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Item Agronomic characteristics, malt quality, and disease resistance of barley germplasm lines with partial Fusarium head blight resistance(Crop Science, 2005-07) Steffenson, Brian; Urrea, Carlos A.; Horsley, Richard D.; Schwarz, Paul B.Fusarium head blight (FHB), incited by Fusarium graminearum Schwabe, has caused devastating losses in both yield and quality of barley (Hordeum vulgare L.) produced in the northern Great Plains from 1993 to 2003. Thirty-five barley germplasm lines with partial resistance to FHB have been identified in exotic and unadapted germplasm lines. Little is known about their agronomic characteristics, malt quality, and reaction to other diseases as compared to adapted cultivars. This information is needed so barley breeders can make informed decisions when planning crosses involving the resistant germplasm lines. The objective of this study was to compare the agronomic performance, malt quality, and disease reaction of barley germplasm lines with partial FHB resistance to cultivars grown in the northern Great Plains. Agronomic and malting data were collected on the 35 germplasm lines and five check cultivars grown in five environments in North Dakota from 1998 to 2000. Data for FHB severity and deoxynivalenol (DON, a mycotoxin produced by F. graminearum) accumulation were obtained for the same 40 entries grown in FHB-epidemic nurseries in North Dakota from 1997 to 1999. Seedling responses to foliar pathogens common in the northern Great Plains were determined in the greenhouse during fall 1997. None of the FHB-resistant barley germplasm lines had acceptable malt quality for all traits. Kernel plumpness, grain protein concentration, and malt extract were the traits impacted most severely. The FHB-resistant barley germplasm lines headed significantly later than the adapted barley cultivars. Most FHB-resistant germplasm lines were susceptible to the common foliar diseases of the northern Great Plains. At least four cycles of breeding will probably be necessary to develop FHB-resistant germplasm lines acceptable to producers and the malting and brewing industry.Item Amplified fragment length polymorphism and virulence polymorphism in Puccinia hordei(Canadian Journal of Plant Pathology, 2007) Sun, Y; Neate, S.M.; Zhong, S; Steffenson, Brian; Friesen, T. L.Puccinia hordei is the causal agent of barley leaf rust. To study the genetic diversity in P. hordei, 45 isolates with diverse virulence patterns and geographical origins were analyzed using amplified fragment length polymorphism markers. Two pathotypes of Puccinia graminis f. sp. tritici and one isolate of P. graminis f. sp. secalis were included in the analysis for comparison. Six primer-pair combinations of amplified fragment length polymorphism were used and a total of 782 polymorphic markers were generated. Cluster analysis showed that P. graminis f. sp. tritici and P. graminis f. sp. secalis were distinctly different from P. hordei. The P. hordei isolates were clustered into five groups: group I contained a single, rare isolate that was virulent on all resistance genes except Rph13 and Rph15 ; group II contained a single isolate found to be virulent on the resistance gene Rph15 ; group III contained 2 isolates; group IV contained 24 isolates, 11 from the United States and 13 from diverse locations around the world; and group V contained 17 isolates, 7 from California, 7 from other states of United States, and 3 from central Europe. The study revealed that molecular diversity in P. hordei can be associated with virulence, but not well with geographic origin.Item Barley stem rust resistance genes: structure and function(Plant Genome, 2009-07) Steffenson, Brian; Kleinhofs, Andris; Brueggeman, Robert; Nirmala, Jayaveeramuthu; Zhang, Ling; Mirlohi, Aghafakhr; Druka, Arnis; Rostoks, NilsRusts are biotrophic pathogens that attack many plant species but are particularly destructive on cereal crops. The stem rusts (caused by Puccinia graminis) have historically caused severe crop losses and continue to threaten production today. Barley (Hordeum vulgare L.) breeders have controlled major stem rust epidemics since the 1940s with a single durable resistance gene Rpg1. As new epidemics have threatened, additional resistance genes were identified to counter new rust races, such as the rpg4/Rpg5 complex locus against races QCCJ and TTKSK. To understand how these genes work, we initiated research to clone and characterize them. The Rpg1 gene encodes a unique protein kinase with dual kinase domains, an active kinase, and a pseudokinase. Function of both domains is essential to confer resistance. The rpg4 and Rpg5 genes are closely linked and function coordinately to confer resistance to several wheat (Triticum aestivum L.) stem rust races, including the race TTKSK (also called Ug99) that