Publications by authors named "Brian J Steffenson"

55 Publications

BED domain-containing NLR from wild barley confers resistance to leaf rust.

Plant Biotechnol J 2021 Jan 8. Epub 2021 Jan 8.

Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia.

Leaf rust, caused by Puccinia hordei, is a devastating fungal disease affecting barley (Hordeum vulgare subsp. vulgare) production globally. Despite the effectiveness of genetic resistance, the deployment of single genes often compromises durability due to the emergence of virulent P. hordei races, prompting the search for new sources of resistance. Here we report on the cloning of Rph15, a resistance gene derived from barley's wild progenitor H. vulgare subsp. spontaneum. We demonstrate using introgression mapping, mutation and complementation that the Rph15 gene from the near-isogenic line (NIL) Bowman + Rph15 (referred to as BW719) encodes a coiled-coil nucleotide-binding leucine-rich repeat (NLR) protein with an integrated Zinc finger BED (ZF-BED) domain. A predicted KASP marker was developed and validated across a collection of Australian cultivars and a series of introgression lines in the Bowman background known to carry the Rph15 resistance. Rph16 from HS-680, another wild barley derived leaf rust resistance gene, was previously mapped to the same genomic region on chromosome 2H and was assumed to be allelic with Rph15 based on genetic studies. Both sequence analysis, race specificity and the identification of a knockout mutant in the HS-680 background suggest that Rph15- and Rph16-mediated resistances are in fact the same and not allelic as previously thought. The cloning of Rph15 now permits efficient gene deployment and the production of resistance gene cassettes for sustained leaf rust control.
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http://dx.doi.org/10.1111/pbi.13542DOI Listing
January 2021

The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles.

Front Plant Sci 2020 21;11:569905. Epub 2020 Dec 21.

International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon.

Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94-97% of the original diversity. The GDP consists of a wide representation of ssp. modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970-2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at = 0.5. analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index ( ) and diversity reduction index () metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology ( and ), plant height () and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.
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http://dx.doi.org/10.3389/fpls.2020.569905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779600PMC
December 2020

A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat.

Nat Biotechnol 2021 Jan 4. Epub 2021 Jan 4.

CSIRO Agriculture and Food, GPO Box 1700, Canberra, Australia.

Breeding wheat with durable resistance to the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), a major threat to cereal production, is challenging due to the rapid evolution of pathogen virulence. Increased durability and broad-spectrum resistance can be achieved by introducing more than one resistance gene, but combining numerous unlinked genes by breeding is laborious. Here we generate polygenic Pgt resistance by introducing a transgene cassette of five resistance genes into bread wheat as a single locus and show that at least four of the five genes are functional. These wheat lines are resistant to aggressive and highly virulent Pgt isolates from around the world and show very high levels of resistance in the field. The simple monogenic inheritance of this multigene locus greatly simplifies its use in breeding. However, a new Pgt isolate with virulence to several genes at this locus suggests gene stacks will need strategic deployment to maintain their effectiveness.
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http://dx.doi.org/10.1038/s41587-020-00770-xDOI Listing
January 2021

Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat.

Plant Genome 2020 11 28;13(3):e20051. Epub 2020 Aug 28.

Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.

Germplasm collections are rich sources of genetic variation to improve crops for many valuable traits. Nested association mapping (NAM) populations can overcome the limitations of genome-wide association studies (GWAS) in germplasm collections by reducing the effect of population structure. We exploited the genetic diversity of the USDA-ARS wheat (Triticum aestivum L.) core collection by developing the Spring Wheat Multiparent Introgression Population (SWMIP). To develop this population, twenty-five core parents were crossed and backcrossed to the Minnesota spring wheat cultivar RB07. The NAM population and 26 founder parents were genotyped using genotyping-by-sequencing and phenotyped for heading date, height, test weight, and grain protein content. After quality control, 20,312 markers with physical map positions were generated for 2,038 recombinant inbred lines (RILs). The number of RILs in each family varied between 58 and 96. Three GWAS models were utilized for quantitative trait loci (QTL) detection and accounted for known family stratification, genetic kinship, and both covariates. GWAS was performed on the whole population and also by bootstrap sampling of an equal number of RILs from each family. Greater power of QTL detection was achieved by treating families equally through bootstrapping. In total 16, 15, 12, and 13 marker-trait associations (MTAs) were identified for heading date, height, test weight, and grain protein content, respectively. Some of these MTAs were coincident with major genes known to control the traits, but others were novel and contributed by the wheat core parents. The SWMIP will be a valuable source of genetic variation for spring wheat breeding.
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http://dx.doi.org/10.1002/tpg2.20051DOI Listing
November 2020

Genome-wide association analysis of natural variation in seed tocochromanols of barley.

Plant Genome 2020 11 28;13(3):e20039. Epub 2020 Sep 28.

USDA-ARS, Cereal Crops Research Unit, 502 Walnut Street, Madison, WI, 53726, USA.

