Genome-Wide Association Mapping of Fusarium Head Blight Resistance in Spring Wheat Lines Developed in the Pacific Northwest and CIMMYT

Evaluation of Fusarium Head Blight Resistance Effects by Haplotype-Based Genome-Wide Association Study in Winter Wheat Lines Derived by Marker Backcrossing Approach

Fusarium head blight (FHB) of wheat caused by Fusarium species is a destructive disease, causing grain yield and quality losses. Developing FHB-resistant cultivars is crucial to minimize the extent of the disease. The first objective of this study was incorporation of Fhb1 from a resistant donor into five Polish wheat breeding lines with good agronomical traits and different origins. We also performed a haplotype-based GWAS to identify chromosome regions in derived wheat families associated with Fusarium head blight resistance. As a result of marker-assisted backcrossing (MABC), five wheat combinations were obtained. Fungal inoculation and disease assessment were conducted for two years, 2019 and 2020. In 2019 the average phenotypic response of type II resistance was 2.2, whereas in 2020 it was 2.1. A haploblock-based GWAS performed on 10 phenotypic traits (related to type of resistance, year of experiment and FHB index) revealed nine marker-trait associations (MTA), among which six belong to chromosome 2D, two to 3B and one to 7D. Phenotypic variation (R²) explained by the identified haplotypes in haploblocks ranged from 6% to 49%. Additionally, an association weight matrix (AWM) was created, giving the partial correlation-information theory (PCIT) pipeline of 171 edges and 19 nodes. The resultant data and high level of explained phenotypic variance of MTA create the opportunity for data utilization in MAS.

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.

Two decades of association mapping: Insights on disease resistance in major crops

Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.

Novel Quantitative Trait Loci for Grain Cadmium Content Identified in Hard White Spring Wheat

Cadmium (Cd) is a heavy metal that can cause a variety of adverse effects on human health, including cancer. Wheat comprises approximately 20% of the human diet worldwide; therefore, reducing the concentrations of Cd in wheat grain will have significant impacts on the intake of Cd in food products. The tests for measuring the Cd content in grain are costly, and the content is affected significantly by soil pH. To facilitate breeding for low Cd content, this study sought to identify quantitative trait loci (QTL) and associated molecular markers that can be used in molecular breeding. One spring wheat population of 181 doubled haploid lines (DHLs), which was derived from a cross between two hard white spring wheat cultivars "UI Platinum" (UIP) and "LCS Star" (LCS), was assessed for the Cd content in grain in multiple field trials in Southeast Idaho, United States. Three major QTL regions, namely, QCd.uia2-5B, QCd.uia2-7B, and QCd.uia2-7D, were identified on chromosomes 5B, 7B, and 7D, respectively. All genes in these three QTL regions were identified from the NCBI database. However, three genes related to the uptake and transport of Cd were used in the candidate gene analysis. The sequences of TraesCS5B02G388000 (TaHMA3) in the QCd.uia2-5B region and TraesCS7B02G320900 (TaHMA2) and TraesCS7B02G322900 (TaMSRMK3) in the QCd.uia2-7B region were compared between UIP and LCS. TaHMA2 on 7B is proposed for the first time as a candidate gene for grain Cd content in wheat. A KASP marker associated with this gene was developed and it will be further validated in near-isogenic lines via a gene-editing system in future studies.

QTL mapping for grain yield and three yield components in a population derived from two high-yielding spring wheat cultivars

Four genomic regions on chromosomes 4A, 6A, 7B, and 7D were discovered, each with multiple tightly linked QTL (QTL clusters) associated with two to three yield components. The 7D QTL cluster was associated with grain yield, fertile spikelet number per spike, thousand kernel weight, and heading date. It was located in the flanking region of FT-D1, a homolog gene of Arabidopsis FLOWERING LOCUS T, a major gene that regulates wheat flowering. Genetic manipulation of yield components is an important approach to increase grain yield in wheat (Triticum aestivum). The present study used a mapping population comprised of 181 doubled haploid lines derived from two high-yielding spring wheat cultivars, UI Platinum and LCS Star. The two cultivars and the derived population were assessed for six traits in eight field trials primarily in Idaho in the USA. The six traits were grain yield, fertile spikelet number per spike, productive tiller number per unit area, thousand kernel weight, heading date, and plant height. Quantitative Trait Locus (QTL) analysis of the six traits was conducted using 14,236 single-nucleotide polymorphism (SNP) markers generated from the wheat 90 K SNP and the exome and promoter capture arrays. Of the 19 QTL detected, 14 were clustered in four chromosomal regions on 4A, 6A, 7B and 7D. Each of the four QTL clusters was associated with multiple yield component traits, and these traits were often negatively correlated with one another. As a result, additional QTL dissection studies are needed to optimize trade-offs among yield component traits for specific production environments. Kompetitive allele-specific PCR markers for the four QTL clusters were developed and assessed in an elite spring wheat panel of 170 lines, and eight of the 14 QTL were validated. The two parents contain complementary alleles for the four QTL clusters, suggesting the possibility of improving grain yield via genetic recombination of yield component loci.