threatens the world's barley and wheat crops. The Rpg5 gene encodes typical resistance gene domains NBS, LRR, and protein kinase but is unique in that all three domains reside in a single gene, a previously unknown structure among plant disease resistance genes. The rpg4 gene encodes an actin depolymerizing factor that functions in cytoskeleton rearrangement.Item The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases(Proceedings of the National Academy of Sciences of the United States of America, 2002-07-09) Steffenson, Brian; Brueggeman, R.; Rostoks, N.; Kudrna, D.; Kilian, A.; Han, F.; Chen, J.; Druka, A.; Kleinhofs, A.Stem rust caused by Puccinia graminis f. sp. tritici was among the most devastating diseases of barley in the northern Great Plains of the U.S. and Canada before the deployment of the stem rust-resistance gene Rpg1 in 1942. Since then, Rpg1 has provided durable protection against stem rust losses in widely grown barley cultivars (cvs.). Extensive efforts to clone Rpg1 by synteny with rice provided excellent flanking markers but failed to yield the gene because it does not seem to exist in rice. Here we report the map-based cloning and characterization of Rpg1. A high-resolution genetic map constructed with 8,518 gametes and a 330-kb bacterial artificial chromosome contig physical map positioned the gene between two crossovers ≈0.21 centimorgan and 110 kb apart. The region including Rpg1 was searched for potential candidate genes by sequencing low-copy probes. Two receptor kinase-like genes were identified. The candidate gene alleles were sequenced from resistant and susceptible cvs. Only one of the candidate genes showed a pattern of apparently functional gene structure in the resistant cvs. and defective gene structure in the susceptible cvs. identifying it as the Rpg1 gene. Rpg1 encodes a receptor kinase-like protein with two tandem protein kinase domains, a novel structure for a plant disease-resistance gene. Thus, it may represent a new class of plant resistance genes.Item A barley UDP-glucosyltransferase provides high levels of resistance to trichothecenes and Fusarium Head Blight in cereals(2017-08) Li, XinFusarium Head Blight (FHB) is a devastating disease that leads to severe economic losses to worldwide wheat (Triticum aestivum) and barley (Hordeum vulgare L.) production. During FHB disease development, the main causal fungal pathogen, Fusarium graminearum can infect a single spikelet and cause disease symptoms throughout the spike in susceptible wheat. Moreover, F. graminearum produces trichothecene mycotoxins (eg., deoxynivalenol (DON), nivalenol (NIV) and their derivatives) that facilitate FHB disease development, and toxin contamination of the grain poses a significant threat to human and animal health. Two major types of resistance have been identified and deployed in breeding programs including: type I (resistance to initial infection) and type II (resistance to spread of the symptoms). Although worldwide efforts have focused on germplasm screening and QTL mapping of FHB resistance, unfortunately, resistance to FHB is quantitatively controlled and only partial. Thus, research efforts have expanded to identifying genes and deploying them in transgenic wheat. Previous gene expression analysis in the barley cultivar ‘Morex’ led to discovery of a UDP-glucosyltransferase gene, HvUGT13248, that was shown to provide DON resistance in transgenic yeast and Arabidopsis thaliana via conjugation of DON to DON-3-O-glucoside (D3G), a much less toxic derivative. To test this promising gene in wheat, we developed transgenic wheat expressing HvUGT13248 and showed that these transgenic plants exhibited significant reduction of disease spread (type II resistance) in the spike compared with nontransformed controls. Expression of HvUGT13248 in transgenic wheat rapidly and efficiently conjugated DON to D3G. Under field conditions, FHB severity was variable between different transgenic lines; however, in some years the transgenic wheat showed significantly less severe disease phenotypes compared with the nontransformed controls. Moreover, HvUGT13248 is also capable of converting NIV to the detoxified derivative, NIV-3-O-β-D-glucoside (NIV3G). An enzymatic assay using HvUGT13248 purified from Escherichia coli showed that HvUGT13248 efficiently catalyzed NIV to NIV3G. Overexpression in yeast, Arabidopsis thaliana and wheat showed enhanced NIV resistance when grown on media containing different levels of NIV. Increased ability to convert nivalenol to NIV3G was observed in transgenic wheat, which also exhibits type II resistance to a NIV-producing F. graminearum strain. Transgenic wheat expressing HvUGT13248 also provides type II resistance to F. graminearum strains producing 3-ADON and NX-2, and resistance to root growth inhibition in 3,15-diANIV-containing media. Moreover, the