Tocochromanols (tocols for short), commonly called Vitamin E, are lipid-soluble plant antioxidants vital for regulating lipid peroxidation in chloroplasts and seeds. Barley (Hordeum vulgare L.) seeds contain all eight different isoforms of tocols; however, the extent of natural variation in their composition and their underlying genetic basis is not known. Tocol levels in barley seeds were quantified in diverse H. vulgare panels comprising 297 wild lines from a diversity panel and 160 cultivated spring-type accessions from the mini-core panel representing the genetic diversity of the USDA barley germplasm collection. Significant differences were observed in the concentration of tocols between the two panels. To identify the genes associated with tocols, genome-wide association analysis was conducted with single nucleotide polymorphisms (SNPs) from Illumina arrays for the mini-core panel and genotyping-by-sequencing for the wild barley panel. Forty unique SNPs in the wild barley and 27 SNPs in the mini-core panel were significantly associated with various tocols. Marker-trait associations (MTAs) were identified on chromosomes 1, 6, and 7 for key genes in the tocol biosynthesis pathway, which have also been reported in other studies. Several novel MTAs were identified on chromosomes 2, 3, 4 and 5 and were found to be in proximity to genes involved in the generation of precursor metabolites required for tocol biosynthesis. This study provides a valuable resource for barley breeding programs targeting specific isoforms of seed tocols and for investigating the physiological roles of these metabolites in seed longevity, dormancy, and germination.
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http://dx.doi.org/10.1002/tpg2.20039DOI Listing
November 2020

Hyperspectral imaging and improved feature variable selection for automated determination of deoxynivalenol in various genetic lines of barley kernels for resistance screening.

Food Chem 2021 May 31;343:128507. Epub 2020 Oct 31.

Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA.

Fusarium head blight (FHB), a fungus disease of small grain cereal crops, results in reduced yields and diminished value of harvested grain due to the presence of deoxynivalenol (DON), a mycotoxin produced by the causal pathogen Fusarium graminearum. DON and other tricothecene mycotoxins pose serious health risks to both humans and livestock, especially swine. Due to these health concerns, barley used for malting, food or feed is routinely assayed for DON levels. Various methods are available for assaying DON levels in grain samples including enzyme-linked immunosorbent assay (ELISA) and gas chromatography-mass spectrometry (GC-MS). ELISA and GC-MS are very accurate; however, assaying grain samples by these techniques are laborious, expensive and destructive. In this study, we explored the feasibility of using hyperspectral imaging (382-1030 nm) to develop a rapid and non-destructive protocol for assaying DON in barley kernels. Samples of 888 and 116 from various genetic lines were selected for calibration and prediction. Full-wavelength locally weighted partial least squares regression (LWPLSR) achieved high accuracy with the coefficient of determination in prediction (R) of 0.728 and root mean square error of prediction (RMSEP) of 3.802. Competitive adaptive reweighted sampling (CARS) was used to choose potential feature wavelengths, and these selected variables were further optimized using the iterative selection of successive projections algorithm (ISSPA). The CARS-ISSPA-LWPLSR model developed using 7 feature variables yielded R of 0.680 and RMSEP of 4.213 in DON content prediction. Based on the 7 wavelengths selected by CARS-ISSPA, partial least square discriminant analysis (PLSDA) discriminated barley kernels having lower DON (less than1.25 mg/kg) levels from those with higher levels (including 1.25-3 mg/kg, 3-5 mg/kg, and 5-10 mg/kg), with Matthews correlation coefficient in cross-validation (M-R) of as high as 0.931. The results demonstrate that hyperspectral imaging have potential for accelerating non-destructive DON assays of barley samples.
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http://dx.doi.org/10.1016/j.foodchem.2020.128507DOI Listing
May 2021

Mutagenesis of  f. sp.  and Selection of Gain-of-Virulence Mutants.

Front Plant Sci 2020 16;11:570180. Epub 2020 Sep 16.

Crop Genetics Department, John Innes Centre, Norwich, United Kingdom.

Wheat stem rust caused by the fungus f. sp. (), is regaining prominence due to the recent emergence of virulent isolates and epidemics in Africa, Europe and Central Asia. The development and deployment of wheat cultivars with multiple stem rust resistance () genes stacked together will provide durable resistance. However, certain disease resistance genes can suppress each other or fail in particular genetic backgrounds. Therefore, the function of each gene must be confirmed after incorporation into an -gene stack. This is difficult when using pathogen disease assays due to epistasis from recognition of multiple avirulence (Avr) effectors. Heterologous delivery of single effectors can circumvent this limitation, but this strategy is currently limited by the paucity of cloned . To accelerate gene cloning, we outline a procedure to develop a mutant population of spores and select for gain-of-virulence mutants. We used ethyl methanesulphonate (EMS) to mutagenize urediniospores and create a library of > 10,000 independent mutant isolates that were combined into 16 bulks of ~658 pustules each. We sequenced random mutants and determined the average mutation density to be 1 single nucleotide variant (SNV) per 258 kb. From this, we calculated that a minimum of three independently derived gain-of-virulence mutants is required to identify a given gene. We inoculated the mutant library onto plants containing , , or and obtained 9, 4, and 14 mutants with virulence toward , , or , respectively. However, only mutants identified on and maintained their virulence when reinolculated onto the lines from which they were identified. We further characterized 8 mutants with virulence toward . These also maintained their virulence profile on the stem rust international differential set containing 20 genes, indicating that they were most likely not accidental contaminants. In conclusion, our method allows selecting for virulent mutants toward targeted resistance () genes. The development of a mutant library from as little as 320 mg spores creates a resource that enables screening against several genes without the need for multiple rounds of spore multiplication and mutagenesis.
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http://dx.doi.org/10.3389/fpls.2020.570180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7533539PMC
September 2020

: A New Gene for Stem Rust Resistance from ssp. .

Phytopathology 2021 Mar 10;111(3):548-558. Epub 2021 Feb 10.

Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A.