Identification of Fusarium head blight resistance loci in two Brazilian wheat mapping populations

Fusarium head blight (FHB) is a disease of wheat (Triticum aestivum L.) that causes major yield losses in South America, as well as many other wheat growing regions around the world. FHB results in low quality, contaminated grain due to the production of mycotoxins such as deoxynivalenol (DON). In Brazil, FHB outbreaks are increasing in frequency and are currently controlled by fungicides which are costly and potentially harmful to the wider environment. To identify the genetic basis of resistance to FHB in Brazilian wheat, two mapping populations (Anahuac 75 × BR 18-Terena and BR 18-Terena × BRS 179) segregating for FHB resistance were phenotyped and quantitative trait loci (QTL) analysis was undertaken to identify genomic regions associated with FHB-related traits. A total of 14 QTL associated with FHB visual symptoms were identified, each of which explained 3.7–17.3% of the phenotypic variance. Two of these QTL were stable across environments. This suggests FHB resistance in Anahuac 75, BR 18-Terena and BRS 179 is controlled by multiple genetic loci that confer relatively minor differences in resistance. A major, novel QTL associated with DON accumulation was also identified on chromosome 4B (17.8% of the phenotypic variance), as well as a major QTL associated with thousand-grain weight on chromosome 6B (16.8% phenotypic variance). These QTL could be useful breeding targets, when pyramided with major sources of resistance such as Fhb1, to improve grain quality and reduce the reliance on fungicides in Brazil and other countries affected by FHB.

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

BACKGROUND

Soil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield.

RESULT

In this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTLs were significantly associated with plant height, spike number, spike length, grain number, thousand kernels weight, yield and biological mass under different salt treatments, with the phenotypic explanation rate (R²) ranging from 9.14 to 50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits such as thousand kernels weight, spike number, spike length, grain number and so on under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding.

CONCLUSION

Utilizing a Wheat660K SNPs chip, QTLs for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.

Characterizing Winter Wheat Germplasm for Fusarium Head Blight Resistance Under Accelerated Growth Conditions

Fusarium head blight (FHB) is one of the economically important diseases of wheat as it causes severe yield loss and reduces grain quality. In winter wheat, due to its vernalization requirement, it takes an exceptionally long time for plants to reach the heading stage, thereby prolonging the time it takes for characterizing germplasm for FHB resistance. Therefore, in this work, we developed a protocol to evaluate winter wheat germplasm for FHB resistance under accelerated growth conditions. The protocol reduces the time required for plants to begin heading while avoiding any visible symptoms of stress on plants. The protocol was tested on 432 genotypes obtained from a breeding program and a genebank. The mean area under disease progress curve for FHB was 225.13 in the breeding set and 195.53 in the genebank set, indicating that the germplasm from the genebank set had higher resistance to FHB. In total, 10 quantitative trait loci (QTL) for FHB severity were identified by association mapping. Of these, nine QTL were identified in the combined set comprising both genebank and breeding sets, while two QTL each were identified in the breeding set and genebank set, respectively, when analyzed separately. Some QTLs overlapped between the three datasets. The results reveal that the protocol for FHB evaluation integrating accelerated growth conditions is an efficient approach for FHB resistance breeding in winter wheat and can be even applied to spring wheat after minor modifications.

