 33540521 PMCID: PMC7867140 DOI: 10.3390/ijms22031460] [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: 12/24/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/28/2022] Open
Abstract
Application of diazotrophs (N2-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph application on microbial communities of major crops. In this study, the diazotrophic and endospore-forming Paenibacillus triticisoli BJ-18 was inoculated into maize soils containing different N levels. The effects of inoculation on the composition and abundance of the bacterial, diazotrophic and fungal communities in the rhizosphere and root/shoot endosphere of maize were evaluated by sequencing the 16S rRNA, nifH gene and ITS (Inter Transcribed Spacer) region. P. triticisoli BJ-18 survived and propagated in all the compartments of the maize rhizosphere, root and shoot. The abundances and diversities of the bacterial and diazotrophic communities in the rhizosphere were significantly higher than in both root and shoot endospheres. Each compartment of the rhizosphere, root and shoot had its specific bacterial and diazotrophic communities. Our results showed that inoculation reshaped the structures of the bacterial, diazotrophic and fungal communities in the maize rhizosphere and endosphere. Inoculation reduced the interactions of the bacteria and diazotrophs in the rhizosphere and endosphere, while it increased the fungal interactions. After inoculation, the abundances of Pseudomonas, Bacillus and Paenibacillus in all three compartments, Klebsiella in the rhizosphere and Paenibacillus in the root and shoot were significantly increased, while the abundances of Fusarium and Giberella were greatly reduced. Paenibacillus was significantly correlated with plant dry weight, nitrogenase, N2-fixing rate, P solubilization and other properties of the soil and plant.
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Affiliation(s)
| | | | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100094, China; (Y.L.); (Q.L.)
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15
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Ge C, Wang YG, Lu S, Zhao XY, Hou BK, Balint-Kurti PJ, Wang GF. Multi-Omics Analyses Reveal the Regulatory Network and the Function of ZmUGTs in Maize Defense Response. FRONTIERS IN PLANT SCIENCE 2021; 12:738261. [PMID: 34630489 PMCID: PMC8497902 DOI: 10.3389/fpls.2021.738261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 05/05/2023]
Abstract
Maize is one of the major crops in the world; however, diseases caused by various pathogens seriously affect its yield and quality. The maize Rp1-D21 mutant (mt) caused by the intragenic recombination between two nucleotide-binding, leucine-rich repeat (NLR) proteins, exhibits autoactive hypersensitive response (HR). In this study, we integrated transcriptomic and metabolomic analyses to identify differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in Rp1-D21 mt compared to the wild type (WT). Genes involved in pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) were enriched among the DEGs. The salicylic acid (SA) pathway and the phenylpropanoid biosynthesis pathway were induced at both the transcriptional and metabolic levels. The DAMs identified included lipids, flavones, and phenolic acids, including 2,5-DHBA O-hexoside, the production of which is catalyzed by uridinediphosphate (UDP)-dependent glycosyltransferase (UGT). Four maize UGTs (ZmUGTs) homologous genes were among the DEGs. Functional analysis by transient co-expression in Nicotiana benthamiana showed that ZmUGT9250 and ZmUGT5174, but not ZmUGT9256 and ZmUGT8707, partially suppressed the HR triggered by Rp1-D21 or its N-terminal coiled-coil signaling domain (CCD21). None of the four ZmUGTs interacted physically with CCD21 in yeast two-hybrid or co-immunoprecipitation assays. We discuss the possibility that ZmUGTs might be involved in defense response by regulating SA homeostasis.
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Affiliation(s)
- Chunxia Ge
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- School of Public Health and Management, Binzhou Medical University, Yantai, China
| | - Yi-Ge Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Shouping Lu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Bing-Kai Hou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Peter J. Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- US Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, Raleigh, NC, United States
| | - Guan-Feng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- *Correspondence: Guan-Feng Wang
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Stasko AK, Batnini A, Bolanos-Carriel C, Lin JE, Lin Y, Blakeslee JJ, Dorrance AE. Auxin Profiling and GmPIN Expression in Phytophthora sojae-Soybean Root Interactions. PHYTOPATHOLOGY 2020; 110:1988-2002. [PMID: 32602813 DOI: 10.1094/phyto-02-20-0046-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Auxin (indole-3-acetic acid, IAA) has been implicated as a susceptibility factor in both beneficial and pathogenic molecular plant-microbe interactions. Previous studies have identified a large number of auxin-related genes underlying quantitative disease resistance loci (QDRLs) for Phytophthora sojae. Thus, we hypothesized that auxin may be involved the P. sojae-soybean interaction. The levels of IAA and related metabolites were measured in mycelia and media supernatant as well as in mock and inoculated soybean roots in a time course assay. The expression of 11 soybean Pin-formed (GmPIN) auxin efflux transporter genes was also examined. Tryptophan, an auxin precursor, was detected in the P. sojae mycelia and media supernatant. During colonization of roots, levels of IAA and related metabolites were significantly higher in both moderately resistant Conrad and moderately susceptible Sloan inoculated roots compared with mock controls at 48 h postinoculation (hpi) in one experiment and at 72 hpi in a second, with Sloan accumulating higher levels of the auxin catabolite IAA-Ala than Conrad. Additionally, one GmPIN at 24 hpi, one at 48 hpi, and three at 72 hpi had higher expression in inoculated compared with the mock control roots in Conrad. The ability of resistant cultivars to cope with auxin accumulation may play an important role in quantitative disease resistance. Levels of jasmonic acid (JA), another plant hormone associated with defense responses, were also higher in inoculated roots at these same time points, suggesting that JA also plays a role during the later stages of infection.
