Browsing by Subject "Fusarium head blight"
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Item Association Mapping and Genome-Wide Prediction of Fusarium Head Blight Resistance in Minnesota Wheat Lines(2021-12) Conley, EmilyTriticum aestivum L. (common wheat) is one of the top three global staple crops, with both record production and consumption forecasted by the USDA for 2021-22. The University of Minnesota’s Wheat Breeding program has developed wheat cultivars and conducted wheat breeding and genetics research for over a century. Breeding for disease resistance is a major priority. Fusarium head blight (FHB), or scab, is a fungal disease of wheat and other small grain crops causing significant yield and quality reduction. FHB has been a major focus for wheat breeding and research. Quantitative trait locus (QTL) mapping studies have identified hundreds of QTL, while only a handful have been successfully deployed in breeding. The University of Minnesota introduced resistant germplasm from Asia in the late 1980s. Genome-wide association mapping (GWAS) uses high density genetic markers and historic linkage disequilibrium to uncover genetic associations between genotypes and phenotypes. Through GWAS, this study identified QTL maintained in the program over decades of phenotypic and marker-assisted selection. Genome-wide selection (GS), a molecular marker-based method for improving quantitative traits, has shown promise for FHB resistance breeding. This study investigated strategies to implement genome-wide selection for FHB resistance during cultivar development. Genome-wide selection has the potential to reduce time and cost and accelerate the rate of genetic gain.Item Characterization and quantitative trait loci (QTL) mapping of Fusarium head blight resistance-related traits in the Japanese wheat landrace, PI 81791 (Sapporo Haru Komugi Jugo)(2010-04) Quirin, Edmund AndrewFusarium head blight (FHB) is a destructive disease of wheat (Triticum aestivum L.). Infection by Fusarium graminearum affects yield and grain quality traits that can lead to substantial economic losses. Developing resistant cultivars has been a major objective of plant breeders for controlling FHB. The objective of this study was to assess FHB resistance in the Japanese landrace, PI 81791 (Sapporo Haru Komugi Jugo), a line that does not possess the widely used Fhb1 QTL for type II resistance. A population of 150 recombinant inbred lines (RILs) was developed from a cross between this genotype and the susceptible variety, Wheaton, and was assessed for several resistance-related traits, including type I and II resistance, post-harvest grain traits, and agronomic traits in four field environments in Minnesota. Type II resistance was also assessed in two greenhouse environments. The RILs were genotyped using 377 microsatellite markers. Composite interval mapping detected QTL for resistance traits on chromosomes 2B, 3A, 3B, 3D, 4A, 4D, 5A, 5B and 6A and for heading date and height on 1B, 2D, 3B and 4D. The resistance QTL on chromosomes 2B, 3B, and 3D explain the largest amount of variation observed for many of the resistance traits analyzed with alleles being inherited from PI 81791. The QTL on chromosome 3B in the interval of Xbarc229 – Xgwm383b appears to be a major novel resistance locus that explains 7 – 21% of the variation observed for various resistance traits. Similar QTL regions to those on chromosome 2B in the interval of Xgwm639b – Xwmc339 and chromosome 3D in the interval of Xwmc533a – Xwmc656 have been previously reported, supporting their use for FHB resistance breeding. Major resistance QTL were also identified on chromosomes 4A, associated with Xbarc233, and 4D, which is associated with the semi-dwarfing gene, Rht-D1. However, these QTL are likely associated with increased susceptibility from PI 81791 and Wheaton, respectively. Additional type II resistance QTL were identified on 3A in greenhouse environments, explaining as much as 23.2 and 15.8% of the phenotypic variation observed.Item Combating Fusarium Head Blight Resistance in Wheat with Genomic Selection and Computer Vision Technology(2022-01) Adeyemo, EmmanuelFusarium head blight (FHB), primarily caused by Fusarium graminarum, Schwabe, is a devastating fungal disease that limits wheat production globally and can significantly reduce yield and grain quality. At the University of Minnesota, screening for FHB begins at the F5 stage and continues annually until the line is released as a cultivar. Before implementing genomic selection at the F5 stage in 2016, we