Genetic Characterization of a Wheat Association Mapping Panel Relevant to Brazilian Breeding Using a High-Density Single Nucleotide Polymorphism Array

Bread wheat (Triticum aestivum L.) is one of the world’s most important crops. Maintaining wheat yield gains across all of its major production areas is a key target toward underpinning global food security. Brazil is a major wheat producer in South America, generating grain yields of around 6.8 million tons per year. Here, we establish and genotype a wheat association mapping resource relevant to contemporary Brazilian wheat breeding programs. The panel of 558 wheat accessions was genotyped using an Illumina iSelect 90,000 single nucleotide polymorphism array. Following quality control, the final data matrix consisted of 470 accessions and 22,475 polymorphic genetic markers (minor allele frequency ≥5%, missing data <5%). Principal component analysis identified distinct differences between materials bred predominantly for the northern Cerrado region, compared to those bred for southern Brazilian agricultural areas. We augmented the genotypic data with 26 functional Kompetitive Allele-Specific PCR (KASP) markers to identify the allelic combinations at genes with previously known effects on agronomically important traits in the panel. This highlighted breeding targets for immediate consideration – notably, increased Fusarium head blight resistance via the Fhb1 locus. To demonstrate the panel’s likely future utility, genome-wide association scans for several phenotypic traits were undertaken. Significant (Bonferroni corrected P < 0.05) marker-trait associations were detected for Fusarium kernel damage (a proxy for type 2 Fusarium resistance), identifying previously known quantitative trait loci in the panel. This association mapping panel represents an important resource for Brazilian wheat breeding, allowing future genetic studies to analyze multiple agronomic traits within a single genetically diverse population.

Identification of a novel genomic region associated with resistance to Fusarium crown rot in wheat

Genome-wide association study (GWAS) on 358 Chinese wheat germplasms and validation in a biparental population identified a novel significant genomic region on 5DL for FCR resistance. Fusarium crown rot (FCR) is a chronic and severe disease in many dryland wheat-producing areas worldwide. In the last few years, the incidence and severity of FCR progressively increased in China, and the disease has currently become a new threat to local wheat crops. Here, we report a genome-wide association study (GWAS) on a set of 358 Chinese germplasms with the wheat 55 K SNP array. A total of 104 SNPs on chromosomes 1BS, 1DS, 2AL, 5AL, 5DS, 5DL, 6BS and 7BL were significantly associated with seedling resistance to FCR in the association panel. Of these SNPs, a novel 13.78 Mb region targeted by five SNPs on chromosome arm 5DL was continually detected in all three trials. The effects of this region on FCR resistance was confirmed in biparental population. qRT-PCR showed that within this 5DL region, several genes encoding TIR-NBS-LRR proteins and proteins related to mycotoxins deoxynivalenol (DON) detoxification increased rapidly in the disease-resistant variety 04 Zhong 36 than the susceptible variety Xinmai 26 after inoculation. Our study provides new insights into gene discovery and creation of new cultivars with desirable alleles for improving FCR resistance in wheat.

Fusarium head blight in wheat: contemporary status and molecular approaches

Fusarium head blight (FHB) disease that occurs in wheat is caused by Fusarium graminearum and is a major risk to wheat yield. Although several research efforts focusing on FHB have been conducted in the past several decades, conditions have become more critical due to the increase in its virulent forms. In such a scenario, conferring complete resistance in plants seems to be difficult for handling this issue. The phenotyping for FHB and finding a solution for it at the genetic level comprises a long-term process as FHB infection is largely affected by environmental conditions. Modern molecular strategies have played a crucial role in revealing the host-pathogen interaction in FHB. The integration of molecular biology-based methods such as genome-wide association studies and marker-based genomic selection has provided potential cultivars for breeding programs. In this review, we aim at outlining the contemporary status of the studies conducted on FHB in wheat. The influence of FHB in wheat on animals and human health is also discussed. In addition, a summary of the advancement in the molecular technologies for identifying and developing the FHB-resistant wheat genetic resources is provided. It also suggests the future measures that are required to reduce the world's vulnerability to FHB which was one of the main goals of the US Wheat and Barley Scab Initiative.

Genome-Wide Association Analysis of Fusarium Head Blight Resistance in Chinese Elite Wheat Lines

