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

Diallel Analysis of Wheat Resistance to Fusarium Head Blight and Mycotoxin Accumulation under Conditions of Artificial Inoculation and Natural Infection

Breeding resistant wheat cultivars to Fusarium head blight (FHB), caused by Fusarium spp., is the best method for controlling the disease. The aim of this study was to estimate general combining ability (GCA) and specific combining ability (SCA) for FHB resistance in a set of eight genetically diverse winter wheat cultivars to identify potential donors of FHB resistance for crossing. FHB resistance of parents and F1 crosses produced by the half diallel scheme was evaluated under the conditions of artificial inoculation with F. graminearum and natural infection. Four FHB related traits were assessed: visual rating index (VRI), Fusarium damaged kernels (FDK), and deoxynivalenol and zearalenone content in the harvested grain samples. Significant GCA effects for FHB resistance were observed for the parental cultivars with high FHB resistance for all studied FHB resistance related traits. The significant SCA and mid-parent heterosis effects for FHB resistance were rare under both artificial inoculation and natural infection conditions and involved crosses between parents with low FHB resistance. A significant negative correlation between grain yield under natural conditions and VRI (r = -0.43) and FDK (r = -0.47) under conditions of artificial inoculation was observed in the set of the studied F1 crosses. Some crosses showed high yield and high FHB resistance, indicating that breeding of FHB resistant genotypes could be performed without yield penalty. These crosses involved resistant cultivars with significant GCA effects for FHB resistance indicating that that they could be used as good donors of FHB resistance.

What Is Fusarium Head Blight (FHB) Resistance and What Are Its Food Safety Risks in Wheat? Problems and Solutions-A Review

The term "Fusarium Head Blight" (FHB) resistance supposedly covers common resistances to different Fusarium spp. without any generally accepted evidence. For food safety, all should be considered with their toxins, except for deoxynivalenol (DON). Disease index (DI), scabby kernels (FDK), and DON steadily result from FHB, and even the genetic regulation of Fusarium spp. may differ; therefore, multitoxin contamination is common. The resistance types of FHB form a rather complex syndrome that has been the subject of debate for decades. It seems that resistance types are not independent variables but rather a series of components that follow disease and epidemic development; their genetic regulation may differ. Spraying inoculation (Type 1 resistance) includes the phase where spores land on palea and lemma and spread to the ovarium and also includes the spread-inhibiting resistance factor; therefore, it provides the overall resistance that is needed. A significant part of Type 1-resistant QTLs could, therefore, be Type 2, requiring the retesting of the QTLs; this is, at least, the case for the most effective ones. The updated resistance components are as follows: Component 1 is overall resistance, as discussed above; Component 2 includes spreading from the ovarium through the head, which is a part of Component 1; Component 3 includes factors from grain development to ripening (FDK); Component 4 includes factors influencing DON contamination, decrease, overproduction, and relative toxin resistance; and for Component 5, the tolerance has a low significance without new results. Independent QTLs with different functions can be identified for one or more traits. Resistance to different Fusarium spp. seems to be connected; it is species non-specific, but further research is necessary. Their toxin relations are unknown. DI, FDK, and DON should be checked as they serve as the basic data for the risk analysis of cultivars. A better understanding of the multitoxin risk is needed regarding resistance to the main Fusarium spp.; therefore, an updated testing methodology is suggested. This will provide more precise data for research, genetics, and variety registration. In winter and spring wheat, the existing resistance level is very high, close to Sumai 3, and provides much greater food safety combined with sophisticated fungicide preventive control and other practices in commercial production.

