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Journal of Integrative Agriculture
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Mining genomic regions and candidate genes underlying QTL Qfcr.caas.7A-2 conferring Fusarium crown rot resistance in wheat via integrated GWAS and BSE-Seq analysis

Peipei Wu1, Hui Zhao1, Minghe Wang1, Ziming Wang1, Ziyu Zhao1,2, Xianrui Guo1, Chunyan Mai3, Huili Li4, Liqiang Yu4, Li Yang1, Hongwei Liu1, Yang Zhou1#, Hongjun Zhang1#

1 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/State Key Laboratory of Crop Gene Resources and Breeding/Engineering Laboratory of Crop Molecular Breeding/State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China

2 College of Agronomy, Qingdao Agricultural University/Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao 266109, China

3 Xinxiang Innovation Center for Breeding Technology of Dwarf-Male-Sterile Wheat, Xinxiang 453731, China

4 Zhaoxian Experiment Station, Shijiazhuang Academy of Agricultural and Forestry Sciences, Zhaoxian 051530, China

 Highlights 

Five Fusarium crown rot (FCR)-resistant wheat accessions were identified, providing valuable genetic resources for FCR resistance breeding.

A novel QTL (Qfcr.caas.7A-2) conferring FCR resistance on chromosome 7A was co-located by GWAS and BSE-Seq analysis.

Two KASP markers KASP-7079 and KASP-3538 were successfully developed and validated for the Qfcr.caas.7A-2 locus.

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摘要  

茎基腐病(FCR是由镰刀菌引起的一种土传病害,对全球小麦生产构成威胁。本研究利用299份小麦品种/品系构成的自然群体进行全基因组关联分析(GWAS),并结合重组自交系(RIL)群体构建的混池进行外显子捕获测序(BSE-Seq),鉴定了小麦抗FCR的数量性状位点(QTL)。表型评价发现5个小麦品种具有与抗性对照品种Sunco相当的抗性水平。通过GWAS分析,在染色体1B2B2D4A5D6D7A7B7D上定位到14QTL,其表型贡献率为3.73-6.64%。其中,位于7A染色体上一个主效QTLQfcr.caas.7A-2)在所有重复鉴定中均稳定检测到。BSE-Seq分析进一步证实了7A染色体存在FCR位点,其相关SNP区域涵盖了Qfcr.caas.7A-2区间。在该区间内,通过表达谱和系统发育树分析,鉴定到一个候选基因TraesCS7A02G535100.1(编码一个RGA5-like蛋白)。针对Qfcr.caas.7A-2位点成功开发并验证了两个竞争性等位基因特异性PCRKASP)标记KASP-7079KASP-3538。这些发现为阐明小麦抗FCR遗传机制提供了有价值的参考,并为抗FCR育种提供了宝贵抗性资源和分子标记。



Abstract  

Fusarium crown rot (FCR), a major soil-borne disease caused by Fusarium species, threatens global wheat production. This study identified quantitative trait locus (QTL) for FCR resistance in wheat using genome-wide association study (GWAS) on a panel of 299 wheat cultivars/lines and bulked segregant exome sequencing (BSE-Seq) on a recombinant inbred line (RIL) population. Phenotypic evaluation revealed five wheat accessions with resistance levels comparable to the resistant control Sunco. Fourteen putative QTLs were mapped on chromosomes B, 2B, 2D, 4A, 5D, 6D, 7A, 7B, and 7D by GWAS, with the phenotypic variation explained by 3.73-6.64%. A major QTL (Qfcr.caas.7A-2) on chromosome 7A was consistently detected across all replications. BSE-Seq analysis confirmed enrichment of associated polymorphisms on chromosome 7A, encompassing the Qfcr.caas.7A-2 interval. Within this region, TraesCS7A02G53500. (encoding an RGA5-like protein) was prioritized as a candidate gene based on expression and phylogenetic analysis. Two kompetitive allele-specific PCR (KASP) markers KASP-7079 and KASP-3538 were successfully developed and validated for Qfcr.caas.7A-2. These findings offer valuable insights into the genetic mechanisms underlying FCR resistance and provide valuable resistance resources and molecular markers for FCR resistance breeding. 

Keywords:  wheat       Fusarium crown rot              GWAS              BSE-Seq              KASP marker              candidate gene  
Online: 10 February 2026  
Fund: 

The work was supported by the National Key Research and Development Program of China (202YFF000200), the Central Public-interest Scientific Institution Basal Research Fund of China (S2025QZ03), and Major Scientific and Technological Tasks of the Chinese Academy of Agricultural Sciences (CAAS-ZDRW202403).

About author:  #Correspondence Yang Zhou, E-mail: zhouyang@caas.cn; Hongjun Zhang, E-mail: zhanghongjun0@caas.cn

Cite this article: 

Peipei Wu, Hui Zhao, Minghe Wang, Ziming Wang, Ziyu Zhao, Xianrui Guo, Chunyan Mai, Huili Li, Liqiang Yu, Li Yang, Hongwei Liu, Yang Zhou, Hongjun Zhang. 2026. Mining genomic regions and candidate genes underlying QTL Qfcr.caas.7A-2 conferring Fusarium crown rot resistance in wheat via integrated GWAS and BSE-Seq analysis. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.02.024

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