Fusarium head blight (FHB) is a devastating wheat disease worldwide. To decipher the genetic architecture of FHB resistance in Chinese germplasm, a Wheat Association Panel for Scab Research (WAPS) consisting of 240 leading Chinese wheat cultivars and elite lines was genotyped using the 90K single nucleotide polymorphism (SNP) arrays. The FHB response was evaluated in the field nurseries in Wuhan in Hubei Province over four consecutive years from 2014 to 2017. Five quantitative trait loci (QTL) were consistently identified on chromosome arms 1AS, 2DL, 5AS, 5AL, and 7DS using a mixed linear model (MLM), explaining 5.6, 10.3, 5.7, 5.4, and 5.6% of phenotypic variation, respectively. The QTL on 5AS, 5AL, and 7DS QTL are probably novel. The allelic frequency analysis indicated that cultivars from the Middle and Lower Yangtze River Valleys harbored more favorable alleles and were therefore more resistant than those from other regions. To facilitate in-house germplasm screening and marker-assisted selection (MAS), SNP-derived PCR markers were developed for the QTL regions on 1AS, 5AS, and 5AL QTL. In addition to the above five QTL, the WAPS population had a very low frequency of Fhb1, confirming that the gene is not widely used in Chinese wheat breeding programs. The resistant lines and molecular markers developed in this study are resources and information for enhancing FHB resistance in breeding populations by marker-assisted recurrent selection and gene stacking.

Characterization of the Genetic Architecture for Fusarium Head Blight Resistance in Durum Wheat: The Complex Association of Resistance, Flowering Time, and Height Genes

Durum wheat is an economically important crop for Canadian farmers. Fusarium head blight (FHB) is one of the most destructive diseases that threatens durum production in Canada. FHB reduces yield and end-use quality and most commonly contaminates the grain with the fungal mycotoxin deoxynivalenol, also known as DON. Serious outbreaks of FHB can occur in durum wheat in Canada, and combining genetic resistance with fungicide application is a cost effective approach to control this disease. However, there is limited variation for genetic resistance to FHB in elite Canadian durum cultivars. To explore and identify useful genetic FHB resistance variation for the improvement of Canadian durum wheat, we assembled an association mapping (AM) panel of diverse durum germplasms and performed genome wide association analysis (GWAS). Thirty-one quantitative trait loci (QTL) across all 14 chromosomes were significantly associated with FHB resistance. On 3BS, a stable QTL with a larger effect for resistance was located close to the centromere of 3BS. Three haplotypes of Fhb1 QTL were identified, with an emmer wheat haplotype contributing to disease susceptibility. The large number of QTL identified here can provide a rich resource to improve FHB resistance in commercially grown durum wheat. Among the 31 QTL most were associated with plant height and/or flower time. QTL 1A.1, 1A.2, 3B.2, 5A.1, 6A.1, 7A.3 were associated with FHB resistance and not associated or only weakly associated with flowering time nor plant height. These QTL have features that would make them good targets for FHB resistance breeding.

Fusarium Head Blight in Durum Wheat: Recent Status, Breeding Directions, and Future Research Prospects

Fusarium head blight (FHB) is a major fungal disease affecting wheat production worldwide. Since the early 1990s, FHB, caused primarily by Fusarium graminearum, has become one of the most significant diseases faced by wheat producers in Canada and the United States. The increasing FHB problem is likely due to the increased adoption of conservation tillage practices, expansion of maize production, use of susceptible wheat varieties in rotation, and climate variability. Durum wheat (Triticum turgidum sp. durum) is notorious for its extreme susceptibility to FHB and breeding for resistance is complicated because sources of FHB resistance are rare in the primary gene pool of tetraploid wheat. Losses due to this disease include yield, test weight, seed quality, food and feed quality, and when severe, market access. More importantly, it is the contamination with mycotoxins, such as deoxynivalenol, in Fusarium-infected durum kernels that causes the most serious economic as well as food and feed safety concerns. Several studies and thorough reviews have been published on germplasm development and breeding for FHB resistance and the genetics and genomics of FHB resistance in bread or common wheat (T. aestivum); however, similar reviews have not been conducted in durum wheat. Thus, the aim of this review is to summarize and discuss the recent research efforts to mitigate FHB in durum wheat, including quantitative trait locus mapping, genome-wide association studies, genomic prediction, mutagenesis and characterization of genes and pathways involved in FHB resistance. It also highlights future directions, FHB-resistant germplasm, and the potential role of morphological traits to enhance FHB resistance in durum wheat.