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Affiliation(s)
- Anna K Stasko
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
- Center for Soybean Research, The Ohio State University, Wooster, OH 44691
| | - Amine Batnini
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
- Center for Soybean Research, The Ohio State University, Wooster, OH 44691
| | - Carlos Bolanos-Carriel
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
- Center for Soybean Research, The Ohio State University, Wooster, OH 44691
| | - Jinshan Ella Lin
- Department of Horticulture and Crop Science and OARDC Metabolite Analysis Cluster, The Ohio State University, Wooster, OH 44691
| | - Yun Lin
- Department of Horticulture and Crop Science and OARDC Metabolite Analysis Cluster, The Ohio State University, Wooster, OH 44691
| | - Joshua J Blakeslee
- Department of Horticulture and Crop Science and OARDC Metabolite Analysis Cluster, The Ohio State University, Wooster, OH 44691
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
- Center for Soybean Research, The Ohio State University, Wooster, OH 44691
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210
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A Comparative Transcriptome Analysis, Conserved Regulatory Elements and Associated Transcription Factors Related to Accumulation of Fusariotoxins in Grain of Rye ( Secale cereale L.) Hybrids. Int J Mol Sci 2020; 21:ijms21197418. [PMID: 33049995 PMCID: PMC7582487 DOI: 10.3390/ijms21197418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 12/19/2022] Open
Abstract
Detoxification of fusariotoxin is a type V Fusarium head blight (FHB) resistance and is considered a component of type II resistance, which is related to the spread of infection within spikes. Understanding this type of resistance is vital for FHB resistance, but to date, nothing is known about candidate genes that confer this resistance in rye due to scarce genomic resources. In this study, we generated a transcriptomic resource. The molecular response was mined through a comprehensive transcriptomic analysis of two rye hybrids differing in the build-up of fusariotoxin contents in grain upon pathogen infection. Gene mining identified candidate genes and pathways contributing to the detoxification of fusariotoxins in rye. Moreover, we found cis regulatory elements in the promoters of identified genes and linked them to transcription factors. In the fusariotoxin analysis, we found that grain from the Nordic seed rye hybrid "Helltop" accumulated 4 times higher concentrations of deoxynivalenol (DON), 9 times higher nivalenol (NIV), and 28 times higher of zearalenone (ZEN) than that of the hybrid "DH372" after artificial inoculation under field conditions. In the transcriptome analysis, we identified 6675 and 5151 differentially expressed genes (DEGs) in DH372 and Helltop, respectively, compared to non-inoculated control plants. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that DEGs were associated with glycolysis and the mechanistic target of rapamycin (mTOR) signaling pathway in Helltop, whereas carbon fixation in photosynthesis organisms were represented in DH372. The gene ontology (GO) enrichment and gene set enrichment analysis (GSEA) of DEGs lead to identification of the metabolic and biosynthetic processes of peptides and amides in DH372, whereas photosynthesis, negative regulation of catalytic activity, and protein-chromophore linkage were the significant pathways in Helltop. In the process of gene mining, we found four genes that were known to be involved in FHB resistance in wheat and that were differentially expressed after infection only in DH372 but not in Helltop. Based on our results, we assume that DH372 employed a specific response to pathogen infection that led to detoxification of fusariotoxin and prevented their accumulation in grain. Our results indicate that DH372 might resist the accumulation of fusariotoxin through activation of the glycolysis and drug metabolism via cytochrome P450. The identified genes in DH372 might be regulated by the WRKY family transcription factors as associated cis regulatory elements found in the in silico analysis. The results of this study will help rye breeders to develop strategies against type V FHB.
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Genome-wide identification of the maize 2OGD superfamily genes and their response to Fusarium verticillioides and Fusarium graminearum. Gene 2020; 764:145078. [PMID: 32858175 DOI: 10.1016/j.gene.2020.145078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 01/05/2023]
Abstract
In maize, eat rot and stalk rot caused by Fusarium verticillioides and Fusarium graminearum lead to contamination of moldy grains to produce mycotoxins. Identification of resistance genes against these pathogens for maize breeding is an effective way for disease control. Several 2-oxoglutarate-dependent dioxygenase (2OGD) proteins have been found to confer resistance to different pathogens in diverse plant species. However, little is known about the 2OGD superfamily in maize. Here, we identified 103 putative 2OGD genes in maize from a genome-wide analysis, and divided them into three classes - DOXA, DOXB, and DOXC. We further comprehensively investigated their gene structure, chromosome distribution, phylogenetic tree, gene-function enrichment, and expression profiles among different tissues. The genes encoding three 2OGD proteins, ACO, F3H, and NCS involved in ethylene biosynthesis, flavonoids biosynthesis, and alkaloids biosynthesis pathways, respectively, were identified to be induced by F. verticillioides and F. graminearum. The promoters of the three genes contain the binding sites for the transcription factor ZmDOF and ZmHSF, which are also induced by the two pathogens. The results imply that the three 2OGDs and the two transcription factors might be involved in the resistance to the two pathogens. This study provided a comprehensive understanding of the 2OGD superfamily in maize and laid the foundation for the further functional analysis of their roles in maize resistance to eat rot and stalk rot.
