Genome-Wide Association Studies for Fusarium Head Blight Resistance and Its Trade-Off With Grain Yield in Soft Red Winter Wheat

Abstract

Identification of quantitative trait loci for Fusarium head blight (FHB) resistance from different sources and pyramiding them into cultivars could provide effective protection against FHB. The objective of this study was to characterize a soft red winter wheat (SRWW) breeding population that has been subjected to intense germplasm introduction and alien introgression for FHB resistance in the past. The population was evaluated under misted FHB nurseries inoculated with Fusarium graminearum infested corn spawn for two years. Phenotypic data included disease incidence (INC), disease severity (SEV), Fusarium damaged kernels (FDK), FHB index (FHBdx), and deoxynivalenol concentration (DON). Genome-wide association studies by using 13,784 SNP markers identified twenty-five genomic regions at -logP ≥ 4.0 that were associated with five FHB-related traits. Of these 25, the marker trait associations that explained more than 5% phenotypic variation were localized on chromosomes 1A, 2B, 3B, 5A, 7A, 7B, and 7D, and from diverse sources including adapted SRWW lines such as Truman and Bess, and unadapted common wheat lines such as Ning7840 and Fundulea 201R. Furthermore, individuals with favorable alleles at the four loci Fhb1, Qfhb.nc-2B.1 (Q2B.1), Q7D.1, and Q7D.2 showed better FDK and DON scores (but not INC, SEV, and FHBdx) compared to other allelic combinations. Our data also showed while pyramiding multiple loci provides protection against FHB disease, it has significant trade-off with grain yield.

Multi-Locus Genome-Wide Association Studies to Characterize Fusarium Head Blight (FHB) Resistance in Hard Winter Wheat

“…Among them, one QTL for FDK was mapped between 611 and 724 Mbp in the ‘Nanda 2419 × Wangshuibai’ population ( Li et al, 2008 ). Additionally, a recent GWAS using soft red winter wheat germplasm reported a QTL for type III and type IV resistance that was mapped at 738 Mbp, which perfectly co-localizes with the MTA from current study ( Gaire et al, 2021 ). Previously, Larkin et al (2020) also reported a QTL for type II resistance at 709 Mbp on chromosome 7A, which is in close proximity to the MTA S7A_713432647 from this study.…”

Evaluation of Methods for Measuring Fusarium-Damaged Kernels of Wheat

“…VIBE was the only platform to effectively detect a significant SNP association within the Fhb1 region [−log 10 (p) of 5.53, S3B_9439629 locus] (Figure 6). While significant SNP associations of other major FHB QTL (F1BJ, F1AN) shown to be present in this population were not detected by VIBE or other platforms, both F1BJ and F1AN were previously detected using DON as a phenotype, rather than FDK as was used to detect Fhb1 [4,16,23]. VIBE proved to be the most effective proxy phenotype to DON among platforms (Figure 4), but still failed to associate with QTL previously detected in GWAS using DON, such as F1BJ and F1AN (Figure 5).…”

“…Consequently, FDK bears a closer relationship with DON content in the physiologically mature grain and has a direct effect on test weight as FDK weigh less than healthy kernels [12,15]. For these reasons, DON and FDK are considered primary traits for their direct effect on yield, quality, and ultimate economic value of the grain, compared to FHB incidence and severity which are considered secondary traits [16].…”

“…Two traditional methods of quantifying FDK are (1) manual separation, or actual enumeration of healthy kernels and FDK, which is time-consuming and labor-intensive but accurate, and (2) visual estimation, often using prepared standards for reference, which is much faster than manual separation but at some cost in accuracy [16,20]. While traditional methods of using a human observer to determine FDK have shown success, these methods are innately prone to human error such as sample bias and lack of objectivity, as results may vary between observers, or even across time with the same observer [21].…”

“…Previously, GWAS has been used to associate FDK with major FHB resistance loci such as Fhb1 [23], F1BJ (FHB_1B_Jamestown) [4,24] and F1AN (FHB_1A_Neuse) [18]. Fhb1 has been previously detected using FDK as a trait, while F1BJ and F1AN have been previously associated with DON directly [16]. Fhb1 has been shown to reduce FDK by 32% and DON accumulation by 20% in soft red winter wheat populations [1].…”