HvUGT13248 transgene was introgressed into the elite wheat cultivars ‘Rollag’ and ‘Linkert’, and greenhouse point inoculation results showed that HvUGT13248 improved FHB resistance in elite backgrounds. HvUGT13248 overexpression in transgenic barley also enhanced DON resistance observed in a root assay. In conclusion, HvUGT13248 is a highly effective FHB resistant gene that can detoxify a wide spectrum of trichothecene chemotypes. Thus, the mechanism of resistance is by rapidly detoxifying trichothecenes to their glucoside forms.Item Biological problem solving through computation(2023-06) Liu, ChaochihAs sequencing becomes more and more affordable, data continues to grow exponentially, and dataset sizes utilized in biological studies continue to increase. There is an increasing importance for reproducible research, especially studies that rely heavily on computational analyses. Custom code written for study-specific goals that are well documented and hosted in source code repositories with version control can accelerate future studies with similar data processing or analysis steps. For example, updating the reference genome positions of old genotyping SNPs as new reference genome versions get released is just as important as handling the latest long-read sequencing technologies. In this dissertation, I present multiple computational solutions to address problems relevant to crop improvement. In Chapter 1 of this dissertation, I use whole-genome sequencing data from 11 barley lines derived from sodium azide mutagenesis to characterize the nature of mutations induced by sodium azide to understand the nature of variants that reduce fitness. In this work, careful variant filtering was performed to identify variants generated by the mutagen. In Chapter 2, I investigate 318 Wild Barley Diversity Collection accessions for evidence of introgression from 2,446 domesticated barley. Information on wild accessions showing crop-to-wild introgression can be used to make informed decisions on wild samples to include in downstream applications. Finally, in Chapter 3, I develop a reproducible computational workflow that automates the scoring of crossovers as a phenotype to provide a means to quickly evaluate the amount of crossover rate variation present in any biparental population. Output from the computational workflow can be used to address limitations imposed by linked selection in breeding populations. For all the chapters, all code used for data processing and analyses is stored in public GitHub repositories to speed up the advancement of future research built upon this work.Item Deciphering lodging resistance in oat and other cereal crops(2019-08) Susko, AlexanderLodging impedes the successful cultivation of oat and other cereal crops in the upper midwestern United States. Lodged cereals not only possess reduced grain yields, but also decreased grain quality. This dissertation first conceives of a camera system to capture plant movement in the wind in the field via a 360-degree field of view camera, followed by a video analysis pipeline to quantify the frequency and amplitude of cereal stem movement under varying wind conditions in the field. The natural oscillating frequencies and amplitudes of stems were dependent on wind speeds and at the cultivar, crop level. Nonetheless, the substantial environmental effects in the field that induce lodging make discovering specific morphologies that confer lodging resistance difficult. Next, in seeking to better identify promising morphological targets for breeding and selecting lodging resistance in cereal crops, a diverse panel of 38 cereal cultivars (oat, wheat, barley) were subjected to replicated testing in a wind tunnel. Wind tunnel testing revealed that a cereal ideotype consisting of low total biomass, high stem strength, and high stem elasticity should confer increased lodging resistance. A field study using the camera system to quantify aspects of plant movement and correlated these phenotypes with physical plant traits is presented next, which indicated that patterns of plant movement are spatially independent in a randomized complete block design of 16 cereal cultivars and that the relationships between plant height, heading date, and plant movement vary among the major cereal crops. Finally, a GWAS and QTL validation study is presented on lodging in oat, which revealed significant marker trait associations for plant height, heading date, and stem snapping, though only QTL for plant height and heading date were successfully validated in derived biparental populations.Item Defining a Cultural Context to Underutilized Crops in the Minnesota Food System(2021) Anderson, Shannon, LeeCulture is a universal component and tool in many contexts that has yet to be adequately defined within a food system. As communities are subject to globalization of the food system(s), not