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Brauer EK, Subramaniam R, Harris LJ. Regulation and Dynamics of Gene Expression During the Life Cycle of Fusarium graminearum. PHYTOPATHOLOGY 2020; 110:1368-1374. [PMID: 32460691 DOI: 10.1094/phyto-03-20-0080-ia] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fungal pathogens survive harsh environments and overcome physical, temporal, and chemical barriers to colonize their hosts and reproduce. Fusarium graminearum was one of the first fungal plant pathogens for which transcriptomic tools were developed, making analysis of gene expression a cornerstone approach in studying its biology. The analysis of gene expression in diverse in vitro conditions and during infection of different cereal crops has revealed subsets of both unique and shared transcriptionally regulated genes. Together with genetic studies, these approaches have enhanced our understanding of the development and infection cycle of this economically important pathogen. Here, we will outline recent advances in transcriptional profiling during sporogenesis, spore germination, vegetative growth, and host infection. Several transcriptional regulators have been identified as essential components in these responses and the role of select transcription factors will be highlighted. Finally, we describe some of the gaps in our understanding of F. graminearum biology and how expression analysis could help to address these gaps.
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Affiliation(s)
- Elizabeth K Brauer
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Linda J Harris
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
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20
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Zhu YX, Ge C, Ma S, Liu XY, Liu M, Sun Y, Wang GF. Maize ZmFNSI Homologs Interact with an NLR Protein to Modulate Hypersensitive Response. Int J Mol Sci 2020; 21:E2529. [PMID: 32260554 PMCID: PMC7177559 DOI: 10.3390/ijms21072529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/11/2022] Open
Abstract
Nucleotide binding, leucine-rich-repeat (NLR) proteins are the major class of resistance (R) proteins used by plants to defend against pathogen infection. The recognition between NLRs and their cognate pathogen effectors usually triggers a rapid localized cell death, termed the hypersensitive response (HR). Flavone synthase I (FNSI) is one of the key enzymes in the flavone biosynthesis pathway. It also displays salicylic acid (SA) 5-hydroxylase (S5H) activity. A close homolog of FNSI/S5H displays SA 3-hydroxylase (S3H) activity. Both FNSI/S5H and S3H play important roles in plant innate immunity. However, the underlying molecular mechanisms and the relationship between S5H and S3H with the NLR-mediated HR are not known in any plant species. In this study, we identified three genes encoding ZmFNSI-1, ZmFNSI-2 and ZmS3H that are significantly upregulated in a maize line carrying an autoactive NLR Rp1-D21 mutant. Functional analysis showed that ZmFNSI-1 and ZmFNSI-2, but not ZmS3H, suppressed HR conferred by Rp1-D21 and its signaling domain CCD21 when transiently expressed in N. benthamiana. ZmFNSI-1 and ZmFNSI-2 physically interacted with CCD21. Furthermore, ZmFNSI-1 and ZmFNSI-2 interacted with HCT, a key enzyme in lignin biosynthesis pathway, which can also suppress Rp1-D21-mediated HR. These results lay the foundation for the further functional analysis of the roles of FNSI in plant innate immunity.
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Affiliation(s)
| | | | | | | | | | | | - Guan-Feng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (Y.-X.Z.); (C.G.); (S.M.); (X.-Y.L.); (M.L.); (Y.S.)
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21
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Fu J, Liu L, Liu Q, Shen Q, Wang C, Yang P, Zhu C, Wang Q. ZmMYC2 exhibits diverse functions and enhances JA signaling in transgenic Arabidopsis. PLANT CELL REPORTS 2020; 39:273-288. [PMID: 31741037 DOI: 10.1007/s00299-019-02490-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/23/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
ZmMYC2 was identified as the key regulator of JA signaling in maize and exhibited diverse functions through binding to many gene promoters as well as enhanced JA signaling in transgenic Arabidopsis. The plant hormone jasmonate (JA) extensively coordinates plant growth, development and defensive responses. MYC2 is the master regulator of JA signaling and has been widely studied in many plant species. However, little is known about this transcription factor in maize. Here, we identified one maize transcription factor with amino acid identity of 47% to the well-studied Arabidopsis AtMYC2, named as ZmMYC2. Gene expression analysis demonstrated inducible expression patterns of ZmMYC2 in response to multiple plant hormone treatments, as well as biotic and abiotic stresses. The yeast two-hybrid assay indicated physical interaction among ZmMYC2 and JA signal repressors ZmJAZ14, ZmJAZ17, AtJAZ1 and AtJAZ9. ZmMYC2 overexpression in Arabidopsis myc2myc3myc4 restored the sensitivity to JA treatment, resulting in shorter root growth and inducible anthocyanin accumulation. Furthermore, overexpression of ZmMYC2 in Arabidopsis elevated resistance to Botrytis cinerea. Further ChIP-Seq analysis revealed diverse regulatory roles of ZmMYC2 in maize, especially in the signaling crosstalk between JA and auxin. Hence, we identified ZmMYC2 and characterized its roles in regulating JA-mediated growth, development and defense responses.