Multi-locus genome-wide association studies reveal the genetic architecture of Fusarium head blight resistance in durum wheat

Durum wheat is more susceptible to Fusarium head blight (FHB) than other types or classes of wheat. The disease is one of the most devastating in wheat; it reduces yield and end-use quality and contaminates the grain with fungal mycotoxins such as deoxynivalenol (DON). A panel of 265 Canadian and European durum wheat cultivars, as well as breeding and experimental lines, were tested in artificially inoculated field environments (2019-2022, inclusive) and two greenhouse trials (2019 and 2020). The trials were assessed for FHB severity and incidence, visual rating index, Fusarium-damaged kernels, DON accumulation, anthesis or heading date, maturity date, and plant height. In addition, yellow pigment and protein content were analyzed for the 2020 field season. To capture loci underlying FHB resistance and related traits, GWAS was performed using single-locus and several multi-locus models, employing 13,504 SNPs. Thirty-one QTL significantly associated with one or more FHB-related traits were identified, of which nine were consistent across environments and associated with multiple FHB-related traits. Although many of the QTL were identified in regions previously reported to affect FHB, the QTL QFhb-3B.2, associated with FHB severity, incidence, and DON accumulation, appears to be novel. We developed KASP markers for six FHB-associated QTL that were consistently detected across multiple environments and validated them on the Global Durum Panel (GDP). Analysis of allelic diversity and the frequencies of these revealed that the lines in the GDP harbor between zero and six resistance alleles. This study provides a comprehensive assessment of the genetic basis of FHB resistance and DON accumulation in durum wheat. Accessions with multiple favorable alleles were identified and will be useful genetic resources to improve FHB resistance in durum breeding programs through marker-assisted recurrent selection and gene stacking.

Genome-wide association analysis of type II resistance to Fusarium head blight in common wheat

Background

Fusarium head blight (FHB) is a disease affecting wheat spikes caused by some Fusarium species and leads to cases of severe yield reduction and seed contamination. Identifying resistance genes/QTLs from wheat germplasm may help to improve FHB resistance in wheat production.

Methods

Our study evaluated 205 elite winter wheat cultivars for FHB resistance. A high-density 90K SNP array was used for genotyping the panel. A genome-wide association study (GWAS) from cultivars from three different environments was performed using a mixed linear model (MLM).

Results

Sixty-six significant marker-trait associations (MTAs) were identified (P < 0.001) on fifteen chromosomes that explained the phenotypic variation ranging from 5.4 to 11.2%. Some important new MTAs in genomic regions involving FHB resistance were found on chromosomes 2A, 3B, 5B, 6A, and 7B. Six MTAs at 92 cM on chromosome 7B were found in cultivars from two different environments. Moreover, there were 11 MTAs consistently associated with diseased spikelet rate and diseased rachis rate as pleiotropic effect loci and D_contig74317_533 on chromosome 5D was novel for FHB resistance. Eight new candidate genes of FHB resistance were predicated in wheat in this study. Three candidate genes, TraesCS5D02G006700, TraesCS6A02G013600, and TraesCS7B02G370700 on chromosome 5DS, 6AS, and 7BL, respectively, were perhaps important in defending against FHB by regulating intramolecular transferase activity, GTP binding, or chitinase activity in wheat, but further validation in needed. In addition, a total of five favorable alleles associated with wheat FHB resistance were discovered. These results provide important genes/loci for enhancing FHB resistance in wheat breeding by marker-assisted selection.

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

Fusarium head blight (FHB), caused by the fungus Fusarium graminearum Schwabe is an important disease of wheat that causes severe yield losses along with serious quality concerns. Incorporating the host resistance from either wild relatives, landraces, or exotic materials remains challenging and has shown limited success. Therefore, a better understanding of the genetic basis of native FHB resistance in hard winter wheat (HWW) and combining it with major quantitative trait loci (QTLs) can facilitate the development of FHB-resistant cultivars. In this study, we evaluated a set of 257 breeding lines from the South Dakota State University (SDSU) breeding program to uncover the genetic basis of native FHB resistance in the US hard winter wheat. We conducted a multi-locus genome-wide association study (ML-GWAS) with 9,321 high-quality single-nucleotide polymorphisms (SNPs). A total of six distinct marker-trait associations (MTAs) were identified for the FHB disease index (DIS) on five different chromosomes including 2A, 2B, 3B, 4B, and 7A. Further, eight MTAs were identified for Fusarium-damaged kernels (FDK) on six chromosomes including 3B, 5A, 6B, 6D, 7A, and 7B. Out of the 14 significant MTAs, 10 were found in the proximity of previously reported regions for FHB resistance in different wheat classes and were validated in HWW, while four MTAs represent likely novel loci for FHB resistance. Accumulation of favorable alleles of reported MTAs resulted in significantly lower mean DIS and FDK score, demonstrating the additive effect of FHB resistance alleles. Candidate gene analysis for two important MTAs identified several genes with putative proteins of interest; however, further investigation of these regions is needed to identify genes conferring FHB resistance. The current study sheds light on the genetic basis of native FHB resistance in the US HWW germplasm and the resistant lines and MTAs identified in this study will be useful resources for FHB resistance breeding via marker-assisted selection.