only is the biodiversity of organisms being affected but cultural diversity as well.1 In order to fully develop and identify barriers and challenges in food systems, culture as operationalized within a system needs to be understood and represented as a part of the entire framework.2 This journal describes independent research conducted remotely within the context of the Barley food system and studies conducted on aspects of the rural food system in an attempt to define tools that can be used for cultural analysis in rural food systems.Item Development Of Barley Introgression Lines Carrying The Leaf Rust Resistance Genes Rph1 To Rph15(2018-07) Martin, MatthewBarley (Hordeum vulgare) is the fourth most planted and harvested grain crop in the world. In many production areas, barley is attacked by the leaf rust pathogen (Puccinia hordei), a basidiomycetous fungus that reduces both its yield and quality. Many leaf rust resistance genes, known as reaction to P. hordei (Rph) genes, have been described in barley. Resistance deployed in cultivars has often been transient due to the pertinacious nature of single gene virulence mutations in P. hodei populations. To differentiate genetic variants for virulence in P. hordei populations, plant pathologists use barley accessions with different resistance genes, referred to as a differential set. The barley leaf rust differential set evolved through time as more Rph genes were described. The sources of Rph1-15 were derived from barleys with diverse geographic origins and agro-morphological traits. Ideal differential sets include lines where single resistance genes are backcrossed into the genetic background of an adapted susceptible cultivar. Sources for Rph1-15, along with many other Rph gene donors were backcrossed to the susceptible cultivar Bowman. Overall, 95 Bowman introgression lines for leaf rust resistance were developed, and a single line was recommended for use as the new backcrossed differential host line for each individual Rph1-15 gene. Genomic positions and gene candidates for Rph1-15 were characterized and the existence of possible new resistance genes was postulated. The new Bowman Rph1-15 differential lines will facilitate the efficient virulence phenotyping of P. hordei and serve as valuable genetic stocks for Rph gene stacking and cloning in barley.Item Disease and insect resistance in cultivated barley accessions from the USDA National Small Grains Collection(Crop Science, 2005) Steffenson, Brian; Bonman, J.Michael; Bockelman, Harold E.; Jackson, Lee F.Cultivated barley (Hordeum vulgare subsp. vulgare L.) accessions from the USDA-ARS National Small Grains Collection (NSGC) have been tested systematically for the past 20 yr for disease and insect resistance. In this study, we analyzed the resistance to barley yellow dwarf (BYD), spot blotch (SB) caused by Cochliobolus sativus (Ito and Kuribayashi) Drechs. ex Dastur, net blotch (NB) caused by Pyrenophora teres f. teres Drechs., stripe rust (SR) caused by Puccinia striiformis Westend. f. sp. hordei, and Russian wheat aphid (RWA), Diuraphis noxia (Mordvilko), with respect to (i) geographic origin of resistant accessions, (ii) relationship to other NSGC descriptor data, and (iii) relationships among resistances. "Centers of concentration" for certain resistances were identified: eastern Africa for several diseases, western Turkey and the Caucasus for SR resistance, eastern Asia for adult plant resistance to NB, and south-central Asia for RWA resistance. Stripe rust resistance was also associated with accessions originating from high altitude in eastern Africa (Ethiopia). Various associations between resistances and grain descriptors, plant habit, and landrace status were also found. Forty-eight accessions showed multiple resistances on the basis of the field disease data and the RWA greenhouse data. Many of these resistant accessions were from Ethiopia, and many were of unknown origin. Stripe rust testing in California and Bolivia supported the conclusion that winter-habit accessions were more resistant to the disease than were spring-habit accessions. Information from this study will be used to guide future NSGC acquisition and evaluation efforts.Item Effect of incubation time and temperature on the phenotypic expression of rpg4 to Puccinia graminis f. sp. tritici in barley(Canadian Journal of Plant Pathology, 1997-03-01) Sun, Yonglian; Steffenson, BrianTo study the effect of incubation time and temperature on the phenotypic expression of rpg4, five barley genotypes with this resistance gene were infected with pathotype QCCJ of Puccinia graminis f. sp. tritici at the seedling stage, then subjected to various times of incubation at either 18-19°C or 27~28°C. Genotypes with rpg4 exhibited low (0, 0;, and 1), mesothetic (e.g. 3-210;, 120;3), and high (3,3) infection types at 18-19°C after