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Affiliation(s)
- Jingye Fu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lijun Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qin Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinqin Shen
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Panpan Yang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chenying Zhu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China.
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Genome-Wide Association and Gene Co-expression Network Analyses Reveal Complex Genetics of Resistance to Goss's Wilt of Maize. G3-GENES GENOMES GENETICS 2019; 9:3139-3152. [PMID: 31362973 PMCID: PMC6778796 DOI: 10.1534/g3.119.400347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Goss’s bacterial wilt and leaf blight is a disease of maize caused by the gram positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn). First discovered in Nebraska, Goss’s wilt has now spread to major maize growing states in the United States and three provinces in Canada. Previous studies conducted using elite maize inbred lines and their hybrids have shown that resistance to Goss’s wilt is a quantitative trait. The objective of this study was to further our understanding of the genetic basis of resistance to Goss’s wilt by using a combined approach of genome-wide association mapping and gene co-expression network analysis. Genome-wide association analysis was accomplished using a diversity panel consisting of 555 maize inbred lines and a set of 450 recombinant inbred lines (RILs) from three bi-parental mapping populations, providing the most comprehensive screening of Goss’s wilt resistance to date. Three SNPs in the diversity panel and 10 SNPs in the combined dataset, including the diversity panel and RILs, were found to be significantly associated with Goss’s wilt resistance. Each significant SNP explained 1–5% of the phenotypic variation for Goss’s wilt (total of 8–11%). To augment the results of genome-wide association mapping and help identify candidate genes, a time course RNA sequencing experiment was conducted using resistant (N551) and susceptible (B14A) maize inbred lines. Gene co-expression network analysis of this time course experiment identified one module of 141 correlated genes that showed differential regulation in response to Cmn inoculations in both resistant and susceptible lines. SNPs inside and flanking these genes explained 13.3% of the phenotypic variation. Among 1,000 random samples of genes, only 8% of samples explained more phenotypic variance for Goss’s wilt resistance than those implicated by the co-expression network analysis. While a statistically significant enrichment was not observed (P < 0.05), these results suggest a possible role for these genes in quantitative resistance at the field level and warrant more research on combining gene co-expression network analysis with quantitative genetic analyses to dissect complex disease resistance traits. The results of the GWAS and co-expression analysis both support the complex nature of resistance to this important disease of maize.
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An Y, Chen L, Li YX, Li C, Shi Y, Song Y, Zhang D, Li Y, Wang T. Candidate loci for the kernel row number in maize revealed by a combination of transcriptome analysis and regional association mapping. BMC PLANT BIOLOGY 2019; 19:201. [PMID: 31096901 PMCID: PMC6521486 DOI: 10.1186/s12870-019-1811-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/30/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND The kernel row number (KRN) of an ear is an important trait related to yield and domestication in maize. Exploring the underlying genetic mechanisms of KRN has great research significance and application potential. RESULTS In the present study, N531 with a KRN of 18-22 and SLN with a KRN of 4-6 were used as the recurrent parent and the donor parent, respectively, to develop two introgression lines (ILs), IL_A and IL_B, both of which have common negative-effect alleles from SLN on chromosomes 1, 5 and 10 and significantly reduced inflorescence meristem (IM) diameter and KRN compared with those of N531. We used RNA-Seq to investigate the transcriptome profiles of 5-mm immature ears of N531, IL_A and IL_B. We identified a total of 2872 differentially expressed genes (DEGs) between N531 and IL_A, 2428 DEGs between N531 and IL_B and 1811 DEGs between IL_A and IL_B. A total of 1252 DEGs were detected as overlapping DEGs, and 89 DEGs were located on the common introgression fragments. Furthermore, three DEGs (Zm00001d013277, Zm00001d015310 and Zm00001d015377) containing three SNPs associated with KRN were identified using regional association mapping. CONCLUSIONS These results will facilitate our understanding of ear development and provide important candidate genes for further study on KRN.