Genetic Mapping and Prediction Analysis of FHB Resistance in a Hard Red Spring Wheat Breeding Population

Fusarium head blight (FHB) is one of the most destructive diseases in wheat worldwide. Breeding for FHB resistance is hampered by its complex genetic architecture, large genotype by environment interaction, and high cost of phenotype screening. Genomic selection (GS) is a powerful tool to enhance improvement of complex traits such as FHB resistance. The objectives of this study were to (1) investigate the genetic architecture of FHB resistance in a North Dakota State University (NDSU) hard red spring wheat breeding population, (2) test if the major QTL Fhb1 and Fhb5 play an important role in this breeding population; and (3) assess the potential of GS to enhance breeding efficiency of FHB resistance. A total of 439 elite spring wheat breeding lines from six breeding cycles were genotyped using genotyping-by-sequencing (GBS) and 102,147 SNP markers were obtained. Evaluation of FHB severity was conducted in 10 unbalanced field trials across multiple years and locations. One QTL for FHB resistance was identified and located on chromosome arm 1AL, explaining 5.3% of total phenotypic variation. The major type II resistance QTL Fhb1 only explained 3.1% of total phenotypic variation and the QTL Fhb5 was not significantly associated with FHB resistance in this breeding population. Our results suggest that integration of many genes with medium/minor effects in this breeding population should provide stable FHB resistance. Genomic prediction accuracies of 0.22-0.44 were obtained when predicting over breeding cycles in this study, indicating the potential of GS to enhance the improvement of FHB resistance.

Genome-Wide Association Mapping of Resistance to Fusarium Head Blight Spread and Deoxynivalenol Accumulation in Chinese Elite Wheat Germplasm

Improving resistance to Fusarium head blight (FHB) in wheat is crucial in the integrated management of the disease and prevention of deoxynivalenol (DON) contamination in grains. To identify novel sources of resistance, a genome-wide association study (GWAS) was performed using a panel of 213 accessions of elite wheat germplasm of China. The panel was evaluated for FHB severity in four environments and DON content in grains in two environments. High correlations across environments and high heritability were observed for FHB severity and DON content in grains. The panel was also genotyped with the 90K Illumina iSelect single nucleotide polymorphism (SNP) array and 11,461 SNP markers were obtained. The GWAS revealed a total of six and three loci significantly associated with resistance to fungal spread and DON accumulation in at least two environments, respectively. QFHB-2BL.1 tagged by IWB52433 and QFHB-3A tagged by IWB50548 were responsible for resistance to both fungal spread and DON accumulation. In summary, this study provided an overview of FHB resistance resources in elite Chinese wheat germplasm and identified novel resistance loci that could be used for wheat improvement.

The role of adapted and non-adapted resistance sources in breeding resistance of winter wheat to Fusarium head blight and deoxynivalenol contamination

Since resistance is the most important agent in regulating deoxynivalenol (DON), breeding for higher resistance is the key to improve food safety. Fusarium damaged kernels (FDK) show a closer correlation with DON than visual symptoms. This implies a difference in genetic regulation. For this reason, the mapping should be extended not only for the visual symptoms, but also for FDK and DON. Quantitative trait loci influencing only Fusarium head blight (FHB) symptoms, may not be relevant for FDK and DON. Type I and II were pooled to overall resistance at spray inoculation. From 2010 to 2016 three selection platforms were compared by checking running variety breeding programs. The use of exotic sources in breeding significantly increased the number of more resistant genotypes in each selection phase from F3-F8 generations compared to the control program where crosses were not planned for FHB resistance and screening in early generations was also not performed. However, also in this breeding platform – at a lower rate – moderately or highly resistant genotypes could be selected. Of them, eight cultivars were/are in commercial production. The Fusarium breeding program using only adapted and more resistant parents generally gave closer results to exotic breeds, and several highly resistant genotypes were produced as a result. For winter wheat the phenotypic screening at high disease pressure is the key to select highly resistant materials. At low infection pressure the high and medium resistant genotypes come in the same group. The use of more isolates increases the chance to have strong selection pressure each year. FHB resistance was combined with leaf rust, yellow rust, powdery mildew, leaf spot resistance and high protein content (15-18%). The cultivar registration and post registration screening is the key in improving food safety in commercial production.