initial incubation at 27-28°C for 0-28, 40-76, and 88 or more hours, respectively. A period of 88 or more hours of initial incubation at high temperature rendered the rpg4 resistance completely ineffective against this pathotype of P. g. f. sp. tritici. In contrast, high, mesothetic, and low infection types were found for the same genotypes at 27-28°C after initial incubation at 18-19°C for 0-40, 52-100, and 112 or more hours, respectively. The resistant infection types conferred by rpg4 are apparently established within the first 112 hours after the end of the infection period since subsequent shifts to higher temperature did not result in marked changes in the resistance response. These data indicate the critical importance of maintaining precise temperature control when assessing the infection phenotypes of barley genotypes carrying the stem rust resistance gene rpg4.Item ELIGULUM-A regulates lateral branch and leaf development. Original figure files(2018-01-05) Okagaki, Ron J; Muehlbauer, Gary J; okaga002@umn.edu; Okagaki, Ron JShoot development is controlled by the actions of the shoot apical and axillary meristems resulting in the development of lateral branches and leaves. The barley (Hordeum vulgare L.) uniculm2 (cul2) mutation blocks axillary meristem development, and mutant plants lack lateral branches, tillers, that normally develop from the crown. A genetic screen for cul2 suppressors recovered two recessive alleles of ELIGULUM-A (ELI-A) that partially rescued the cul2 tillering phenotype. Mutations in ELI-A produce shorter plants with fewer tillers, disrupt the leaf blade – sheath boundary resulting in a liguleless leaf, and secondary cell wall formation is reduced. ELI-A encodes a previously un-annotated plant gene that is conserved in land plants. ELI-A transcript accumulates at the preligule boundary, the developing ligule, leaf margins, cells destined to develop secondary cell walls, and cells surrounding leaf vascular bundles. Recent studies have identified commonalities in the genetic control of boundaries during leaf and lateral organ development. Interestingly, we observed ELI-A transcript at the preligule boundary, indicating a role in establishing the boundary between the blade and sheath. However, we did not observe ELI-A transcript at the axillary meristem boundary in leaf axils, indicating that it does not play a role in establishing the boundary for axillary meristem development. Our results provide a new player in the model for leaf and lateral branch development in which ELI-A acts as a boundary gene for ligule development but not during lateral branch development.Item Exploring Variation for Fusarium Head Blight Resistance and Deoxynivalenol Distribution in the Naked Barley Diversity Panel(2022-07) Hawkins, JohnHull-less or naked barley (Hordeum vulgare L.) is a grain of growing importance in food, feed, and malting applications. Fusarium Head Blight (FHB), a disease caused by fungi in the genus Fusarium, causes significant damage to barley grain through accumulation of mycotoxins and undesirable fungal proteins and reduction of grain mass and malting quality. The most important Fusarium mycotoxin in North America is deoxynivalenol (DON). Naked barley accumulates significant amounts of DON in hull tissue, which is discarded at threshing, providing a mechanism for limiting FHB discounts due to mycotoxin contamination. For this research, genome wide association studies were performed using the Naked Barley Diversity Panel genotyped with an array of 50,000 single nucleotide polymorphisms (SNPs) and phenotyped for traits associated with DON distribution in the barley spike. Three notable quantitative trait loci (QTLs) for disease related traits were discovered. A QTL on the short arm of chromosome 3H, linked to a hydroxyproline rich glycoprotein gene was associated with reduced FHB severity. Another QTL on the long arm of 3H, linked to sdw1, was associated with shorter plants, greater FHB severity under grain spawn inoculation, and earlier heading. A third QTL on the short arm of 2H, linked to PPD-H1, was associated with taller plants, later heading, and a greater proportion of the total DON being localized in the hull. Overall, there appears to be potential for the improvement of FHB resistance and DON mitigation in naked barley.Item Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross(Genome, 2007) Steffenson, Brian; Gyenis, L.; Yun, S.J.; Smith, K.P.; Bossolini, E.; Sanguineti, M.C.; Muehlbauer, G.J.Hordeum vulgare subsp. spontaneum is the progenitor of cultivated barley (Hordeum vulgare L.). Domestication combined with plant breeding has led to the morphological and agronomic characteristics of modern barley cultivars. The objective of this study was to map the genetic factors that morphologically and agronomically differentiate wild barley from modern barley