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Affiliation(s)
- Yixin An
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yong-Xiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Gurunathan S, Qasim M, Park C, Yoo H, Choi DY, Song H, Park C, Kim JH, Hong K. Cytotoxicity and Transcriptomic Analysis of Silver Nanoparticles in Mouse Embryonic Fibroblast Cells. Int J Mol Sci 2018; 19:ijms19113618. [PMID: 30453526 PMCID: PMC6275036 DOI: 10.3390/ijms19113618] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/27/2018] [Accepted: 11/13/2018] [Indexed: 12/16/2022] Open
Abstract
The rapid development of nanotechnology has led to the use of silver nanoparticles (AgNPs) in biomedical applications, including antibacterial, antiviral, anti-inflammatory, and anticancer therapies. The molecular mechanism of AgNPs-induced cytotoxicity has not been studied thoroughly using a combination of cellular assays and RNA sequencing (RNA-Seq) analysis. In this study, we prepared AgNPs using myricetin, an anti-oxidant polyphenol, and studied their effects on NIH3T3 mouse embryonic fibroblasts as an in vitro model system to explore the potential biomedical applications of AgNPs. AgNPs induced loss of cell viability and cell proliferation in a dose-dependent manner, as evident by increased leakage of lactate dehydrogenase (LDH) from cells. Reactive oxygen species (ROS) were a potential source of cytotoxicity. AgNPs also incrementally increased oxidative stress and the level of malondialdehyde, depleted glutathione and superoxide dismutase, reduced mitochondrial membrane potential and adenosine triphosphate (ATP), and caused DNA damage by increasing the level of 8-hydroxy-2′-deoxyguanosine and the expressions of the p53 and p21 genes in NIH3T3 cells. Thus, activation of oxidative stress may be crucial for NIH3T3 cytotoxicity. Interestingly, gene ontology (GO) term analysis revealed alterations in epigenetics-related biological processes including nucleosome assembly and DNA methylation due to AgNPs exposure. This study is the first demonstration that AgNPs can alter bulk histone gene expression. Therefore, our genome-scale study suggests that the apoptosis observed in NIH3T3 cells treated with AgNPs is mediated by the repression of genes required for cell survival and the aberrant enhancement of nucleosome assembly components to induce apoptosis.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Muhammad Qasim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Hyunjin Yoo
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Dong Yoon Choi
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
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Gurunathan S, Qasim M, Park C, Yoo H, Kim JH, Hong K. Cytotoxic Potential and Molecular Pathway Analysis of Silver Nanoparticles in Human Colon Cancer Cells HCT116. Int J Mol Sci 2018; 19:E2269. [PMID: 30072642 PMCID: PMC6121495 DOI: 10.3390/ijms19082269] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/29/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
Silver nanoparticles (AgNPs) have gained attention for use in cancer therapy. In this study, AgNPs were biosynthesized using naringenin. We investigated the anti-colon cancer activities of biogenic AgNPs through transcriptome analysis using RNA sequencing, and the mechanisms of AgNPs in regulating colon cancer cell growth. The synthesized AgNPs were characterized using UV⁻visible spectroscopy (UV⁻vis), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), and transmission electron microscopy (TEM). The AgNPs were spherical with sizes of 2⁻10 nm. Cytotoxicity assays indicated that the AgNPs in HCT116 colorectal cancer cells were very effective at low concentrations. The viability and proliferation of colon cancer cells treated with 5 µg/mL biogenic AgNPs were reduced by 50%. Increased lactate dehydrogenase leakage (LDH), reactive oxygen species (ROS) generation, malondialdehyde (MDA), and decreased dead-cell protease activity and ATP generation were observed. This impaired mitochondrial function and DNA damage led to cell death. The AgNPs upregulated and downregulated the most highly ranked biological processes of oxidation⁻reduction and cell-cycle regulation, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that AgNPs upregulated GADD45G in the p53 pathway. Thus, the AgNP tumor suppressive effects were mediated by cell apoptosis following DNA damage, as well as by mitochondrial dysfunction and cell-cycle arrest following aberrant regulation of p53 effector proteins. It is of interest to mention that, to the best of our knowledge, this study is the first report demonstrating cellular responses and molecular pathways analysis of AgNPs in HCT116 colorectal cancer cells.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Muhammad Qasim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Hyunjin Yoo
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
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Du L, Gu T, Zhang Y, Huang Z, Wu N, Zhao W, Chang G, Xu Q, Chen G. Transcriptome profiling to identify key mediators of granulosa cell proliferation upon FSH stimulation in the goose (Anser cygnoides). Br Poult Sci 2018; 59:416-421. [PMID: 29723039 DOI: 10.1080/00071668.2018.1459474] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
1. The low reproductive performance of geese has seriously hampered the development of the industry. Reproductive performance, particularly the egg laying rate mainly depends on the development of the follicle. Previous studies have shown that follicle-stimulating hormone (FSH) plays an important role in the process of follicular development, but the exact underlying mechanism remains unclear. 2. This study showed that FSH stimulated granulosa cell proliferation in a dose-dependent manner. The effect of FSH treatment on granulosa cell proliferation was greatest at a dose of 100 mIU/ml FSH for 24 h. 3. Secondly, the effect of different concentrations of FSH on goose granulosa cell proliferation was investigated, and de novo transcriptome assembly and gene expression analysis performed using short-read sequencing technology (Illumina). High-throughput sequencing results yielded 62.61 M reads and 7.8 G base pairs from granulosa cells treated with 100 mIU/ml FSH. These reads were assembled into 65,757 unigenes (mean length: 705 bp) with an N50 of 903 bp. A total of 110 upregulated and 510 downregulated differentially expressed genes (DEGs) were identified by RNA-seq. 4. Functional analysis by gene ontology (GO) and KEGG pathway annotation indicated that hormone biosynthesis (GO:0042446), positive regulation of hormone secretion (GO:0046887), steroid biosynthesis, oxidative phosphorylation and carbon metabolism pathways were involved in FSH-mediated proliferation of goose granulosa cells. 5. After screening, a group of key responsive genes including superoxide dismutase 1, fatty acyl-CoA reductase 1, transforming growth factor-beta receptor-associated protein 1 and follistatin were tested by real-time reverse transcription PCR to confirm differential expression in granulosa cells stimulated by FSH. 6. FSH-stimulated goose granulosa cells and DEG profiling data provided comprehensive gene expression information at the transcriptional level that could promote better understanding of the molecular mechanisms underlying follicle development in response to FSH stimulation.