QTL identification and KASP marker development for productive tiller and fertile spikelet numbers in two high-yielding hard white spring wheat cultivars

Selecting high-yielding wheat cultivars with more productive tillers per unit area (PTN) combined with more fertile spikelets per spike (fSNS) is difficult. QTL mapping of these traits may aid understanding of this bottleneck and accelerate precision breeding for high yield via marker-assisted selection. PTN and fSNS were assessed in four to five trials from 2015 to 2017 in a doubled haploid population derived from two high-yielding cultivars "UI Platinum" and "SY Capstone." Two QTL for PTN (QPTN.uia-4A and QPTN.uia-6A) and four QTL for fSNS (QfSNS.uia-4A, QfSNS.uia-5A, QfSNS.uia-6A, and QfSNS.uia-7A) were identified. The effects of the QTL were primarily additive and, therefore, pyramiding of multiple QTL may increase PTN and fSNS. However, the two QTL for PTN were positioned in the flanking regions for the two QTL for fSNS on chromosomes 4A and 6A, respectively, suggesting either possible pleiotropic effect of the same QTL or tightly linked QTL and explaining the difficulty of selecting both high PTN and fSNS in phenotypic selection. Kompetitive allele-specific PCR (KASP) markers for all identified QTL were developed and validated in a recombinant inbred line (RIL) population derived from the same two cultivars. In addition, KASP markers for three of the QTL (QPTN.uia-6A, QfSNS.uia-6A, and QfSNS.uia-7A) were further validated in a diverse spring wheat panel, indicating their usefulness under different genetic backgrounds. These KASP markers could be used by wheat breeders to select high PTN and fSNS.

Evaluation of the Potential for Genomic Selection to Improve Spring Wheat Resistance to Fusarium Head Blight in the Pacific Northwest

Fusarium Head Blight (FHB) has emerged in spring wheat production in Pacific Northwest during the last decade due to factors including climate changes, crop rotations, and tillage practices. A breeding population with 170 spring wheat lines was established and screened over a 2-year period in multiple locations for FHB incidence (INC), severity (SEV), and deposition of the mycotoxin, deoxynivalenol (DON). A genome-wide association study suggested that the detectable number of genetic loci and effects are limited for marker-assisted selection. In conjunction with the success of breeding on FHB resistance in other programs, genomic selection (GS) was suggested as a better option. To evaluate the prediction accuracy of GS in the current breeding population, we conducted a variety of validations by varying proportions of testing populations and cohorts based on both FHB resistance and market class, including soft white spring (SWS), hard white spring (HWS), and hard red spring (HRS). We found that INC had higher heritability, higher correlation across years and locations, and higher prediction accuracy than SEV and DON. Prediction accuracy varied among the scenarios that restricted the testing population to a certain cohort. For a small set of newly developed or introduced lines (<17), prediction accuracy will be about 60% if the lines have similar genetic relationships as those among the current 170-line training population. However, we expect a lower prediction accuracy if new lines are selected for a specific characteristic, such as FHB resistance or market class. With the exception of DON in the SWS lines, the current training population is capable of making reasonably accurate predictions for FHB-resistant lines in most of the major market classes. For SWS, adding more lines or further phenotyping is required to improve prediction accuracy. These results demonstrate the potential and challenges of GS, especially for developing FHB-resistant varieties in the SWS market class.

QTL identification and KASP marker development for productive tiller and fertile spikelet numbers in two high-yielding hard white spring wheat cultivars

Selecting high-yielding wheat cultivars with more productive tillers per unit area (PTN) combined with more fertile spikelets per spike (fSNS) is difficult. QTL mapping of these traits may aid understanding of this bottleneck and accelerate precision breeding for high yield via marker-assisted selection. PTN and fSNS were assessed in four to five trials from 2015 to 2017 in a doubled haploid population derived from two high-yielding cultivars "UI Platinum" and "SY Capstone." Two QTL for PTN (QPTN.uia-4A and QPTN.uia-6A) and four QTL for fSNS (QfSNS.uia-4A, QfSNS.uia-5A, QfSNS.uia-6A, and QfSNS.uia-7A) were identified. The effects of the QTL were primarily additive and, therefore, pyramiding of multiple QTL may increase PTN and fSNS. However, the two QTL for PTN were positioned in the flanking regions for the two QTL for fSNS on chromosomes 4A and 6A, respectively, suggesting either possible pleiotropic effect of the same QTL or tightly linked QTL and explaining the difficulty of selecting both high PTN and fSNS in phenotypic selection. Kompetitive allele-specific PCR (KASP) markers for all identified QTL were developed and validated in a recombinant inbred line (RIL) population derived from the same two cultivars. In addition, KASP markers for three of the QTL (QPTN.uia-6A, QfSNS.uia-6A, and QfSNS.uia-7A) were further validated in a diverse spring wheat panel, indicating their usefulness under different genetic backgrounds. These KASP markers could be used by wheat breeders to select high PTN and fSNS.