Background-dependent genetic architecture of Fusarium head blight resistance in U.S. hard winter wheat

Abstract

Fusarium head blight (FHB), caused primarily by Fusarium graminearum, is one of the most destructive diseases of wheat worldwide, causing substantial yield losses and mycotoxin contamination of grain. Deployment of major resistance quantitative trait loci (QTL) through marker-assisted breeding is an effective strategy for improving resistance; however, the effectiveness of QTL combinations and the genomic architecture of introgression populations remain incompletely understood. This study evaluated the effects of three major FHB resistance QTL, Fhb1, Fhb7, and Fhb9, in four U.S. hard winter wheat genetic backgrounds (Guardian, KS Providence, NE18445, and OK19225) and assessed the utility of genotyping-by-sequencing (GBS) for characterizing introgression populations. A total of 470 BC₂F₄ lines carrying different QTL combinations were evaluated for Type II FHB resistance and agronomic traits. The effectiveness of QTL combinations varied among genetic backgrounds, with Fhb7 providing the most consistent contribution to resistance across populations. In most backgrounds, two-QTL combinations provided resistance levels comparable to those of three-QTL combinations, indicating diminishing returns from pyramiding all three loci. Genome-wide characterization using GBS-derived sliding window bin maps showed recurrent-parent genome recovery ranged from 78.8% to 90.3% and substantial differences in donor genome retention and recombination patterns among populations. Donor introgressions occurred as discrete chromosomal segments and showed greater similarity within populations than among lines carrying the same FHB QTL combinations. GBS-derived bin maps effectively detected Fhb1 and Fhb7 introgressions but showed limited ability to identify Fhb9. SNP x QTL analyses identified several background-specific loci associated with variation in FHB resistance, particularly in the NE18445 population. Overall, these results demonstrate that the effectiveness of major FHB resistance QTL depends on genetic background and highlight the value of GBS-derived bin mapping for genome-wide characterization of breeding populations.