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Integrating BSA-Seq and RNA-Seq to Identify Major QTLs and Candidate Genes Conferring Resistance to Fusarium Ear Rot
Shufeng Sun1,2,3, Jie Xu3, Jiaxin Huang1,3
1College of Agronomy, Shenyang Agricultural University, Dongling Street, Shenhe District, Shenyang 110866, China.
Plants (Basel, Switzerland)
|March 28, 2026
Summary
Researchers identified a new major gene, qFER4, on chromosome 4 that significantly enhances maize resistance to Fusarium ear rot (FER). This discovery provides a foundation for breeding improved, disease-resistant maize varieties.
Area of Science:
- Plant Genetics and Breeding
- Molecular Plant Pathology
- Agricultural Science
Background:
- Fusarium ear rot (FER), caused by *Fusarium verticillioides*, is a major agricultural problem, reducing maize yield and kernel quality.
- Understanding the genetic basis of maize resistance to FER is crucial for developing resistant cultivars.
- Previous studies have identified some resistance factors, but a comprehensive understanding of major genetic loci is still needed.
Purpose of the Study:
- To identify major quantitative trait loci (QTL) conferring resistance to *Fusarium verticillioides* in maize.
- To investigate the molecular mechanisms underlying FER resistance.
- To identify candidate genes within the identified QTL for future functional analysis and breeding applications.
Main Methods:
- Bulked segregant analysis sequencing (BSA-Seq) and RNA sequencing (RNA-Seq) were integrated to map QTL.
- An F2 population derived from a cross between resistant (3IBZ2) and susceptible (KW5G321) maize inbred lines was used.
- Transcriptome profiling was performed at 36 and 72 hours post inoculation (hpi) to analyze gene expression changes.
Main Results:
- A major QTL, designated *qFER4*, was identified on chromosome 4, conferring partial dominance for FER resistance.
- Transcriptome analysis revealed significant enrichment of defense-related pathways, including phenylpropanoid biosynthesis and MAPK signaling.
- Four candidate genes within the *qFER4* interval were identified, with *Zm00001d053393* showing significant structural variations potentially leading to gain-of-function.
Conclusions:
- This study successfully identified a novel, major-effect QTL (*qFER4*) associated with *Fusarium* ear rot resistance in maize.
- The candidate gene *Zm00001d053393* presents a promising target for understanding FER resistance mechanisms.
- The findings provide valuable genetic resources for breeding FER-resistant maize varieties.
