Identification and genome-wide association analysis of seedling-stage Fusarium crown rot resistance in 200 wheat cultivars from Henan province, China

Fusarium crown rot (FCR) is a globally prevalent soil-borne fungal disease of wheat. In recent years, its incidence has steadily increased in the middle-lower Yangtze River and Huang-Huai wheat-growing regions of China. However, wheat cultivars with strong resistance remain scarce. As a result, the identification of resistant germplasm and the discovery of resistance genes have become key priorities in resistance breeding. In this study, the dominant FCR pathogen Fusarium pseudograminearum strain WZ-8A, isolated from the Huang-Huai wheat region, was used to evaluate seedling-stage resistance in 133 landrace cultivars and 67 modern cultivars from Henan province. Phenotypic data were integrated with wheat 660K SNP genotyping data to perform a genome-wide association study (GWAS). The results revealed that only eight cultivars—Tutoumai (Qixian), Zaoyangmai, Baiquan 41, Kaimai 18, Zhoumai 24, 04 Zhong 36, Yumai 35, and Zhongyu 3—exhibited moderate resistance. GWAS identified 30 significant loci, with two SNPs (AX-111055517 and AX-110584552) consistently detected across multiple models and environments. Functional annotation and expression analysis of candidate regions suggested that TraesCS4B02G048500 may be a key resistance gene. This study identified eight moderately resistant wheat accessions at the seedling stage, and the significant loci and putative genes discovered provide valuable resources, insights, and a theoretical foundation for future FCR resistance breeding and related research.