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

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. 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 1B, 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, TraesCS7A02G535100 . 1 (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.