Identification of two major QTL associated with Fusarium crown rot resistance in wheat

Fusarium crown rot (FCR), caused by the fungal genus Fusarium, is a severe soil-borne disease of wheat (Triticum aestivum) worldwide. In this study, we identified five quantitative trait loci (QTL) associated with FCR resistance on chromosomes 3A, 3B, 4B (two QTL), and 6A using a population of 128 F₇ recombinant inbred lines (RILs) derived from a cross between the two Chinese cultivars 04zhong 36 and Jinxiu 21. Of these QTL, two major QTL, QFcr.cau-3A and QFcr.cau-4B.1, were stably detected across multiple trials and explained 14.06% and 18.09%, respectively, of the phenotypic variance based on best linear unbiased prediction (BLUP) data. The resistance alleles at these two loci were derived from the parental lines 04zhong36 (QFcr.cau-3A) and Jinxiu 21 (QFcr.cau-4B.1), respectively. We confirmed the effects and stability of QFcr.cau-3A and QFcr.cau-4B.1 in an independent RIL population and in a collection of wheat accessions, respectively. Additionally, we detected a major and stable QTL for plant height, QPh.cau-4B, that overlapped with QFcr.cau-4B.1. The allele of QPh.cau-4B conferring tallness was from Jinxiu 21. Conditional QTL mapping indicated that although QFcr.cau-4B.1 and QPh.cau-4B showed significant interactions, the effect of QFcr.cau-4B.1 remained significant after the effects of plant height were removed. Field inoculation experiments with the 60 RILs showing the greatest sensitivity or resistance to FCR at the seedling stage detected a significant and positive correlation between seedling and adult plant resistance (correlation coefficient = 0.71). The confidence intervals for QFcr.cau-3A and QFcr.cau-4B.1 contain 264 and 240 high-confidence genes, respectively. Based on gene annotation, sequence variation, and expression patterns, three genes (TraesCS3A02G373300, TraesCS3A02G376500, and TraesCS4B02G222600) were considered as potential candidates for QFcr.cau-3A and QFcr.cau-4B.1. Our results provide valuable resources for the cloning of FCR resistance loci that can be utilized in FCR resistance breeding programs.