Wheat stem rust (causal organism: f. sp. ) is an important fungal disease that causes significant yield losses in barley. The deployment of resistant cultivars is the most effective means of controlling this disease. Stem rust evaluations of a diverse collection of wild barley ( ssp. ) identified two Jordanian accessions (WBDC094 and WBDC238) with resistance to a virulent pathotype ( f. sp. HKHJC) from the United States. To elucidate the genetics of stem rust resistance, both accessions were crossed to the susceptible landrace Hiproly. Segregation ratios of F and F progeny indicated that a single dominant gene confers resistance to f. sp. HKHJC. Molecular mapping of the resistance locus was performed in the Hiproly/WBDC238 F population based on 3,329 single-nucleotide polymorphism markers generated by genotyping-by-sequencing. Quantitative trait locus analysis positioned the resistance gene to the long arm of chromosome 3H between the physical/genetic positions of 683.8 Mbp/172.9 cM and 693.7 Mbp/176.0 cM. Because this resistance gene is novel, it was assigned the new gene locus symbol of with a corresponding allele symbol of . At the seedling stage, confers resistance against a number of other important f. sp. pathotypes from the United States (MCCFC, QCCJB, and TTTTF) and Africa (TTKSK) as well as an isolate (92-MN-90) of the rye stem rust pathogen (. f. sp. ) from Minnesota. The resistance conferred by can be readily transferred into breeding programs because of its simple inheritance and clear phenotypic expression.
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http://dx.doi.org/10.1094/PHYTO-08-20-0325-RDOI Listing
March 2021

The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley.

Plant Biotechnol J 2021 Feb 6;19(2):273-284. Epub 2020 Sep 6.

John Innes Centre, Norwich Research Park, Norwich, UK.

In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley's genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley.
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http://dx.doi.org/10.1111/pbi.13460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7868974PMC
February 2021

Identification of quantitative trait loci for net form net blotch resistance in contemporary barley breeding germplasm from the USA using genome-wide association mapping.

Theor Appl Genet 2020 Mar 3;133(3):1019-1037. Epub 2020 Jan 3.

Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA.

Key Message: Association mapping study conducted in a population of 3490 elite barley breeding lines from ten barley breeding programs of the USA identified 12 QTLs for resistance/susceptibility to net form of net blotch. Breeding resistant varieties is the best management strategy for net form of net blotch (NFNB) in barley (Hordeum vulgare L.) caused by Pyrenophora teres f. teres (Ptt). Several resistance QTL have been previously identified in barley via linkage mapping and genome-wide association studies (GWAS). A GWAS conducted in a collection of advanced breeding lines (n = 3490) representing elite germplasm from ten barley breeding programs of the USA identified 42 unique marker-trait associations (MTA) for NFNB resistance. The lines were genotyped with 3072 SNP markers and phenotyped with four Ptt isolates in controlled environment. The lines were used to construct 13 different GWAS panels. Efficient mixed model association method with principal components and kinship was used for GWAS. Significance threshold for MTA was set at a false discovery rate of 0.05. Two, eight, six, one and 25 MTA were identified in chromosomes 1H, 3H, 4H, 5H and 6H, respectively. Based on genetic positions and linkage disequilibrium, these MTA's correspond to two, three, two, one and four QTLs in chromosome 1H, 3H, 4H, 5H and 6H, respectively. A comparison with previous linkage and GWAS studies revealed several previously identified and novel QTLs. Moreover, different genomic regions were found to be responsible for NFNB resistance in two-row versus six-row germplasm. The germplasm-specific SNP markers with additive effects and allelic distribution is reported to facilitate breeders in selection of markers for MAS to introgress novel net blotch resistance.
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http://dx.doi.org/10.1007/s00122-019-03528-5DOI Listing
March 2020

Virulence of Leaf Rust Physiological Races in Iran From 2010 to 2017.

Plant Dis 2020 Feb 18;104(2):363-372. Epub 2019 Dec 18.

Department of Plant Pathology, University of Minnesota, Minneapolis, MN, U.S.A.

The wheat leaf rust fungus, , has widespread geographical distribution in Iran within the Fertile Crescent region of the Middle East where wheat was domesticated and originated. Therefore, it is of great importance to identify the prevalence and distribution of pathotypes in this area. From 2010 to 2017, 241 single-uredinium isolates of . were purified from 175 collections of made from various hosts in 14 provinces of Iran, and they were tested on 20 Thatcher near-isogenic lines carrying single-leaf rust resistance genes. In total, 86 pathotypes were identified, of which the pathotypes FDTTQ, FDKPQ, FDKTQ, and FDTNQ were most prevalent. No virulence for was detected, whereas virulence for was found only on bread wheat in a few provinces in 2016. Only isolates from durum wheat and wild barley were virulent to . Although virulence for , , and was observed in some years, the virulence frequency for these genes was lower than that of the other genes. collections from host plants with different ploidy levels or genetically dissimilar backgrounds were grouped individually according to genetic distance. Based on these results, collections from barley, durum wheat, oat, triticale, and wild barley were different from those of bread wheat.
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http://dx.doi.org/10.1094/PDIS-06-19-1340-REDOI Listing
February 2020

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation.

Nat Commun 2019 11 7;10(1):5068. Epub 2019 Nov 7.

Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.

Parasexuality contributes to diversity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, are a major threat to global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt, with no recombination or chromosome reassortment. These findings indicate that nuclear exchange between dikaryotes can generate genetic diversity and facilitate the emergence of new lineages in asexual fungal populations.
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http://dx.doi.org/10.1038/s41467-019-12927-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838127PMC
November 2019

Variability in temperature-independent transpiration responses to evaporative demand correlate with nighttime water use and its circadian control across diverse wheat populations.

Planta 2019 Jul 3;250(1):115-127. Epub 2019 Apr 3.

Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Twin Cities, MN, USA.