evaluated ~ 3,000 F5 lines annually in field nurseries. The use of genomic selection allowed the prediction of untested lines with a training population of 500 lines selected by pedigree information. The first study showed that a set of 200 lines selected by genomic relationship led to predictive abilities of up to 0.49, whereas a larger, randomly selected subset of 500 F5 lines had a maximum predictive ability of 0.34. While the addition of parents also led to increased predictive abilities, the increments were not significant in most cases. The second study examined the merit of incorporating available germplasm into our existing genomic selection pipeline. We observed that training populations that contained historical data were less useful while those that included a subset of 200 F5 lines selected by genomic relationship, were more effective for predicting FHB. The third study demonstrated the use of computer vision to estimate the percentage of kernels damaged by Fusarium. We utilized 85 samples containing five check cultivars with varying levels of FHB susceptibility and maturity and achieved an accuracy of 90%. Additional studies should be done to assess the utilization of this technology among our experimental lines.Item Factors affecting Fusarium head blight development and trichothecene accumulation in fusarium-infected wheat heads.(2010-06) Gautam, PravinFusarium head blight (FHB), primarily caused by Fusarium graminearum Schwabe, is an economically important disease as it results in yield loss and quality losses of infected grain and the accumulation of mycotoxins produced by the invading fungus. Environmental factors, host genetics, and isolate aggressiveness impact FHB development and subsequently trichothecene production and accumulation. Though it is well established that moisture around anthesis promotes FHB development and trichothecene accumulation, the role of moisture, either in the form of rainfall or mist-irrigation during the period from anthesis to harvest has been largely overlooked. A three year field experiment was conducted in 2006, 2007 and 2008 to examine the influence of environmental factors, especially moisture, host resistance, and pathogen variation with respect to mycotoxin production capacity and pathogen aggressiveness, on infection, FHB development and mycotoxin production and accumulation in planta. In mature harvested grain FHB severity, visually scabby kernel (VSK) and mycotoxin concentration were significantly higher in Wheaton (FHB susceptible) than in the other two cultivars examined, Alsen and 2375. Although FHB severities were not significantly different in plots receiving different durations of mist-irrigation, VSK were significantly lower in the treatments receiving the least amount of mist-irrigation (14 DAI) than for treatments receiving mist-irrigation for longer periods, suggesting that extended periods of moisture promote disease development. DON concentration in harvested grain was, however, significantly lower in the treatment receiving the longest duration of mist-irrigation than those treatments receiving less water. In the whole head samples, which were collected 0, 7, 11, 14, 21, 28 and 41 days after inoculation, DON and other trichothecenes either declined with increased durations of mist-irrigation or remained low while water was being applied by the misting system. However, trichothecene accumulation was observed to increase after the cessation of mist-irrigation, with increases being most pronounced for the treatments with shorter mist-irrigation periods. The largest reduction in DON observed as a result of extended mist-irrigation periods was seen in the susceptible cultivar Wheaton. The influence of host resistance and pathogen variation on infection, FHB infection, disease development and mycotoxin accumulation in planta was examined in the series of greenhouse experiments utilizing point and spray inoculations. The levels of FHB severity and mycotoxins were higher in spray inoculated experiment than point inoculation in all cultivars examined. Wheaton (FHB susceptible) had the highest FHB severity and levels of mycotoxins. Alsen (moderately resistant to FHB) had significantly lower FHB severities, DON, 15-ADON, 3-ADON and NIV than either 2375 or Wheaton. Though there were no significant differences in initial infection among cultivars examined, Alsen had reduced spread of FHB symptoms from initial infection presumably due to type II resistance. DON production did not peak in all treatments, but where evident, the peak was