cultivars. To address this objective, we identified quantitative trait loci (QTLs) associated with plant height, flag leaf width, spike length, spike width, glume length in relation to seed length, awn length, fragility of ear rachis, endosperm width and groove depth, heading date, flag leaf length, number of tillers per plant, and kernel color in a Harrington/OUH602 advanced backcross (BC2F8) population. This population was genotyped with 113 simple sequence repeat markers. Thirty QTLs were identified, of which 16 were newly identified in this study. One to 4 QTLs were identified for each of the traits except glume length, for which no QTL was detected. The portion of phenotypic variation accounted for by individual QTLs ranged from about 9% to 54%. For traits with more than one QTL, the phenotypic variation explained ranged from 25% to 71%. Taken together, our results reveal the genetic architecture of morphological and agronomic traits that differentiate wild from cultivated barley.Item Genetic characterization of multiple disease resistance and agronomical/nutritional traits in hordeum(2013-08) Mamo, Bullo ErenaBarley is an economically important crop plant whose yield and quality is affected by multiple diseases. Landrace and wild barley gene pools can be utilized to enhance disease resistance and nutrition in cultivated barley. To identify and map resistance loci for three important diseases (stem rust, spot blotch and Fusarium head blight [FHB]), and enhanced accumulation of two vital micronutrients (zinc and iron), genetic mapping was employed. The genetics of resistance to stem rust race TTKSK in Swiss landrace and wild barley accessions at the seedling stage was conducted through bi-parental mapping. Genetic analysis of F2:3 families derived from these accessions revealed that a single gene that maps to chromosome 5HL — at or in close proximity to the complex stem rust resistance locus rpg4/Rpg5 confers resistance. An association mapping approach was utilized to identify Quantitative Trait Loci (QTL) associated with disease resistance and zinc and iron concentration in 298 Ethiopian and Eritrean barley landraces genotyped with 7,842 single nucleotide polymorphism (SNP) markers. For stem rust race TTKSK, five seedling resistance loci were identified: one each on chromosome 2HS, 2HL, 3HL, 4HL, and 5HS. The ones on chromosomes 2HL and 4HL are novel, whereas the other three mapped to regions coincident with previously reported stem rust resistance QTL. For stem rust race MCCFC at the adult plant stage, one locus coincident with a known race TTKSK resistance QTL was identified on chromosome 5HL. For spot blotch, SNP markers located in close proximity with known adult plant spot blotch resistance QTL were found on chromosomes 2HL and 4HS in six-rowed barley landraces. For FHB, one common resistance QTL on chromosome 2HL, also associated with deoxynivalenol (DON) concentration, was identified. A locus mapping to a region of chromosome 4HL, known to contain QTL associated with DON, also was detected. The loci identified on chromosomes 2HL and 4HL associated with FHB and/or DON were not associated with heading date or plant height. Two novel loci associated with grain zinc concentration were identified on chromosomes 4HS and 6HL. For kernel weight, a known QTL region on chromosome 2HL was detected.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 Genetically engineered stem rust resistance in barley using the Rpg1 gene(Proceedings of the National Academy of Sciences of the United States of America, 2003-01-07) Steffenson, Brian; Horvath, Henriette; Rostoks, Nils; Brueggeman, Robert; Wettstein, Diter von; Kleinhofs, AndrisThe stem-rust-susceptible barley cv. Golden Promise was transformed by Agrobacterium-mediated transformation of immature zygotic embryos with the Rpg1 genomic clone of cv. Morex containing a 520-bp 5′ promoter region, 4,919-bp gene region, and 547-bp 3′ nontranscribed sequence. Representatives of 42 transgenic barley lines obtained were characterized for their seedling infection response to pathotype Pgt-MCC of the stem rust fungus Puccinia graminis f. sp. tritici. Golden Promise was converted from a highly susceptible cultivar into a highly resistant one by transformation with the dominant Rpg1 gene. A single copy of the gene was sufficient to confer resistance against stem rust, and progenies from several transformants segregated in a 3:1 ratio for resistance/susceptibility as expected for Mendelian inheritance. These results unequivocally demonstrate that the DNA segment isolated by map-based cloning is the functional Rpg1 gene for stem rust, resistance. One of the remarkable aspects about the transformants is that they exhibit a higher level of resistance than the original sources of Rpg1 (cvs. Chevron and Peatland). In most cases, the Golden Promise transformants exhibited a highly resistant reaction where no visible sign of infection was evident. Hypersensitive necrotic “fleck” reactions were also observed, but less frequently. With both infection types, pathogen sporulation was prevented. Southern blot and RT-PCR analysis revealed that neither Rpg1 gene copy number nor expression levels could account for the increased resistance observed in Golden Promise transformants. Nevertheless, this research demonstrates that stem-rust-susceptible barley can be made resistant by transformation with the cloned Rpg1 gene.