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Zhou G, Ma L, Zhao C, Xie F, Xu Y, Wang Q, Hao D, Gao X. Genome-wide association study and molecular marker development for susceptibility to Gibberella ear rot in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:222. [PMID: 39276212 DOI: 10.1007/s00122-024-04711-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/04/2024] [Indexed: 09/16/2024]
Abstract
KEY MESSAGES Sixty-nine quantitative trait nucleotides conferring maize resistance to Gibberella ear rot were detected, including eighteen novel loci. Four candidate genes were predicted, and four kompetitive allele-specific PCR markers were developed. Maize Gibberella ear rot (GER), caused by Fusarium graminearum, is one of the most devastating diseases in maize-growing regions worldwide. Enhancing maize cultivar resistance to this disease requires a comprehensive understanding of the genetic basis of resistance to GER. In this study, 334 maize inbred lines were phenotyped for GER resistance in five environments and genotyped using the Affymetrix CGMB56K SNP Array, and a genome-wide association study of resistance to GER was performed using a 3V multi-locus random-SNP-effect mixed linear model. A total of 69 quantitative trait nucleotides (QTNs) conferring resistance to GER were detected, and all of them explained individually less than 10% of the phenotypic variation, suggesting that resistance to GER is controlled by multiple minor-effect genetic loci. A total of 348 genes located around the 200-kb genomic region of these 69 QTNs were identified, and four of them (Zm00001d029648, Zm00001d031449, Zm00001d006397, and Zm00001d053145) were considered candidate genes conferring susceptibility to GER based on gene expression patterns. Moreover, four kompetitive allele-specific PCR markers were developed based on the non-synonymous variation of these four candidate genes and validated in two genetic populations. This study provides useful genetic resources for improving resistance to GER in maize.
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Affiliation(s)
- Guangfei Zhou
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, 226012, China.
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
- Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry/College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Liang Ma
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, 226012, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry/College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Caihong Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry/College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fugui Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry/College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Qing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry/College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Derong Hao
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, 226012, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
- Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry/College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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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 J, Shi H, Yang Y, Zeng C, Jia Z, Ma T, Wu M, Du J, Huang N, Pan G, Li Z, Yuan G. Kernel Bioassay Evaluation of Maize Ear Rot and Genome-Wide Association Analysis for Identifying Genetic Loci Associated with Resistance to Fusarium graminearum Infection. J Fungi (Basel) 2023; 9:1157. [PMID: 38132758 PMCID: PMC10744209 DOI: 10.3390/jof9121157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae) is one of the most destructive diseases in maize, which severely reduces yield and contaminates several potential mycotoxins in the grain. However, few efforts had been devoted to dissecting the genetic basis of maize GER resistance. In the present study, a genome-wide association study (GWAS) was conducted in a maize association panel consisting of 303 diverse inbred lines. The phenotypes of GER severity were evaluated using kernel bioassay across multiple time points in the laboratory. Then, three models, including the fixed and random model circulating probability unification model (FarmCPU), general linear model (GLM), and mixed linear model (MLM), were conducted simultaneously in GWAS to identify single-nucleotide polymorphisms (SNPs) significantly associated with GER resistance. A total of four individual significant association SNPs with the phenotypic variation explained (PVE) ranging from 3.51 to 6.42% were obtained. Interestingly, the peak SNP (PUT-163a-71443302-3341) with the greatest PVE value, was co-localized in all models. Subsequently, 12 putative genes were captured from the peak SNP, and several of these genes were directly or indirectly involved in disease resistance. Overall, these findings contribute to understanding the complex plant-pathogen interactions in maize GER resistance. The regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the kernel bioassay that can be used for evaluating and selecting elite germplasm resources with GER resistance in maize.
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Affiliation(s)
- Jihai Zhang
- Yibin Academy of Agricultural Sciences, Yibin 644600, 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - Ning Huang
- Yibin Academy of Agricultural Sciences, Yibin 644600, 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
| | - Zhilong Li
- Yibin Academy of Agricultural Sciences, Yibin 644600, China
| | - 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
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