Identification of QTLs for Resistance to Fusarium Head Blight Using a Doubled Haploid Population Derived from Southeastern United States Soft Red Winter Wheat Varieties AGS 2060 and AGS 2035

Comprehensive genome-wide analysis of wheat xylanase inhibitor protein (XIP) genes: unveiling their role in Fusarium head blight resistance and plant immune mechanisms

In this comprehensive genome-wide study, we identified and classified 83 Xylanase Inhibitor Protein (XIP) genes in wheat, grouped into five distinct categories, to enhance understanding of wheat's resistance to Fusarium head blight (FHB), a significant fungal threat to global wheat production. Our analysis reveals the unique distribution of XIP genes across wheat chromosomes, particularly at terminal regions, suggesting their role in the evolutionary expansion of the gene family. Several XIP genes lack signal peptides, indicating potential alternative secretion pathways that could be pivotal in plant defense against FHB. The study also uncovers the sequence homology between XIPs and chitinases, hinting at a functional diversification within the XIP gene family. Additionally, the research explores the association of XIP genes with plant immune mechanisms, particularly their linkage with plant hormone signaling pathways like abscisic acid and jasmonic acid. XIP-7A3, in particular, demonstrates a significant increase in expression upon FHB infection, highlighting its potential as a key candidate gene for enhancing wheat's resistance to this disease. This research not only enriches our understanding of the XIP gene family in wheat but also provides a foundation for future investigations into their role in developing FHB-resistant wheat cultivars. The findings offer significant implications for wheat genomics and breeding, contributing to the development of more resilient crops against fungal diseases.

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.

Update on the state of research to manage Fusarium head blight

Fusarium head blight (FHB) is one of the most devastating diseases of cereal crops, causing severe reduction in yield and quality of grain worldwide. In the United States, the major causal agent of FHB is the mycotoxigenic fungus, Fusarium graminearum. The contamination of grain with mycotoxins, including deoxynivalenol and zearalenone, is a particularly serious concern due to its impact on the health of humans and livestock. For the past few decades, multidisciplinary studies have been conducted on management strategies designed to reduce the losses caused by FHB. However, effective management is still challenging due to the emergence of fungicide-tolerant strains of F. graminearum and the lack of highly resistant wheat and barley cultivars. This review presents multidisciplinary approaches that incorporate advances in genomics, genetic-engineering, new fungicide chemistries, applied biocontrol, and consideration of the disease cycle for management of FHB.

Novel genomic regions on chromosome 5B controlling wheat powdery mildew seedling resistance under Egyptian conditions

Wheat powdery mildew (PM) causes significant yield losses worldwide. None of the Egyptian wheat cultivars was detected to be highly resistant to such a severe disease. Therefore, a diverse spring wheat panel was evaluated for PM seedling resistance using different Bgt conidiospores collected from Egyptian fields in two growing seasons. The evaluation was done in two separate experiments. Highly significant differences were found between the two experiments suggesting the presence of different isolates populations. Highly significant differences were found among the tested genotypes confirming the ability to improve PM resistance using the recent panel. Genome-wide association study (GWAS) was done for each experiment separately and a total of 71 significant markers located within 36 gene models were identified. The majority of these markers are located on chromosome 5B. Haplotype block analysis identified seven blocks containing the significant markers on chromosome 5B. Five gene models were identified on the short arm of the chromosome. Gene enrichment analysis identified five and seven pathways based on the biological process and molecular functions respectively for the detected gene models. All these pathways are associated with disease resistance in wheat. The genomic regions on 5B seem to be novel regions that are associated with PM resistance under Egyptian conditions. Selection of superior genotypes was done and Grecian genotypes seem to be a good source for improving PM resistance under Egyptian conditions.

Phenotyping Fusarium head blight through seed morphology characteristics using RGB imaging