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Affiliation(s)
- L Du
- a Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education , Yangzhou University , Yangzhou , PR China
| | - T Gu
- a Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education , Yangzhou University , Yangzhou , PR China
| | - Y Zhang
- a Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education , Yangzhou University , Yangzhou , PR China
| | - Zhengyang Huang
- a Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education , Yangzhou University , Yangzhou , PR China
| | - N Wu
- a Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education , Yangzhou University , Yangzhou , PR China
| | - W Zhao
- a Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education , Yangzhou University , Yangzhou , PR China
| | - G Chang
- a Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education , Yangzhou University , Yangzhou , PR China
| | - Q Xu
- a Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education , Yangzhou University , Yangzhou , PR China
| | - G Chen
- a Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education , Yangzhou University , Yangzhou , PR China
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Ghorbani A, Izadpanah K, Dietzgen RG. Changes in maize transcriptome in response to maize Iranian mosaic virus infection. PLoS One 2018; 13:e0194592. [PMID: 29634778 PMCID: PMC5892904 DOI: 10.1371/journal.pone.0194592] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/06/2018] [Indexed: 12/14/2022] Open
Abstract
Background Maize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) causes an economically important disease in maize and other gramineous crops in Iran. MIMV negative-sense RNA genome sequence of 12,426 nucleotides has recently been completed. Maize Genetics and Genomics database shows that 39,498 coding genes and 4,976 non-coding genes of maize have been determined, but still some transcripts could not be annotated. The molecular host cell responses of maize to MIMV infection including differential gene expression have so far not been elucidated. Methodology/Principal findings Complementary DNA libraries were prepared from total RNA of MIMV-infected and mock-inoculated maize leaves and sequenced using Illumina HiSeq 2500. Cleaned raw transcript reads from MIMV-infected maize were mapped to reads from uninfected maize and to a maize reference genome. Differentially expressed transcripts were characterized by gene ontology and biochemical pathway analyses. Transcriptome data for selected genes were validated by real-time quantitative PCR. Conclusion/Significance Approximately 42 million clean reads for each treatment were obtained. In MIMV-infected maize compared to uninfected plants, 1689 transcripts were up-regulated and 213 transcripts were down-regulated. In response to MIMV infection, several pathways were activated in maize including immune receptor signaling, metabolic pathways, RNA silencing, hormone-mediated pathways, protein degradation, protein kinase and ATP binding activity, and fatty acid metabolism. Also, several transcripts including those encoding hydrophobic protein RCI2B, adenosylmethionine decarboxylase NAC transcription factor and nucleic acid binding, leucine-rich repeat, heat shock protein, 26S proteasome, oxidoreductases and endonuclease activity protein were up-regulated. These data will contribute to the identification of genes and pathways involved in plant-virus interactions that may serve as future targets for improved disease control.
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
| | | | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
- * E-mail:
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Kazan K, Gardiner DM. Transcriptomics of cereal-Fusarium graminearum interactions: what we have learned so far. MOLECULAR PLANT PATHOLOGY 2018; 19:764-778. [PMID: 28411402 PMCID: PMC6638174 DOI: 10.1111/mpp.12561] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/11/2017] [Accepted: 04/11/2017] [Indexed: 05/16/2023]
Abstract
The ascomycete fungal pathogen Fusarium graminearum causes the globally important Fusarium head blight (FHB) disease on cereal hosts, such as wheat and barley. In addition to reducing grain yield, infection by this pathogen causes major quality losses. In particular, the contamination of food and feed with the F. graminearum trichothecene toxin deoxynivalenol (DON) can have many adverse short- and long-term effects on human and animal health. During the last decade, the interaction between F. graminearum and both cereal and model hosts has been extensively studied through transcriptomic analyses. In this review, we present an overview of how such analyses have advanced our understanding of this economically important plant-microbe interaction. From a host point of view, the transcriptomes of FHB-resistant and FHB-susceptible cereal genotypes, including near-isogenic lines (NILs) that differ by the presence or absence of quantitative trait loci (QTLs), have been studied to understand the mechanisms of disease resistance afforded by such QTLs. Transcriptomic analyses employed to dissect host responses to DON have facilitated the identification of the genes involved in toxin detoxification and disease resistance. From the pathogen point of view, the transcriptome of F. graminearum during pathogenic vs. saprophytic growth, or when infecting different cereal hosts or different tissues of the same host, have been studied. In addition, comparative transcriptomic analyses of F. graminearum knock-out mutants with altered virulence have provided new insights into pathogenicity-related processes. The F. graminearum transcriptomic data generated over the years are now being exploited to build a systems level understanding of the biology of this pathogen, with an ultimate aim of developing effective and sustainable disease prevention strategies.