Main Conclusion: Nocturnal transpiration, through its circadian control, plays a role in modulating daytime transpiration response to increasing evaporative demand, to potentially enable drought tolerance in wheat. Limiting plant transpiration rate (TR) in response to increasing vapor pressure deficit (VPD) has been suggested to enable drought tolerance through water conservation. However, there is very little information on the extent of diversity of TR response curves to "true" VPD (i.e., independent from temperature). Furthermore, new evidence indicate that water-saving could operate by modulating nocturnal TR (TR), and that this response might be coupled to daytime gas exchange. Based on 3 years of experimental data on a diverse group of 77 genotypes from 25 countries and 5 continents, a first goal of this study was to characterize the functional diversity in daytime TR responses to VPD and TR in wheat. A second objective was to test the hypothesis that these traits could be coupled through the circadian clock. Using a new gravimetric phenotyping platform that allowed for independent temperature and VPD control, we identified three and fourfold variation in daytime and nighttime responses, respectively. In addition, TR was found to be positively correlated with slopes of daytime TR responses to VPD, and we identified pre-dawn variation in TR that likely mediated this relationship. Furthermore, pre-dawn increase in TR positively correlated with the year of release among drought-tolerant Australian cultivars and with the VPD threshold at which they initiated water-saving. Overall, the study indicates a substantial diversity in TR responses to VPD that could be leveraged to enhance fitness under water-limited environments, and that TR and its circadian control may play an important role in the expression of water-saving.
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http://dx.doi.org/10.1007/s00425-019-03151-0DOI Listing
July 2019

Resistance gene cloning from a wild crop relative by sequence capture and association genetics.

Nat Biotechnol 2019 02 4;37(2):139-143. Epub 2019 Feb 4.

John Innes Centre, Norwich Research Park, Norwich, UK.

Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel.
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http://dx.doi.org/10.1038/s41587-018-0007-9DOI Listing
February 2019

Introgression of / Into Barley Germplasm Provides Insights Into the Genetics of Resistance to f. sp. Race TTKSK and Resources for Developing Resistant Cultivars.

Phytopathology 2019 Jun 7;109(6):1018-1028. Epub 2019 May 7.

1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331.

Stem rust (incited by f. sp. ) is a devastating disease of wheat and barley in many production areas. The widely virulent African f. sp. race TTKSK is of particular concern, because most cultivars are susceptible. To prepare for the possible arrival of race TTKSK in North America, we crossed a range of barley germplasm-representing different growth habits and end uses-with donors of stem rust resistance genes and . The former confers resistance to prevalent races of f. sp. in North America, and the latter confers resistance to TTKSK and other closely related races from Africa. We produced doubled haploids from these crosses and determined their allele type at the loci and haplotype at 7,864 single-nucleotide polymorphism loci. The doubled haploids were phenotyped for TTKSK resistance at the seedling stage. Integration of genotype and phenotype data revealed that (i) was not associated with TTKSK resistance, (ii) was necessary but was not sufficient for resistance, and (iii) specific haplotypes at two quantitative trait loci were required for to confer resistance to TTKSK. To confirm whether lines found resistant to TTKSK at the seedling resistance were also resistant at the adult plant stage, a subset of doubled haploids was evaluated in Kenya. Additionally, adult plant resistance to leaf rust and stripe rust (incited by and f. sp. , respectively) was also assessed on the doubled haploids in field trials at three locations in the United States over a 2-year period. Doubled haploids were identified with adult plant resistance to all three rusts, and this germplasm is available to the research and breeding communities.
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http://dx.doi.org/10.1094/PHYTO-09-18-0350-RDOI Listing
June 2019

Resistance of Aegilops longissima to the Rusts of Wheat.

Plant Dis 2018 Jun 2;102(6):1124-1135. Epub 2018 Apr 2.

School of Public Health, University of Minnesota, Minneapolis, 55455.

Stem rust (caused by Puccinia graminis f. sp. tritici), leaf rust (P. triticina), and stripe rust (P. striiformis f. sp. tritici) rank among the most important diseases of wheat worldwide. The development of resistant cultivars is the preferred method of controlling rust diseases because it is environmentally benign and also cost effective. However, new virulence types often arise in pathogen populations, rendering such cultivars vulnerable to losses. The identification of new sources of resistance is key to providing long-lasting disease control against the rapidly evolving rust pathogens. Thus, the objective of this research was to evaluate the wild wheat relative Aegilops longissima for resistance to stem rust, leaf rust, and stripe rust at the seedling stage in the greenhouse. A diverse collection of 394 accessions of the species, mostly from Israel, was assembled for the study, but the total number included in any one rust evaluation ranged from 308 to 379. With respect to stem rust resistance, 18.2 and 80.8% of accessions were resistant to the widely virulent U.S. and Kenyan P. graminis f. sp. tritici races of TTTTF and TTKSK, respectively. The percentage of accessions exhibiting resistance to the U.S. P. triticina races of THBJ and BBBD was 65.9 and 52.2%, respectively. Over half (50.1%) of the Ae. longissima accessions were resistant to the U.S. P. striiformis f. sp. tritici race PSTv-37. Ten accessions (AEG-683-23, AEG-725-15, AEG-803-49, AEG-1274-20, AEG-1276-22, AEG-1471-15, AEG-1475-19, AEG-2974-0, AEG-4005-20, and AEG-8705-10) were resistant to all races of the three rust pathogens used in this study. Distinct differences in the geographic distribution of resistance and susceptibility were found in Ae. longissima accessions from Israel in response to some rust races. To P. graminis f. sp. tritici race TTKSK, populations with a very high frequency of resistance were concentrated in the central and northern part of Israel, whereas populations with a comparatively higher frequency of susceptibility were concentrated in the southern part of the country. The reverse trend was observed with respect to P. striiformis f. sp. tritici race PSTv-37. The results from this study demonstrate that Ae. longissima is a rich source of rust resistance genes for wheat improvement.
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http://dx.doi.org/10.1094/PDIS-06-17-0880-REDOI Listing
June 2018

QTL Mapping of Fusarium Head Blight and Correlated Agromorphological Traits in an Elite Barley Cultivar Rasmusson.