earlier in 2375 (11 dai) than Alsen and Wheaton (21 or 14 dai). Multiple peaks and declines in DON levels were also evident. The performance of isolates was highly variable, though generally isolates Butte86Ada-11 and B63A were the most aggressive isolates and 49-3 and B45A were the least. The impact of free moisture, such as that from irrigation systems or rainfall, on mycotoxin accumulation was evaluated in greenhouse experiments. Despite the similar levels of FHB severity observed, the levels of mycotoxins were significantly less in the plants that received a single six hour wetting treatment compared to the respective control. The loss of DON and other mycotoxins was evident in all cultivars examined. Further, DON and 15-ADON were detected in run-off water. The results of these studies suggest that the availability of free moisture such as from mist-irrigation or rainfall may increase FHB severity and VSK, although DON and other trichothecene concentrations may be concomitantly reduced. Leaching appears to contribute to reductions in DON following wetting events.Item Fine mapping coincident QTL on a chromosome 6H introgression region from unadapted germplasm into elite malting barley(2017-01) Yin, LuBreeders strive to improve a cultivar for multiple traits. This can be challenging when these traits are unfavorably associated. This study fine maps several traits associated with the centromeric region of chromosome 6H by mendelizing the region using near-isogenic lines (NILs). A NIL carrying an introgression from the landrace Chevron for this region was crossed to a malting cultivar Lacey to create 1941 F2 individuals from which recombinant NILs (rNILs) for the introgressed region were developed. We developed a dense genetic map using 249 F4-derived rNILs and phenotyped 101 of them in field and greenhouse trials for fourteen traits. We observed transgressive segregation for Fusarium head blight (FHB) severity, grain protein concentration (GPC), days to senescence, normalized difference vegetation index (NDVI), seedling net blotch, and heading date. We detected QTL for eleven traits. For ten of the traits, we detected multiple QTL with opposite allelic effects for each of them. Six traits that showed transgressive segregation mapped to multiple QTL with opposite allelic effects. QTL for deoxynivalenol (DON) accumulation mapped to separate regions to that for GPC and FHB severity, suggesting DON accumulation was likely associated through linkage rather than pleiotropy to GPC and FHB severity. While there was no recombinant line possessing all favorable alleles in this region, we identified two rNILs with numerically lower FHB severity and DON accumulation and GPC similar to Lacey. Seven traits (NDVI, days to senescence, percent stem breakage, GPC, heading date, adult net blotch severity and seedling net blotch severity) mapped to a single region, close to the physical location of the NAM-1/Gpc-1 gene. This gene is known to encode a NAC transcription factor that might be involved in nitrogen remobilization from leaves to grains during senescence. Findings in this study about coincident QTL controlling days to senescence, NDVI, percent stem breakage, and GPC might aid in the understanding of nitrogen remobilization process. Our fine mapping study revealed a complex genetic architecture for eleven traits associated with this chromosome 6H region and highlights the need for recombination to uncouple unfavorable linkages in breeding programs.Item Genetic variance, transgressive segregation, and genomic selection prediction accuracy for Fusarium head blight resistance in advanced multi-parent barley breeding populations(2013-04) Kumar, Leticia M.The contemporary era of molecular breeding includes predicting breeding values based on allelic value estimations with genome-wide markers. The overarching objective of this thesis is to assess the potential use of genomic markers in predicting genetic variance, transgressive segregation, and breeding values within barley breeding populations in the context of Fusarium head blight (FHB) resistance. Chapter One investigates prediction of genetic variance and transgressive segregation using measures of phenotypic and genotypic parental dissimilarity. To a limited extent, phenotypic dissimilarity could predict transgressive segregation and genetic variance while genetic dissimilarity using a subset of FHB-associated single nucleotide polymorphism markers could predict genetic variance in both populations. Homogeneity of genomic selection prediction accuracy