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Identification of Resistance of Maize Germplasm Resources to Disease

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 August 2026 | Viewed by 7768

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Special Issue Editors

Dr. Canxing Duan

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Guest Editor

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
Interests: maize; germplasm resources; fungal disease; resistance identification; resistance genes; gene mapping; maize–pathogen interactions

Dr. Yanyong Cao

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Guest Editor

Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
Interests: maize disease; maize–pathogen interactions; resistance genes; maize genome editing; maize transformation

Special Issue Information

Dear Colleagues,

Maize (Zea mays L.) is an important crop widely utilized for food, feed, industrial raw material, and energy. However, maize yield and quality are seriously threatened by numerous diseases caused by diverse pathogens. The major maize diseases include northern corn leaf blight (NCLB), southern corn leaf blight (SCLB), southern corn rust (SCR), grey leaf spot (GLS), Curvularia leaf spot, white spot, stalk rot, ear rot, head smut, common smut, banded leaf, and sheath blight, etc. These diseases, which can occur year-round or intermittently in different ecological zones, often lead to substantial economic losses. Developing maize cultivars with broad resistance to multiple diseases through breeding is the most effective approach for combating diseases. The identification of resistant maize germplasm and discovery of resistance genes are major steps toward this goal. Maize germplasm resources, including wild relatives, landrace, traditional varieties, and farmer’s varieties, encompass a vast array of genetic variations that could be served as the primary gene pool for enhancing maize resistance and genetic improvement.

The primary objective of this Special Issue is to publish innovative research, short communications, and comprehensive review articles focusing on, but not limited to: the precise characterization of maize germplasm for disease resistance via the application of phenomics, genomics, or molecular markers; the development and utilization of novel molecular markers for resistance breeding; or comparative studies on different molecular marker systems associated with maize diseases resistance to assess the genetic structure of maize germplasm or populations. Maize–pathogen interactions and resistance gene mining and cloning are also within the scope of this Special Issue.

Dr. Canxing Duan
Dr. Yanyong Cao
Guest Editors

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Keywords

maize germplasm
maize disease
resistance identification
resistance genes
molecular markers
maize–microbe interactions

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Published Papers (7 papers)

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Research

22 pages, 10666 KB

Open AccessArticle

Bulked Segregant Analysis Revealed the Common Resistant QTLs Associated with Fusarium Ear Rot and Gibberella Ear Rot in Maize

by Haiyan Zhang, Weili Cai, Wenyi Li, Luyao Duan, Zhenyu Zhang, Chengjia Zou, Ling Li, Lin Li, Runtian Xiao, Lina Cui and Xiao Li

Plants 2026, 15(9), 1401; https://doi.org/10.3390/plants15091401 - 4 May 2026

Viewed by 81

Abstract

Maize ear rot, primarily caused by Fusarium verticillioides (Fusarium ear rot, FER) and Fusarium graminearum (Gibberella ear rot, GER), is a devastating disease that causes significant yield losses and mycotoxin contamination. Breeding resistant varieties is the most effective control strategy, but this requires the identification of stable genetic loci for resistance. In this study, we employed bulked segregant analysis (BSA) on two F₂ mapping populations to identify quantitative trait loci (QTLs) conferring resistance to FER and GER. We identified five and eleven QTLs for FER and GER, respectively. Notably, chromosome 4 was identified as a major hotspot for resistance to both diseases, and there was a co-localization of the FER QTL (qFER4.05) and GER QTL (qGER4.05-1) within a 58.58–71.34 Mb interval on bin 4.05, suggesting a potential locus for broad-spectrum resistance. Within this overlapping region, we identified 18 high-confidence candidate genes, including genes encoding leucine-rich repeat receptor-like kinases (LRR-RLKs), remorin, cytochrome P450 monooxygenases, and wall-associated receptor kinase-like (WAKL) protein, all with established roles in plant defense. These findings advance the understanding of the genetic architecture of ear rot resistance and provide critical resources for marker-assisted breeding to develop maize hybrids with durable resistance to both FER and GER. Full article

(This article belongs to the Special Issue Identification of Resistance of Maize Germplasm Resources to Disease)

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20 pages, 4245 KB

Open AccessArticle

Integrated Transcriptomic and Metabolic Analyses Reveal Key Defense Pathways Against Fusarium Infection in Maize Kernels

by Yuying Jia, Xin Qi, Xinfang Liu, Jun Ma, Mo Zhang, Chengtao Sun, Zhiyan Cao, Chunsheng Xue and Yanbo Wang