Front Plant Sci 2018 28;9:1260. Epub 2018 Aug 28.

Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States.

Fusarium head blight (FHB) is an important fungal disease affecting the yield and quality of barley and other small grains. Developing and deploying resistant barley cultivars is an essential component of an integrated strategy for reducing the adverse effects of FHB. Genetic mapping studies have revealed that resistance to FHB and the accumulation of pathogen-produced mycotoxins are controlled by many quantitative trait loci (QTL) with minor effects and are highly influenced by plant morphological traits and environmental conditions. Some prior studies aimed at mapping FHB resistance have used populations derived from crossing a Swiss landrace Chevron with elite breeding lines/cultivars. Both Chevron and Peatland, a sib-line of Chevron, were used as founders in the University of Minnesota barley breeding program. To understand the native resistance that might be present in the Minnesota breeding materials, a cross of an elite cultivar with a susceptible unadapted genotype is required. Here, a mapping population of 93 recombinant inbred lines (RILs) was developed from a cross between a moderately susceptible elite cultivar 'Rasmusson' and a highly susceptible Japanese landrace PI 383933. This population was evaluated for FHB severity, deoxynivalenol (DON) accumulation and various agromorphological traits. Genotyping of the population was performed with the barley iSelect 9K SNP chip and 1,394 SNPs were used to develop a genetic map. FHB severity and DON accumulation were negatively correlated with plant height (HT) and spike length (SL), and positively correlated with spike density (SD). QTL analysis using composite interval mapping (CIM) identified the largest effect QTL associated with FHB and DON on the centromeric region of chromosome 7H, which was also associated with HT, SL, and SD. A minor FHB QTL and a minor DON QTL were detected on chromosome 6H and chromosome 3H, respectively, and the Rasmusson alleles contributed to resistance. The 3H DON QTL likely represents native resistance in elite germplasm as the marker haplotype of Rasmusson at this QTL is distinct from that of Chevron. This study highlights the relationship between FHB resistance/susceptibility and morphological traits and the need for breeders to account for morphology when developing FHB resistant genotypes.
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http://dx.doi.org/10.3389/fpls.2018.01260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127635PMC
August 2018

Correction to: Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79.

Theor Appl Genet 2018 10;131(10):2267

Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.

Unfortunately, one co-author name was incorrectly published in the original publication. The complete correct name should read as follows.
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http://dx.doi.org/10.1007/s00122-018-3170-yDOI Listing
October 2018

Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79.

Theor Appl Genet 2018 Oct 14;131(10):2245-2266. Epub 2018 Aug 14.

Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.

Key message Major stem rust resistance QTLs proposed to be Rpg2 from Hietpas-5 and Rpg3 from GAW-79 were identified in chromosomes 2H and 5H, respectively, and will enhance the diversity of stem rust resistance in barley improvement programs. Stem rust is a devastating disease of cereal crops worldwide. In barley (Hordeum vulgare ssp. 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 serious losses for more than 60 years; however, widely virulent Pgt races from Africa in the Ug99 group threaten the crop. The accessions Hietpas-5 (CIho 7124) and GAW-79 (PI 382313) both possess moderate-to-high levels of adult plant resistance to stem rust and are the sources of the resistance genes Rpg2 and Rpg3, respectively. To identify quantitative trait loci (QTL) for stem rust resistance in Hietpas-5 and GAW-79, two biparental populations were developed with Hiproly (PI 60693), a stem rust-susceptible accession. Both populations were phenotyped to the North American Pgt races of MCCFC, QCCJB, and HKHJC in St. Paul, Minnesota, and to African Pgt races (predominately TTKSK in the Ug99 group) in Njoro, Kenya. In the Hietpas-5/Hiproly population, a major effect QTL was identified in chromosome 2H, which is proposed as the location for Rpg2. In the GAW-79/Hiproly population, a major effect QTL was identified in chromosome 5H and is the proposed location for Rpg3. These QTLs will enhance the diversity of stem rust resistance in barley improvement programs.
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http://dx.doi.org/10.1007/s00122-018-3149-8DOI Listing
October 2018

The gene conferring susceptibility to spot blotch caused by Cochliobolus sativus is located at the Mla locus in barley cultivar Bowman.

Theor Appl Genet 2018 Jul 16;131(7):1531-1539. Epub 2018 Apr 16.

Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA.

Key Message: We identified, fine mapped, and physically anchored a dominant spot blotch susceptibility gene Scs6 to a 125 kb genomic region containing the Mla locus on barley chromosome 1H. Spot blotch caused by Cochliobolus sativus is an important disease of barley, but the molecular mechanisms underlying resistance and susceptibility to the disease are not well understood. In this study, we identified and mapped a gene conferring susceptibility to spot blotch caused by the pathotype 2 isolate (ND90Pr) of C. sativus in barley cultivar Bowman. Genetic analysis of F and F progeny as well as F families from a cross between Bowman and ND 5883 indicated that a single dominant gene (designated as Scs6) conferred spot blotch susceptibility in Bowman. Using a doubled haploid (DH) population derived from a cross between Calicuchima-sib (resistant) and Bowman-BC (susceptible), we confirmed that Scs6, contributed by Bowman-BC, was localized at the same locus as the previously identified spot blotch resistance allele Rcs6, which was contributed by Calicuchima-sib and mapped on the short arm of chromosome 1H. Using a genome-wide putative linear gene index of barley (Genome Zipper), 13 cleaved amplified polymorphism markers were developed from 11 flcDNA and two EST sequences and mapped to the Scs6/Rcs6 region on a linkage map constructed with the DH population. Further fine mapping with markers developed from barley genome sequences and F recombinants derived from Bowman × ND 5883 and Bowman × ND B112 crosses delimited Scs6 in a 125 kb genomic interval harboring the Mla locus on the reference genome of barley cv. Morex. This study provides a foundational step for further cloning of Scs6 using a map-based approach.
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http://dx.doi.org/10.1007/s00122-018-3095-5DOI Listing
July 2018

Genome Targeted Introgression of Resistance to African Stem Rust from into Bread Wheat.