among families for FHB severity and deoxynivalenol concentration was examined in Chapter Two. Accuracy between predicted and observed values for both traits varied among families. Potential factors for limited ability to predict individual family performance are discussed.Item Genetics of Fusarium head blight resistance in barley and of rust resistance in the wild wheat relative Aegilops longissima(2023-05) Page, RaeThe use of crop wild relatives, landraces, unadapted accessions, and/or diverse panels of germplasm for discovery and deployment of disease resistance genes and/or alleles is extremely valuable in breeding crop varieties to changing disease pressures. This thesis explores two diverse germplasm panels for disease resistance in distinct pathosystems: quantitative resistance to Fusarium head blight (FHB) in barley and qualitative resistance to rust pathogens in a wild wheat relative. Fusarium head blight (FHB), a devastating disease of barley caused primarily by the fungus Fusarium graminearum, causes significant yield losses and grain contamination with mycotoxins. Enhancing resistance to FHB and the resultant accumulation of mycotoxins, such as deoxynivalenol (DON), is one of the most effective and economical methods of reducing losses caused by this disease. A diverse panel of 234 barley accessions from world-wide origins was assembled to assess the most promising FHB resistant germplasm and perform a genome-wide association study (GWAS) for FHB/DON. Multiple FHB and DON quantitative trait loci (QTL) were detected, some independent of QTL influencing heading date and plant height. These significant marker-trait associations were used to generate multi-marker haplotypes. Haplotype-trait associations were tested to analyze their diversity and effects within the panel. The rust diseases are major limiting factors in worldwide wheat production. These diseases include leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst). Aegilops longissima, a wild grass closely related to the D subgenome of modern bread wheat, has been shown to carry resistance to rust and other diseases, although it remains underutilized as a resource for discovery of novel rust resistance genes. A panel of 404 Ae. longissima accessions was evaluated for resistance to several races of Pt, Pgt, and Pst. GWAS was conducted to map rust resistance loci. Nine key candidate markers were identified as promising for further investigation due to their detection via multiple GWAS models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.Item Genetics of Resistance to Fusarium Head Blight and Spot Blotch in Hordeum(2016-05) Haas, MatthewFusarium head blight (FHB) and spot blotch are two important diseases of barley (Hordeum vulgare) in the Upper Midwest. FHB is caused by Fusarium graminearum which produces deoxynivalenol (DON), a toxin harmful to humans and animals. To characterize the genetic architecture of resistance to FHB and DON accumulation, two wild barley (PI 466423 and W-365) accessions with partial resistance were used as donor parents in advanced backcross populations with six-rowed Minnesota malting barley cultivars. The largest effect quantitative trait locus (QTL) identified in the populations was mapped at or near the photoperiod response gene Ppd-H1, which affects heading date and plant height. This result suggests that the QTL for reduced FHB and DON are a pleiotropic effect of that locus. For over 50 years, spot blotch, caused by Cochliobolus sativus, has been controlled in the Upper Midwest through the deployment of durable resistance derived from the breeding line NDB112. Recently, C. sativus isolates (e.g. ND4008) with virulence for the NDB112 resistance have been reported in the region. PI 466423 is resistant to isolate ND4008; therefore, the Rasmusson/PI 466423 population was used to map QTL for resistance to virulent isolate. Four resistance QTL were identified in chromosomes 1H, 2H, 4H, and 5H. The QTL on chromosomes 1H, 4H, and 5H were contributed by PI 466423, while the one on chromosome 2H was contributed by Rasmusson. A gamma radiation-induced susceptibility mutant from cultivar Morex was used in an RNAseq experiment to study the early infection response of barley to C. sativus. Differential expression analysis between the two genotypes revealed a role for lipid signaling in the resistance response, which may activate the jasmonic acid pathway.Item Phenotypic and genotypic data of barley Gen10 population to study a pericentromeric region on chromosome 