Multi-trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat

Multi-trait genomic prediction (MTGP) can improve selection accuracy for economically valuable 'primary' traits by incorporating data on correlated secondary traits. Resistance to Fusarium head blight (FHB), a fungal disease of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), is evaluated using four genetically correlated traits: incidence (INC), severity (SEV), Fusarium damaged kernels (FDK), and deoxynivalenol content (DON). Both FDK and DON are primary traits; DON evaluation is expensive and usually requires several months for wheat breeders to get results from service laboratories performing the evaluations. We evaluated MTGP for DON using three soft red winter wheat breeding datasets: two diversity panels from the University of Illinois (IL) and Purdue University (PU) and a dataset consisting of 2019-2020 University of Illinois breeding cohorts. For DON, relative to single-trait (ST) genomic prediction, MTGP including phenotypic data for secondary traits on both validation and training sets, resulted in 23.4 and 10.6% higher predictive abilities in IL and PU panels, respectively. The MTGP models were advantageous only when secondary traits were included in both training and validation sets. In addition, MTGP models were more accurate than ST models only when FDK was included, and once FDK was included in the model, adding additional traits hardly improved accuracy. Evaluation of MTGP models across testing cohorts indicated that MTGP could increase accuracy by more than twofold in the early stages. Overall, we show that MTGP can increase selection accuracy for resistance to DON accumulation in wheat provided FDK is evaluated on the selection candidates.

Genetic Trends in Fusarium Head Blight Resistance from 20 Years of Winter Wheat Breeding and Cooperative Testing in the Northern U.S.A

Fusarium head blight (FHB) is a devastating disease of wheat and barley. In the U.S.A., a significant long-term investment in breeding FHB-resistant cultivars began after the 1990s. However, to this date, no study has been performed to understand and monitor the rate of genetic progress in FHB resistance as a result of this investment. Using 20 years of data (1998 to 2018) from the Northern Uniform and Preliminarily Northern Uniform winter wheat scab nurseries that consisted of 1,068 genotypes originating from nine different institutions, we studied the genetic trends in FHB resistance within the northern soft red winter wheat growing region using mixed model analyses. For the FHB resistance traits incidence, severity, Fusarium-damaged kernels, and deoxynivalenol content, the rate of genetic gain in disease resistance was estimated to be 0.30 ± 0.1, 0.60 ± 0.09, and 0.37 ± 0.11 points per year, and 0.11 ± 0.05 parts per million per year, respectively. Among the five FHB-resistance quantitative trait loci assayed for test entries from 2012 to 2018, the frequencies of favorable alleles from Fhb 2DL Wuhan1 W14, Fhb Ernie 3Bc, and Fhb 5A Ning7840 were close to zero across the years. The frequency of the favorable at Fhb1 and Fhb 5A Ernie ranged from 0.08 to 0.33 and 0.06 to 0.20, respectively, across years, and there was no trend in changes in allele frequencies over years. Overall, this study showed that substantial genetic progress has been made toward improving resistance to FHB. It is apparent that today's investment in public wheat breeding for FHB resistance is achieving results and will continue to play a vital role in reducing FHB levels in growers' fields.