Plants 2026, 15(8), 1148; https://doi.org/10.3390/plants15081148 - 9 Apr 2026

Viewed by 421

Abstract

Fusarium ear rot (FER), caused by F. verticillioides, is a devastating disease in maize, leading to substantial yield losses and mycotoxin contamination. Therefore, revealing the molecular mechanisms underlying FER resistance is essential for crop breeding. Here, we performed integrated transcriptomic and metabolomic analyses on two maize inbred lines with contrasting FER resistance: the resistant line ZL30-12 (ZL30) and the susceptible line 92C0468U (92C). Following F. verticillioides inoculation, ZL30 exhibited sustained inhibition of fungal colonization and fumonisin accumulation, whereas 92C showed progressive disease development and elevated fumonisin levels. Both transcriptomic and metabolomic analyses converged on the phenylpropanoid pathway, with DEGs enriched in phenylpropanoid metabolism and DAMs enriched in phenylpropanoid biosynthesis, highlighting its central role in resistance. Further integrative analysis revealed that the lignin biosynthetic process, a key branch of phenylpropanoid metabolism, plays an important role in resistance. Several key DEGs (ZmPAL, ZmHCT, peroxidases, and ZmCOMT) and DAMs (sinapic acid, sinapaldehyde, coniferin, cinnamic acid, and caffeic acid) were differentially regulated between the two lines. Correlation analysis revealed a significant correlation between ZmCOMT expression and sinapic acid accumulation. RT-qPCR validation confirmed the expression patterns of key lignin-associated genes. The elevated activation of lignin biosynthesis in ZL30, via time-dependent induction of key genes (ZmPAL, ZmHCT, and peroxidases), suggests an increase in lignin accumulation, which likely reinforces cell wall integrity and restricts fungal invasion, thereby contributing to FER resistance. Collectively, these findings provide insights into the molecular mechanisms of FER resistance and identify key lignin-associated genes as promising targets for maize breeding. Full article

(This article belongs to the Special Issue Identification of Resistance of Maize Germplasm Resources to Disease)

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18 pages, 3397 KB

Open AccessArticle

Integrating BSA-Seq and RNA-Seq to Identify Major QTLs and Candidate Genes Conferring Resistance to Fusarium Ear Rot in Maize

by Shufeng Sun, Jie Xu, Jiaxin Huang, Yuying Fan, Gongjian Li, Zhuanfang Hao, Jianfeng Weng, Zhennan Xu and Xinhai Li

Plants 2026, 15(6), 985; https://doi.org/10.3390/plants15060985 - 23 Mar 2026

Viewed by 584

Abstract

Fusarium ear rot (FER), caused by Fusarium verticillioides, is a devastating disease that substantially reduces maize yield and compromises kernel quality. To investigate the genetic and molecular basis of resistance, an F₂ population derived from a cross between the resistant inbred line 3IBZ2 and the susceptible inbred line KW5G321 was analysed. By integrating bulked segregant analysis sequencing (BSA-Seq) with RNA sequencing (RNA-Seq), a major quantitative trait locus (QTL), designated qFER4, was identified on chromosome 4. Genetic analysis further demonstrated that qFER4 confers resistance through partial dominance. Transcriptome profiling of the resistant line revealed 7684 and 7906 differentially expressed genes (DEGs) at 36 and 72 h post inoculation (hpi), respectively. These DEGs were significantly enriched in defence-related biological processes and pathways, including phenylpropanoid biosynthesis, jasmonic acid signalling, MAPK cascades, and plant-pathogen interactions. By combining QTL mapping with transcriptome analyses, four candidate genes within the qFER4 interval were screened. Sequence analysis identified extensive structural variations in the promoter and coding regions of Zm00001d053393, including a premature stop codon predicted to lead to a gain-of-function mutation. In contrast, the other three genes exhibited only minor promoter polymorphisms with identical coding sequences between the parental lines. Overall, this study identifies a novel major-effect QTL and candidate gene associated with FER resistance, providing a foundation for gene function and a valuable genetic resource for breeding FER-resistant maize varieties. Full article

(This article belongs to the Special Issue Identification of Resistance of Maize Germplasm Resources to Disease)