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 Genetics, Sources, and Mapping of Stem Rust Resistance in Barley(2017-04) Case, AustinStem rust is a devastating disease of cereal crops worldwide. In barley (Hordeum vulgare), the disease is caused by two pathogens: Puccinia graminis f. sp. secalis (Pgs) and Puccinia graminis f. sp. tritici (Pgt). In North America, the stem rust resistance gene Rpg1 has protected barley from losses for more 60 years; however, widely virulent Pgt races from Africa in the Ug99 group threaten the crop. To identify novel quantitative trait loci (QTL) for stem rust resistance, bi-parental and association mapping studies were undertaken in the Barley iCore Collection (BCC) held by the USDA National Small Grains Collection. Association mapping studies of the BCC were conducted for seedling resistance to Pgt race TTKSK (Ug99 group) in the greenhouse and adult plant resistance (APR) to Pgt TTKSK composite in Njoro, Kenya and Pgt race QCCJB in St. Paul, MN. A major effect QTL (Rpg-qtl-5H-11_11355) for APR in all locations was identified on chromosome 5H. This QTL represents a unique locus for APR and has been confirmed in other studies. Subsequently, 290 of the most resistant BCC accessions, the BCC Selects (BCCS), were screened for resistance Pgt races MCCFC, QCCJB, HKHJC, TTKSK, TTKST, TKTTF, and TRTTF, and also Pgs isolate 92-MN-90. From this investigation, four BCCS accessions were postulated to carry Rpg1, 14 to carry Rpg2, 91 to carry Rpg3, four to carry rpg4/Rpg5, and 59 to carry potentially novel resistance genes. To map the APR genes of Rpg2 and Rpg3 in Hietpas-5 (CIho 7124) and GAW-79 (PI 382313), respectively, two biparental populations were developed with Hiproly (PI 60693), a stem rust susceptible accession. Both populations were phenotyped to the domestic Pgt races of MCCFC, QCCJB, and HKHJC in St. Paul and to Pgt TTKSK composite in Njoro. In the Heitpas-5/Hiproly population, a major effect QTL was identified on chromosome 2H, which is proposed as the location for Rpg2. In the GAW-79/Hiproly population, a major effect QTL was identified on chromosome 5H and is the proposed location for Rpg3. The resistance sources identified and characterized in this study enhance barley breeding programs focused on stem rust resistance.Item Genome-wide association mapping of fusarium head blight resistance and agromorphological traits in barley landraces from Ethiopia and Eritrea(Crop Science, 2015-06-12) Steffenson, Brian; Mamo, Bullo ErenaFusarium head blight (FHB), caused primarily by Fusarium graminearum, is an important disease of barley (Hordeum vulgare L.), and other cereals. In barley, the genetic basis of FHB resistance has been intensively studied through linkage mapping that identified several quantitative trait loci (QTL). However, our understanding and application of these QTL in breeding is still limited due to the complex nature and low-to-moderate heritability of FHB resistance. Previous studies used either breeding lines, unimproved varieties, or germplasm selections. Here, we used association mapping in barley landraces to identify QTL associated with FHB severity, deoxynivalenol (DON) concentration and correlated agromorphological traits. Diverse barley landraces (n = 298) from Ethiopia and Eritrea were evaluated for the traits under field conditions for 2 yr (2011–2012) in Crookston, MN, and genotyped with 7842 single nucleotide polymorphism (SNP) markers. Association mapping analysis using a mixed model corrected for pairwise relatedness between individuals identified one common resistance QTL on barley chromosome 2HL significantly associated with both FHB severity and DON concentration and another one on 4HL associated with DON concentration. The QTL identified on 2HL is associated with the row-type locus Vrs1. Both of these QTL were not significantly associated with heading date or plant height unlike other QTL reported in previous studies. Thus, the resistant accessions carrying these QTL may be used in breeding programs without the confounding effects from these agromorphological traits. Importantly, these QTL could be new alleles preserved in this unique germplasm, and the linked SNP markers found may be useful in marker-assisted introgression of resistance.
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