Plant Genome 2017 11;10(3)

Many accessions of the wheat wild relative Sharon goatgrass ( Eig., ) are resistant to African races of the stem rust pathogen (i.e., Ug99 group races), which currently threaten wheat production worldwide. A procedure was designed to introgress the respective resistances to specific bread wheat genomes by producing plants homozygous for the A and B genomes and hemizygous for the D and S genomes or homozygous for the A and D genomes and hemizygous for the B and S genomes. In these genotypes, which lack the allele, homeologous pairing was expected mainly between chromosomes of the D and S genomes or B and S genomes, respectively. An antigametocidal (AG) wheat mutant () was used to overcome gametocidal effects. Wheat lines initially found resistant at the seedling stage were also highly resistant at the adult plant stage in rust nurseries established in the field. DNA of 41 selected homozygous resistant lines, analyzed by the Axiom wheat 820K SNP array, showed alien chromatin mainly in wheat chromosomes 1B, 1D, and 5B. This work suggests that, in most cases, it is possible to target introgressions into the homeologous chromosome of a selected genome of bread wheat.
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http://dx.doi.org/10.3835/plantgenome2017.07.0061DOI Listing
November 2017

Genome-wide association study of stem rust resistance in a world collection of cultivated barley.

Theor Appl Genet 2018 Jan 24;131(1):107-126. Epub 2017 Nov 24.

Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.

Key Message: QTL conferring a 14-40% reduction in adult plant stem rust severity to multiple races of Pgt were found on chromosome 5H and will be useful in barley breeding. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt) is an important disease of barley. The resistance gene Rpg1 has protected the crop against stem rust losses for over 70 years in North America, but is not effective against the African Pgt race TTKSK (and its variants) nor the domestic race QCCJB. To identify resistance to these Rpg1-virulent races, the Barley iCore Collection, held by the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection was evaluated for adult plant resistance (APR) and seedling resistance to race TTKSK and APR to race QCCJB and the Pgt TTKSK composite of races TTKSK, TTKST, TTKTK, and TTKTT. Using a genome-wide association study approach based on 6224 single nucleotide polymorphic markers, seven significant loci for stem rust resistance were identified on chromosomes 1H, 2H, 3H, and 5H. The most significant markers detected were 11_11355 and SCRI_RS_177017 at 71-75 cM on chromosome 5H, conferring APR to QCCJB and TTKSK composite. Significant markers were also detected for TTKSK seedling resistance on chromosome 5H. All markers detected on 5H were independent of the rpg4/Rpg5 complex at 152-168 cM. This study verified the importance of the 11_11355 locus in conferring APR to races QCCJB and TTKSK and suggests that it may be effective against other races in the Ug99 lineage.
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http://dx.doi.org/10.1007/s00122-017-2989-yDOI Listing
January 2018

Genome-Wide Association Mapping of Stem Rust Resistance in subsp. .

G3 (Bethesda) 2017 10 5;7(10):3491-3507. Epub 2017 Oct 5.

Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108

Stem rust was one of the most devastating diseases of barley in North America. Through the deployment of cultivars with the resistance gene , losses to stem rust have been minimal over the past 70 yr. However, there exist both domestic (QCCJB) and foreign (TTKSK aka isolate Ug99) pathotypes with virulence for this important gene. To identify new sources of stem rust resistance for barley, we evaluated the Wild Barley Diversity Collection (WBDC) (314 ecogeographically diverse accessions of subsp. ) for seedling resistance to four pathotypes (TTKSK, QCCJB, MCCFC, and HKHJC) of the wheat stem rust pathogen ( f. sp. , ) and one isolate (92-MN-90) of the rye stem rust pathogen ( f. sp. , ). Based on a coefficient of infection, the frequency of resistance in the WBDC was low ranging from 0.6% with HKHJC to 19.4% with 92-MN-90. None of the accessions was resistant to all five cultures of A genome-wide association study (GWAS) was conducted to map stem rust resistance loci using 50,842 single-nucleotide polymorphic markers generated by genotype-by-sequencing and ordered using the new barley reference genome assembly. After proper accounting for genetic relatedness and structure among accessions, 45 quantitative trait loci were identified for resistance to across all seven barley chromosomes. Three novel loci associated with resistance to TTKSK, QCCJB, MCCFC, and 92-MN-90 were identified on chromosomes 5H and 7H, and two novel loci associated with resistance to HKHJC were identified on chromosomes 1H and 3H. These novel alleles will enhance the diversity of resistance available for cultivated barley.
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http://dx.doi.org/10.1534/g3.117.300222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633397PMC
October 2017

Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis.

Theor Appl Genet 2017 Jun 8;130(6):1207-1222. Epub 2017 Mar 8.

John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.