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15 pages, 1260 KB

Open AccessArticle

Identification and Analysis of Resistance to Northern Corn Leaf Blight in Maize Germplasm Resources

by Bing Meng, Junwei Yang, Lixiu Tong, Qingli Liu, Dongfeng Zhang, Wen-Xue Li, Jianjun Wang, Yunbi Xu, Zifeng Guo and Canxing Duan

Plants 2025, 14(20), 3171; https://doi.org/10.3390/plants14203171 - 15 Oct 2025

Viewed by 1335

Abstract

Northern corn leaf blight (NCLB), caused by the fungus Exserohilum turcicum, is one of the most significant foliar diseases in maize worldwide, with its severity being highly influenced by environmental conditions. An effective strategy used to control NCLB involves screening diverse maize germplasm for resistant sources through multi-environment inoculation assays, ultimately aiming to develop resistant varieties. This study systematically evaluated 711 maize germplasm accessions with rich genetic diversity. The evaluation was conducted under four location–year environment combinations (Shangluo, Shaanxi Province, China in 2014–2015 and Xinzhou, Shanxi Province, China in 2021–2022) using artificial inoculation with physiological race 123N (or races 1, 2, 3, N). The results showed that the estimated variances of genotype, environment, and genotype-by-environment interaction were all highly significant (p < 0.01). Significant correlations (p < 0.01) were observed among replicates within each environment, with correlation coefficients (r) ranging from 0.67 to 0.88. At the Xinzhou trial in 2021, four replicates were inoculated with four physiological races (1, 2, 3, and N), revealing highly significant correlations (r = 0.77–0.80, p < 0.01) among them. The disease severity of the tropical germplasm was significantly lower (p < 0.001) than that of the temperate germplasm. Among the temperate subgroups, the PA and PB (groups A and B germplasms derived from modern US hybrids) subgroups exhibited lower disease severity, with the PB subgroup showing the lowest, while the Iodent and Reid subgroups exhibited higher susceptibility. The disease severity responses to the four physiological races were highly positively correlated (r = 0.77–0.80, p < 0.001), and their correlations with the composite inoculation (race 123N) ranged from 0.65 to 0.83. Based on the resistance evaluations across four location–year environment combinations, the 711 maize accessions were classified into five categories: 20 were highly resistant, 236 resistant, 205 moderately resistant, 237 susceptible, and 13 highly susceptible. The findings indicate that the tropical germplasm and the temperate PB subgroup are major sources of NCLB resistance. Full article

(This article belongs to the Special Issue Identification of Resistance of Maize Germplasm Resources to Disease)

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20 pages, 8487 KB

Open AccessArticle

Precise Identification and Analysis of Maize Germplasm Resistance to Ear Rot Caused by Six Fusarium Species

by Shuai Li, Lihong Zhu, Yongxiang Li, Yaxuan Guo, Yuhang Zhang, Chaosong Huang, Wenqi Wu, Suli Sun, Zixiang Cheng and Canxing Duan

Plants 2025, 14(15), 2280; https://doi.org/10.3390/plants14152280 - 24 Jul 2025

Viewed by 1447

Abstract

Maize (Zea may L.) is one of the most important crops worldwide, but ear rot poses a significant threat to its production. Diverse pathogens cause ear rot in China, with Fusarium spp. being predominant, especially Fusarium graminearum and Fusarium verticillioides. Current methods for the control of ear rot are limited, making the use of resistant germplasm resources an effective and economical management strategy. Earlier research focused on resistance to Fusarium ear rot (FER; caused by F. verticillioides) and Gibberella ear rot (GER; caused by F. graminearum), but assessing maize resistance to multiple major Fusarium spp. is critical in ensuring maize production. Thus, the resistance of 343 maize germplasm resources to ear rot caused by six Fusarium spp. (F. verticillioides, F. graminearum, F. proliferatum, F. meridionale, F. subglutinans, and F. temperatum) was evaluated in this study. Over three years, 69 and 77 lines resistant to six and five ear rot diseases, respectively, and 139 lines resistant to both FER and GER were identified. Moreover, the 343 germplasm resources were divided into eight heterotic groups, of which PH4CV was the most resistant one, whereas NSS and Pioneer Female were the least resistant ones. These findings provide a basis for the development of maize cultivars with broad-spectrum ear rot resistance. Full article

(This article belongs to the Special Issue Identification of Resistance of Maize Germplasm Resources to Disease)