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Affiliation(s)
- Kemal Kazan
- CSIRO Agriculture and Food Queensland Bioscience PrecinctSt. LuciaQld4067Australia
- Queensland Alliance for Agriculture & Food Innovation (QAAFI)University of Queensland, Queensland Bioscience PrecinctSt. LuciaQld4067Australia
| | - Donald M. Gardiner
- CSIRO Agriculture and Food Queensland Bioscience PrecinctSt. LuciaQld4067Australia
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Liu G, Liu J, Zhang C, You X, Zhao T, Jiang J, Chen X, Zhang H, Yang H, Zhang D, Du C, Li J, Xu X. Physiological and RNA-seq analyses provide insights into the response mechanism of the Cf-10-mediated resistance to Cladosporium fulvum infection in tomato. PLANT MOLECULAR BIOLOGY 2018; 96:403-416. [PMID: 29383477 DOI: 10.1007/s11103-018-0706-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/20/2018] [Indexed: 05/22/2023]
Abstract
Based on the physiological and RNA-seq analysis, some progress has been made in elucidating the Cf-10-mediated resistance responses to C. fulvum infection in tomato. GO and KEGG enrichment analysis revealed that the DEGs were significantly associated with defense-signaling pathways like oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Leaf mold, caused by the fungus Cladosporium fulvum, is one of the most common diseases affecting tomatoes worldwide. Cf series genes including Cf-2, Cf-4, Cf-5, Cf-9 and Cf-10 play very important roles in resisting tomato leaf mold. Understanding the molecular mechanism of Cf gene-mediated resistance is thus the key to facilitating genetic engineering of resistance to C. fulvum infection. Progress has been made in elucidating two Cf genes, Cf -19 and Cf -12, and how they mediate resistance responses to C. fulvum infection in tomato. However, the mechanism of the Cf-10- mediated resistance response is still unclear. In the present study, RNA-seq was used to analyze changes in the transcriptome at different stages of C. fulvum infection. A total of 2,242 differentially expressed genes (DEGs) responsive to C. fulvum between 0 and 16 days post infection (dpi) were identified, including 1,501 upregulated and 741 downregulated genes. The majority of DEGs were associated with defense-signaling pathways including oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Four DEGs associated with plant-pathogen interaction were uniquely activated in Cf-10 tomato and validated by qRT-PCR. In addition, physiological indicators including reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were measured at 0-21 dpi, and hormone expression [Jasmonic acid (JA) and salicylic acid (SA)] was estimated at 0 and 16 dpi to elucidate the mechanism of the Cf-10-mediated resistance response. C. fulvum infection induced the activities of POD, CAT and SOD, and decreased ROS levels. JA was determined to participate in the resistance response to C. fulvum during the initial infection period. The results of this study provide accountable evidence for the physiological and transcriptional regulation of the Cf-10-mediated resistance response to C. fulvum infection, facilitating further understanding of the molecular mechanism of Cf-10-mediated resistance to C. fulvum infection.
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Affiliation(s)
- Guan Liu
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Junfang Liu
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Chunli Zhang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaoqing You
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Tingting Zhao
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Xiuling Chen
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - He Zhang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Huanhuan Yang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Dongye Zhang
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Chong Du
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Jingfu Li
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China.
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Gao FX, Wang Y, Zhang QY, Mou CY, Li Z, Deng YS, Zhou L, Gui JF. Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes. BMC Genomics 2017; 18:561. [PMID: 28738780 PMCID: PMC5525251 DOI: 10.1186/s12864-017-3945-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 07/13/2017] [Indexed: 01/25/2023] Open
Abstract
Background Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their resistances to herpesvirus and the underlying mechanism remain unknown. Results To reveal their susceptibility differences, we firstly performed herpesvirus challenge experiments in three gynogenetic clones of gibel carp, including the leading variety clone A+, candidate variety clone F and wild clone H. Three clones showed distinct resistances to CaHV. Moreover, 8772, 8679 and 10,982 differentially expressed unigenes (DEUs) were identified from comparative transcriptomes between diseased individuals and control individuals of clone A+, F and H, respectively. Comprehensive analysis of the shared DEUs in all three clones displayed common defense pathways to the herpesvirus infection, activating IFN system and suppressing complements. KEGG pathway analysis of specifically changed DEUs in respective clones revealed distinct immune responses to the herpesvirus infection. The DEU numbers identified from clone H in KEGG immune-related pathways, such as “chemokine signaling pathway”, “Toll-like receptor signaling pathway” and others, were remarkably much more than those from clone A+ and F. Several IFN-related genes, including Mx1, viperin, PKR and others, showed higher increases in the resistant clone H than that in the others. IFNphi3, IFI44-like and Gig2 displayed the highest expression in clone F and IRF1 uniquely increased in susceptible clone A+. In contrast to strong immune defense in resistant clone H, susceptible clone A+ showed remarkable up-regulation of genes related to apoptosis or death, indicating that clone A+ failed to resist virus offensive and evidently induced apoptosis or death. Conclusions Our study is the first attempt to screen distinct resistances and immune responses of three gynogenetic gibel carp clones to herpesvirus infection by comprehensive transcriptomes. These differential DEUs, immune-related pathways and IFN system genes identified from susceptible and resistant clones will be beneficial to marker-assisted selection (MAS) breeding or molecular module-based resistance breeding in gibel carp. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3945-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan-Xiang Gao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Cheng-Yan Mou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yuan-Sheng Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Sun D, Zhang W, Mou Z, Chen Y, Guo F, Yang E, Wang W. Transcriptome Analysis Reveals Silver Nanoparticle-Decorated Quercetin Antibacterial Molecular Mechanism. ACS APPLIED MATERIALS & INTERFACES 2017; 9:10047-10060. [PMID: 28240544 DOI: 10.1021/acsami.7b02380] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Facile and simple method is developed to synthesize silver-nanoparticle-decorated quercetin nanoparticles (QA NPs). Modification suggests that synergistic quercetin (Qe) improves the antibacterial effect of silver nanoparticles (Ag NPs). Characterization experiment indicates that QA NPs have a diameter of approximately 10 nm. QA NPs show highly effective antibacterial activities against drug-resistant Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). We explore antibacterial mechanisms using S. aureus and E. coli treated with QA NPs. Through morphological changes in E. coli and S. aureus, mechanisms are examined for bacterial damage caused by particulate matter from local dissociation of silver ion and Qe from QA NPs trapped inside membranes. Moreover, we note that gene expression profiling methods, such as RNA sequencing, can be used to predict discover mechanisms of toxicity of QA NPs. Gene ontology (GO) assay analyses demonstrate the molecular mechanism of the antibacterial effect of QA NPs. Regarding cellular component ontology, "cell wall organization or biogenesis" (GO: 0071554) and "cell wall macromolecule metabolic process" (GO: 0044036) are the most represented categories. The present study reports that transcriptome analysis of the mechanism offers novel insights into the molecular mechanism of antibacterial assays.
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Affiliation(s)
- Dongdong Sun
- School of Life Sciences, Anhui Agricultural University , Hefei 230036, China
| | - Weiwei Zhang
- School of Life Sciences, Anhui Agricultural University , Hefei 230036, China
| | - Zhipeng Mou
- School of Life Sciences, Anhui Agricultural University , Hefei 230036, China
| | - Ying Chen
- School of Life Sciences, Anhui Agricultural University , Hefei 230036, China
| | - Feng Guo
- School of Life Sciences, Anhui Agricultural University , Hefei 230036, China
| | - Endong Yang
- School of Life Sciences, Anhui Agricultural University , Hefei 230036, China
| | - Weiyun Wang
- School of Life Sciences, Anhui Agricultural University , Hefei 230036, China
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Chen Q, Song J, Du WP, Xu LY, Jiang Y, Zhang J, Xiang XL, Yu GR. Identification, Mapping, and Molecular Marker Development for Rgsr8.1: A New Quantitative Trait Locus Conferring Resistance to Gibberella Stalk Rot in Maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1355. [PMID: 28824686 PMCID: PMC5540892 DOI: 10.3389/fpls.2017.01355] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/20/2017] [Indexed: 05/20/2023]
Abstract
Maize stalk rot is a major fungal disease worldwide, and is difficult to control by chemical methods. Therefore, in maize breeding, quantitative trait loci (QTLs) conferring resistance are important for controlling the disease. Next-generation sequencing technologies are considered a rapid and efficient method to establish the association of agronomic traits with molecular markers or candidate genes. In the present study, we employed QTL-seq, which is a whole-genome resequencing-based approach, to identify candidate genomic regions conferring resistance to maize stalk rot. A novel resistance QTL Rgsr8.1 was finely mapped, conferring broad-spectrum resistance to Gibberella stalk rot (GSR). Segregation analysis in F2 and BC1F1 populations, which were derived from a cross between 18327 (Susceptible) and S72356 (Resistant), indicated that the resistance to GSR was likely to be a quantitatively inherited trait in maize. The result of QTL-seq showed that the resistance to GSR was mapped on chromosome 8 from 161.001 to 170.6 Mb. Based on the simple sequence repeat (SSR) markers, single-nucleotide polymorphism (SNP) markers, and the recombinant test, the location of Rgsr8.1 was narrowed down to 2.04 Mb, flanked by SSR-65 and SNP-25 markers at the physical location from 164.69 to 166.72 Mb based on the maize reference genome. In this region, two candidate resistant genes were found with, one auxin-responsive elements and the other encoding a disease resistance protein. In summary, these results will be useful in maize breeding programs to improve the resistance to GSR in maize.
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Liu Y, Guo Y, Ma C, Zhang D, Wang C, Yang Q. Erratum to: Transcriptome analysis of maize resistance to Fusarium graminearum. BMC Genomics 2016; 17:830. [PMID: 27782800 PMCID: PMC5080770 DOI: 10.1186/s12864-016-3107-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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