Key Message: We identified two novel wheat stem rust resistance genes, Sr-1644-1Sh and Sr-1644-5Sh in Aegilops sharonensis that are effective against widely virulent African races of the wheat stem rust pathogen. Stem rust is one of the most important diseases of wheat in the world. When single stem rust resistance (Sr) genes are deployed in wheat, they are often rapidly overcome by the pathogen. To this end, we initiated a search for novel sources of resistance in diverse wheat relatives and identified the wild goatgrass species Aegilops sharonesis (Sharon goatgrass) as a rich reservoir of resistance to wheat stem rust. The objectives of this study were to discover and map novel Sr genes in Ae. sharonensis and to explore the possibility of identifying new Sr genes by genome-wide association study (GWAS). We developed two biparental populations between resistant and susceptible accessions of Ae. sharonensis and performed QTL and linkage analysis. In an F recombinant inbred line and an F population, two genes were identified that mapped to the short arm of chromosome 1S, designated as Sr-1644-1Sh, and the long arm of chromosome 5S, designated as Sr-1644-5Sh. The gene Sr-1644-1Sh confers a high level of resistance to race TTKSK (a member of the Ug99 race group), while the gene Sr-1644-5Sh conditions strong resistance to TRTTF, another widely virulent race found in Yemen. Additionally, GWAS was conducted on 125 diverse Ae. sharonensis accessions for stem rust resistance. The gene Sr-1644-1Sh was detected by GWAS, while Sr-1644-5Sh was not detected, indicating that the effectiveness of GWAS might be affected by marker density, population structure, low allele frequency and other factors.
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http://dx.doi.org/10.1007/s00122-017-2882-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440502PMC
June 2017

Mapping quantitative trait loci conferring resistance to a widely virulent isolate of Cochliobolus sativus in wild barley accession PI 466423.

Theor Appl Genet 2016 Oct 17;129(10):1831-42. Epub 2016 Jun 17.

Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA.

Key Message: This research characterized the genetics of resistance of wild barley accession PI 466423 to a widely virulent pathotype of Cochliobolus sativus . Breeding lines were identified that combine the Midwest Six-rowed Durable Resistance Haplotype and resistance to the virulent isolate ND4008. Spot blotch, caused by Cochliobolus sativus, is a historically important foliar disease of barley (Hordeum vulgare L.) in the Upper Midwest region of the USA. However, for the last 50 years this disease has been of little consequence due to the deployment of resistant six-rowed malting cultivars. These durably resistant cultivars carry the Midwest Six-rowed Durable Resistant Haplotype (MSDRH) comprised of three Quantitative Trait Loci (QTL) on chromosomes 1H, 3H and 7H, originally contributed by breeding line NDB112. Recent reports of C. sativus isolates (e.g. ND4008) with virulence on NDB112 indicate that widely grown cultivars of the region are vulnerable to spot blotch epidemics. Wild barley (H. vulgare ssp. spontaneum), the progenitor of cultivated barley, is a rich source of novel alleles, especially for disease resistance. Wild barley accession PI 466423 is highly resistant to C. sativus isolate ND4008. To determine the genetic architecture of resistance to isolate ND4008 in PI 466423, we phenotyped and genotyped an advanced backcross population (N = 244) derived from the wild accession and the recurrent parent 'Rasmusson', a Minnesota cultivar with the MSDRH. Disease phenotyping was done on BC2F4 seedlings in the greenhouse using isolate ND4008. The Rasmusson/PI 466423 population was genotyped with 7842 single nucleotide polymorphic markers. QTL analysis using composite interval mapping revealed four resistance loci on chromosomes 1H, 2H, 4H and 5H explaining 10.3, 7.4, 6.4 and 8.4 % of the variance, respectively. Resistance alleles on chromosomes 1H, 4H and 5H were contributed by PI 466423, whereas the one on chromosome 2H was contributed by Rasmusson. All four resistance QTL are likely coincident with previously identified QTL. Agronomically advanced two- and six-rowed lines combining the MSDRH and resistance alleles to isolate ND4008 have been identified and are being utilized in breeding. These results reaffirm the value of using wild relatives as a source of novel resistance alleles.
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http://dx.doi.org/10.1007/s00122-016-2742-yDOI Listing
October 2016

Sources of Stem Rust Resistance in Wheat-Alien Introgression Lines.

Plant Dis 2016 Jun 23;100(6):1101-1109. Epub 2016 Mar 23.

Department of Plant Breeding, Swedish University of Agricultural Sciences.

Stem rust is one of the most devastating diseases of wheat. Widely virulent races of the pathogen in the Ug99 lineage (e.g., TTKSK) are threatening wheat production worldwide; therefore, there is an urgent need to enhance the diversity of resistance genes in the crop. The objectives of this study were to identify new sources of resistance in wheat-alien introgression derivatives from Secale cereale, Leymus mollis, L. racemosus, and Thinopyrum junceiforme, postulate genes conferring the resistance, and verify the postulated genes by use of molecular markers. From seedling tests conducted in the greenhouse, the presence of seven known stem rust resistance genes (Sr7b, Sr8a, Sr9d, Sr10, Sr31, Sr36, and SrSatu) was postulated in the wheat-alien introgression lines. More lines possessed a high level of resistance in the field compared with the number of lines that were resistant at the seedling stage. Three 2R (2D) wheat-rye substitution lines (SLU210, SLU238, and SLU239) seemed likely to possess new genes for resistance to stem rust based on their resistance pattern to 13 different stem rust races but the genes responsible could not be identified. Wheat-rye, wheat-L. racemosus, and wheat-L. mollis substitutions or translocations with single and multiple interchanges of chromosomes, in particular of the B and D chromosomes of wheat, were verified by a combination of genomic in situ hybridization and molecular markers. Thus, the present study identified novel resistance genes originating from different alien introgressions into the wheat genome of the evaluated lines. Such genes may prove useful in enhancing the diversity of stem rust resistance in wheat against widely virulent pathogen races such as those in the Ug99 lineage.
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http://dx.doi.org/10.1094/PDIS-12-15-1448-REDOI Listing
June 2016

Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley.

Genetics 2016 07 10;203(3):1453-67. Epub 2016 May 10.

Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108

The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC2F4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r(2) = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for high-resolution gene mapping and discovery of novel allelic variation using wild barley germplasm.
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http://dx.doi.org/10.1534/genetics.116.190736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937491PMC
July 2016

A new 2DS·2RL Robertsonian translocation transfers stem rust resistance gene Sr59 into wheat.

Theor Appl Genet 2016 Jul 29;129(7):1383-1392. Epub 2016 Mar 29.

Department of Plant Breeding, Swedish University of Agricultural Sciences, PO Box 101, 23053, Alnarp, Sweden.

Key Message: A new stem rust resistance gene Sr59 from Secale cereale was introgressed into wheat as a 2DS·2RL Robertsonian translocation. Emerging new races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici), from Africa threaten global wheat (Triticum aestivum L.) production. To broaden the resistance spectrum of wheat to these widely virulent African races, additional resistance genes must be identified from all possible gene pools. From the screening of a collection of wheat-rye (Secale cereale L.) chromosome substitution lines developed at the Swedish University of Agricultural Sciences, we described the line 'SLU238' 2R (2D) as possessing resistance to many races of P. graminis f. sp. tritici, including the widely virulent race TTKSK (isolate synonym Ug99) from Africa. The breakage-fusion mechanism of univalent chromosomes was used to produce a new Robertsonian translocation: T2DS·2RL. Molecular marker analysis and stem rust seedling assays at multiple generations confirmed that the stem rust resistance from 'SLU238' is present on the rye chromosome arm 2RL. Line TA5094 (#101) was derived from 'SLU238' and was found to be homozygous for the T2DS·2RL translocation. The stem rust resistance gene on chromosome 2RL arm was designated as Sr59. Although introgressions of rye chromosome arms into wheat have most often been facilitated by irradiation, this study highlights the utility of the breakage-fusion mechanism for rye chromatin introgression. Sr59 provides an additional asset for wheat improvement to mitigate yield losses caused by stem rust.
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http://dx.doi.org/10.1007/s00122-016-2710-6DOI Listing
July 2016

A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family.

PLoS One 2015 8;10(7):e0130890. Epub 2015 Jul 8.

ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.

Cellulose is a fundamentally important component of cell walls of higher plants. It provides a scaffold that allows the development and growth of the plant to occur in an ordered fashion. Cellulose also provides mechanical strength, which is crucial for both normal development and to enable the plant to withstand both abiotic and biotic stresses. We quantified the cellulose concentration in the culm of 288 two--rowed and 288 six--rowed spring type barley accessions that were part of the USDA funded barley Coordinated Agricultural Project (CAP) program in the USA. When the population structure of these accessions was analysed we identified six distinct populations, four of which we considered to be comprised of a sufficient number of accessions to be suitable for genome-wide association studies (GWAS). These lines had been genotyped with 3072 SNPs so we combined the trait and genetic data to carry out GWAS. The analysis allowed us to identify regions of the genome containing significant associations between molecular markers and cellulose concentration data, including one region cross-validated in multiple populations. To identify candidate genes we assembled the gene content of these regions and used these to query a comprehensive RNA-seq based gene expression atlas. This provided us with gene annotations and associated expression data across multiple tissues, which allowed us to formulate a supported list of candidate genes that regulate cellulose biosynthesis. Several regions identified by our analysis contain genes that are co-expressed with cellulose synthase A (HvCesA) across a range of tissues and developmental stages. These genes are involved in both primary and secondary cell wall development. In addition, genes that have been previously linked with cellulose synthesis by biochemical methods, such as HvCOBRA, a gene of unknown function, were also associated with cellulose levels in the association panel. Our analyses provide new insights into the genes that contribute to cellulose content in cereal culms and to a greater understanding of the interactions between them.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130890PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4496100PMC
April 2016

Resistance of Aegilops Species from Israel to Widely Virulent African and Israeli Races of the Wheat Stem Rust Pathogen.

Plant Dis 2014 Oct;98(10):1309-1320

Department of Plant Pathology, University of Minnesota.

Widely virulent races of the stem rust pathogen (Puccinia graminis f. sp. tritici) such as those isolated from Africa (e.g., TTKSK, isolate synonym Ug99) threaten wheat production worldwide. To identify Aegilops accessions with effective resistance to such virulent stem rust races, up to 10 different species from Israel were evaluated against African races TTKSK, TTKST, and TTTSK and the Israeli race TTTTC as seedlings in the greenhouse. A wide diversity of stem rust reactions was observed across the Aegilops spp. and ranged from highly resistant (i.e., infection type 0) to highly susceptible (infection type 4). The frequency of resistance within a species to races TTTTC and TTKSK ranged from 7 and 14%, respectively, in Aegilops searsii to 98 and 100% in AE. speltoides. In all, 346 accessions were found resistant to the three African races and 138 accessions were resistant (or heterogeneous with a resistant component) to all four races. The species with broadly resistant accessions included Ae. longissima (59 accessions), Ae. peregrina (47 accessions), Ae. sharonensis (15 accessions), Ae. geniculata (9 accessions), Ae. kotschyi (5 accessions), and Ae. bicornis (3 accessions). Few geographical trends or correlations with climatic variables were observed with respect to stem rust resistance in the Aegilops spp. The exception was Ae. longissima infected with race TTTTC, where a high frequency of resistance was found in central and northern Israel and a very low frequency in southern Israel (Negev desert region). This geographical trend followed a pattern of annual precipitation in Israel, and a significant correlation was found between this variable and resistance in Ae. longissima. Although difficult, it is feasible to transfer resistance genes from Aegilops spp. into wheat through conventional wide-crossing schemes or, alternatively, a cloning and transformation approach. The broadly resistant accessions identified in this study will be valuable in these research programs.
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http://dx.doi.org/10.1094/PDIS-01-14-0062-REDOI Listing
October 2014