Fusarium head blight (FHB) is an economically important disease affecting wheat and thus poses a major threat to wheat production. Several studies have evaluated the effectiveness of image analysis methods to predict FHB using disease-infected grains; however, few have looked at the final application, considering the relationship between cost and benefit, resolution, and accuracy. The conventional screening of FHB resistance of large-scale samples is still dependent on low-throughput visual inspections. This study aims to compare the performance of two cost-benefit seed image analysis methods, the free software "SmartGrain" and the fully automated commercially available instrument "Cgrain Value™" by assessing 16 seed morphological traits of winter wheat to predict FHB. The analysis was carried out on a seed set of FHB which was visually assessed as to the severity. The dataset is composed of 432 winter wheat genotypes that were greenhouse-inoculated. The predictions from each method, in addition to the predictions combined from the results of both methods, were compared with the disease visual scores. The results showed that Cgrain Value™ had a higher prediction accuracy of R ² = 0.52 compared with SmartGrain for which R ² = 0.30 for all morphological traits. However, the results combined from both methods showed the greatest prediction performance of R ² = 0.58. Additionally, a subpart of the morphological traits, namely, width, length, thickness, and color features, showed a higher correlation with the visual scores compared with the other traits. Overall, both methods were related to the visual scores. This study shows that these affordable imaging methods could be effective to predict FHB in seeds and enable us to distinguish minor differences in seed morphology, which could lead to a precise performance selection of disease-free seeds/grains.

Utilizing genomics and historical data to optimize gene pools for new breeding programs: A case study in winter wheat

With the rapid generation and preservation of both genomic and phenotypic information for many genotypes within crops and across locations, emerging breeding programs have a valuable opportunity to leverage these resources to 1) establish the most appropriate genetic foundation at program inception and 2) implement robust genomic prediction platforms that can effectively select future breeding lines. Integrating genomics-enabled¹ breeding into cultivar development can save costs and allow resources to be reallocated towards advanced (i.e., later) stages of field evaluation, which can facilitate an increased number of testing locations and replicates within locations. In this context, a reestablished winter wheat breeding program was used as a case study to understand best practices to leverage and tailor existing genomic and phenotypic resources to determine optimal genetics for a specific target population of environments. First, historical multi-environment phenotype data, representing 1,285 advanced breeding lines, were compiled from multi-institutional testing as part of the SunGrains cooperative and used to produce GGE biplots and PCA for yield. Locations were clustered based on highly correlated line performance among the target population of environments into 22 subsets. For each of the subsets generated, EMMs and BLUPs were calculated using linear models with the ‘lme4’ R package. Second, for each subset, TPs representative of the new SC breeding lines were determined based on genetic relatedness using the ‘STPGA’ R package. Third, for each TP, phenotypic values and SNP data were incorporated into the ‘rrBLUP’ mixed models for generation of GEBVs of YLD, TW, HD and PH. Using a five-fold cross-validation strategy, an average accuracy of r = 0.42 was obtained for yield between all TPs. The validation performed with 58 SC elite breeding lines resulted in an accuracy of r = 0.62 when the TP included complete historical data. Lastly, QTL-by-environment interaction for 18 major effect genes across three geographic regions was examined. Lines harboring major QTL in the absence of disease could potentially underperform (e.g., Fhb1 R-gene), whereas it is advantageous to express a major QTL under biotic pressure (e.g., stripe rust R-gene). This study highlights the importance of genomics-enabled breeding and multi-institutional partnerships to accelerate cultivar development.

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.

The Change in Winter Wheat Response to Deoxynivalenol and Fusarium Head Blight Through Technological and Agronomic Progress

Fusarium head blight (FHB) in wheat causes yield loss, quality reduction, and mycotoxin contamination in temperate wheat production areas worldwide. The objective of this study was to quantify the progress of agronomic and FHB management strategies over the past two decades in FHB suppression and agronomic performance of winter wheat in environments favorable for FHB. Field experiments were conducted in environments typical of FHB epidemics to compare common agronomic and FHB management practices used in the 1996 era compared with those used in 2016. The experiments included a comparison of three different nitrogen (N) fertilizer application rates and six old (1996-era) and new (modern-era) winter wheat cultivars representing combinations of susceptibility and era to FHB, with and without a fungicide applied at flowering (pydiflumetofen + propiconazole). To mimic environments favorable for infection (similar to 1996 in Ontario, Canada), plots were challenged at 50% anthesis with F. graminearum macroconidia suspension followed by mist irrigation. The modern management strategy of using moderately resistant cultivars, a fungicide applied at flowering, and a high rate of N fertilizer reduced total deoxynivalenol by 67%, reduced Fusarium-damaged kernels by 49%, reduced FHB index by 86%, increased grain test weight by 11%, and increased grain yield by 31% compared with the standard management practice of seeding highly susceptible cultivars with no fungicide and a lower rate of N fertilizer recommended in the 1996 era. This study enabled a published economic assessment of the return on investment for the improvements in cultivars, fungicide, and N fertilizer applications since 1996.