6H(2021-06-01) Yin, Lu; Huang, Yadong; Sallam, Ahmad; Heinen, Shane; Li, Lin; Beaubien, Karen; Dill-Macky, Ruth; Dong, Yanhong; Steffenson, Brian; Smith, Kevin; Muehlbauer, Gary; smith376@umn.edu; Smith, Kevin; University of Minnesota Barley Breeding and Genetics (Smith Lab)The phenotypic and genotypic data of the Gen10 population used to study a genetic region on chromosome 6H of barley associated with multiple traits. Gen10 is a population of ~100 Chevron-derived recombinant near-isogenic lines that contained the Fusarisum head blight/kernel discoloration resistance locus from Chevron, a landrace, in the genetic background of Lacey, an elite malting barley variety.Item Sources of FHB Resistance, Genetics and Mapping of Stem Rust Resistance in Kenyan and Ethiopian Spring Wheat Germplasm(2019-11) KOSGEY, ZENNAHFusarium head blight (FHB or scab) and stem rust are important diseases of wheat. Fusarium graminearum is considered the primary causal agent of FHB. This study evaluated 215 wheat genotypes from Kenya and Ethiopia for their response to F. graminearum in inoculated and mist-irrigated nurseries established in St. Paul, MN in 2016, St. Paul, MN in 2017 and Crookston, MN in 2017. Six genotypes with stable resistance across the three test locations were identified. Positive associations were identified between FHB index, VSK, and DON and negative associations were identified between FHB index, plant height, and heading dates. The response of select genotypes was confirmed under greenhouse conditions. These studies identified resistance sources that can be used to improve the resistance levels in Kenyan and Ethiopian wheat germplasm. Stem rust caused by Puccinia graminis f. sp. tritici remains a threat to wheat production in East African wheat growing regions. In this study, we characterized the genetics of stem rust resistance, identified QTLs and markers associated with the resistance in spring wheat line CI 14275. The RILs together with their parents were evaluated at the seedling stage in a biosafety level 3 greenhouse against Pgt races TTKSK and TRTTF and in the USDA-ARS Cereal Disease Lab greenhouse against Pgt races TPMKC, TTTTF, and RTQQC. Screening for resistance to Pgt races in the field was undertaken in Kenya, Ethiopia, and the US in 2016, 2017, and 2018. One and three complementary genes conferred resistance to races TTTTF and RTQQC, respectively. The QTL QSr.cdl-2BS.2, that conferred resistance in Kenya and Ethiopia was validated and the marker Excalibur_c7963_1722 was shown to have potential in marker assisted selection. This is the first study to both detect and validate an adult plant stem rust resistance QTL on chromosome arm 2BS. The QSr.cdl-3B.1 is likely Sr12, QSr.cdl-4AL.1 is postulated as Sr7a, QSr.cdl-6BL.1 is likely Sr11, and QSr.cdl-6AS.1 appears to be a new QTL. Combination of QSr.cdl-2BS.2, QSr.cdl-3B.1, and QSr.cdl-6AS.1 has the potential to reduce stem rust severity in Africa. The work presented on FHB and stem rust provides resources for wheat improvement in East Africa.Item Using near isogenic barley lines to validate Deoxynivalenol (DON) QTL previously identified through association analysis(2013-01) Navara, Stephanie LynnFusarium head blight (FHB) is a serious disease of cereal grains caused by the fungal pathogen Fusarium graminearum. Deoxynivalenol (or DON), the associated trichothecene mycotoxin is of special concern to barley producers and consumers. A recent association mapping (AM) study of U.S. six-row spring barley identified several modest effect quantitative trait loci (QTL) for DON and FHB. To date, few studies have attempted to verify the results of association analyses, particularly for complex traits such as FHB and DON resistance in barley. Despite control measures used to mitigate the effects of population structure and multiple testing in AM, false positives may still occur. To verify previously reported associations we evaluated the effects of nine DON QTL using near isogenic lines (NILs) for each QTL region. Families of contrasting homozygous haplotypes for each region were derived from lines in the original AM populations that were heterozygous for DON QTL. Seventeen NIL families were evaluated for FHB and DON in three field experiments. Significant differences between contrasting NIL haplotypes were detected for three QTL across environments and/or genetic backgrounds, thereby confirming QTL from the original AM study. Several explanations for those QTL that were not confirmed are discussed, including the effect of genetic background and incomplete sampling of relevant haplotypes.