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16 pages, 1874 KB

Open AccessArticle

Genome-Wide Association Study and RNA-Seq Elucidate the Genetic Mechanisms Behind Aphid (Rhopalosiphum maidis F.) Resistance in Maize

by Doudou Sun, Yijun Wei, Chunyan Han, Xiaopeng Li, Zhen Zhang, Shiwei Wang, Zijian Zhou, Jingyang Gao, Jiafa Chen and Jianyu Wu

Plants 2025, 14(11), 1614; https://doi.org/10.3390/plants14111614 - 25 May 2025

Cited by 4 | Viewed by 1399

Abstract

Maize is a crucial food crop and industrial raw material, significantly contributing to national food security. Aphids are one of the most prevalent and destructive pests in maize production, necessitating the exploration of pest-resistant germplasm and the development of resistant varieties as the most fundamental and effective strategy for mitigating aphid-induced damage. This study established an aphid resistance evaluation system and identified 17 elite resistant inbred lines through multi-year screening. A genome-wide association study (GWAS) revealed 22 significant single-nucleotide polymorphisms (SNPs) associated with aphid resistance, including genes involved in benzoxazinoid (Bx) biosynthesis (such as Bx2), insect resistance-related transcription factors (such as WRKY23), plant lectins, and other resistance pathways. RNA-seq analysis of the samples before and after aphid infestation detected 1037 differentially expressed genes (DEGs) in response to aphid infestation, with KEGG enrichment highlighting benzoxazinoid biosynthesis and starch/sucrose metabolism as primary response pathways. Integrating GWAS and RNA-seq results revealed the presence of several benzoxazinoid synthesis-related genes on the short arm of chromosome 4 (Chr4S). FMqRrm1, a Kompetitive Allele-Specific PCR (KASP) marker, was derived from the Chr4S region. We subsequently utilized this marker for marker-assisted selection (MAS) to introgress the Chr4S region from the aphid-resistant inbred line into two aphid-susceptible inbred lines. The results demonstrated that the Chr4S favorable allele significantly reduced aphid occurrence by 1.5 to 2.1 grades. This study provides a critical theoretical foundation and practical guidance for understanding the molecular mechanism of aphid resistance in maize and molecular breeding for aphid resistance. Full article

(This article belongs to the Special Issue Identification of Resistance of Maize Germplasm Resources to Disease)

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17 pages, 2810 KB

Open AccessArticle

The Involvement of Glycerophospholipids in Susceptibility of Maize to Gibberella Root Rot Revealed by Comparative Metabolomics and Mass Spectrometry Imaging Joint Analysis

by Qing Wang, Zi’an Zhao, Xin Li and Xiquan Gao

Plants 2025, 14(9), 1376; https://doi.org/10.3390/plants14091376 - 1 May 2025

Cited by 2 | Viewed by 1509

Abstract

Gibberella root rot (GRR), caused by Fusarium graminearum, is one of the major threats to maize production. However, the mechanism underlying maize’s response to GRR is not fully understood. Multi-omics study incorporating metabolomics reveals insights into maize–pathogen interactions. Using metabolomics and mass spectrometry imaging (MSI), maize inbred lines with GRR resistance (W438) and susceptibility (335M) were deployed to characterize specific metabolites associated with GRR. Analysis of significantly altered metabolites suggested that glycerophospholipid metabolism was highly associated with GRR resistance or susceptibility. Furthermore, the distinct accumulation of lysophosphatidylethanolamine (lysoPE) and lysophosphatidylcholine (lysoPC) from glycerophospholipid metabolism, along with the significant up-regulation of phospholipase (PLA) gene in the susceptible line, suggested that high levels of lysoPC and lysoPE contributed to GRR susceptibility. Meanwhile, genes encoding lysophospholipase (LPLA), the detoxification enzymes of lysoPC, were significantly activated in both genotypes. However, the significantly higher expression of LPLAs in the resistant line corresponded to a significant increase in the content of non-toxic sn-glycero-3-phosphocholine, whereas this increase was not observed in the susceptible line. MSI analysis revealed the involvement of other potential phospholipids in GRR susceptibility. Taken together, maintaining an appropriate concentration of lysophospholipids is crucial for their role in the signaling pathway that triggers GRR resistance without causing damage to maize roots. Full article

(This article belongs to the Special Issue Identification of Resistance of Maize Germplasm Resources to Disease)

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