Genetic analysis of leaf and stripe rust resistance in the spring wheat (Triticum aestivum L.) cross RL4452/AC Domain

Leaf rust and stripe rust of wheat (Triticum aestivum L.) are caused by the fungal pathogens Puccinia triticina, and Puccinia striiformis f.sp. tritici, respectively. In North America, the incorporation of adult-plant resistance (APR) genes into breeding lines has been an important strategy to achieve durable resistance to both diseases. Previously, the spring wheat cultivar AC Domain was reported to express an effective level of adult-plant resistance (APR) to leaf rust under field conditions. Early gene postulation work had suggested AC Domain might carry the APR gene Lr34 due to its phenotypic similarity to other Lr34 carrying lines. However, new gene specific markers have shown that AC Domain is not a carrier of Lr34. The objective of this research was to genetically localize the resistance in AC Domain, which is important because the cultivar has frequently been used as a parent in Canadian breeding programs, primarily for its value as a source of pre-harvest sprouting resistance. A mapping population of 185 doubled haploid (DH) lines derived from the cross ‘RL4452’ by ‘AC Domain’ was used for this study. RL4452 is a known carrier of Lr34. During 2011-2012, the DH population was evaluated in field leaf rust nurseries at Saskatoon, SK and Portage, MB and at a stripe rust nursery at Lethbridge, AB. Field results indicated that rust resistance in the mapping population was variable, with lines ranging from highly resistant, to highly susceptible. DH lines carrying Lr34 showed a high level of resistance to both diseases. Thus, the non-Lr34 carriers were genotyped using select SSR markers, and by an Illumina 9k Infinium iSelect SNP assay for subsequent quantitative trait loci (QTL) analysis. QTL analysis revealed that AC Domain donated a major resistance QTL located on chromosome 2BS, that mapped 46 cM proximal to markers linked to Lr16, and explained a significant portion of the leaf and stripe rust phenotypic variance in all test environments. In addition, this QTL was significantly associated with the expression leaf tip necrosis (LTN), reduction in area under the disease progress curve (AUDPC), and coefficient of infection (CI). In certain environments the interaction between the 2B QTL and Lr34 was additive resulting in a superior level of rust resistance. Indoor rust testing showed AC Domain was susceptible to both diseases at the seedling stage. Taken together these results suggest that the identified resistance in AC Domain is likely due to the presence of an APR gene, on chromosome 2BS

A study of solid-stem expression in durum and common wheat

The wheat stem sawfly (WSS) is a damaging insect pest of wheat in North America. Resistance to WSS has primarily been achieved by introgressing the stem-solidness QTL SSt1 into elite cultivars. This thesis comprehensively examined the expression of SSt1 from both the phenotypic and genetic perspective. The first study investigated the influence of four sowing densities on pith expression for two newly released solid-stemmed durum cultivars, CDC Fortitude and AAC Raymore. Both cultivars had strong pith expression (average stem-solidness > 3.9) across all environments and sowing densities, in contrast to the common wheat cultivar Lillian (average stem-solidness = 2.2). Increasing sowing density had a positive effect on grain yield in all cultivars, but was negatively associated with stem-solidness. These findings suggest that, unlike with Lillian, altering sowing density is not required to achieve effective sawfly resistance with CDC Fortitude and AAC Raymore. For the second study, we improved the resolution of the SSt1 interval in durum and common wheat by localizing coincident QTL near the telomere of 3BL (LOD = 94 - 127, R2 = 78 - 92 %). The SSt1 interval spanned a 1.6 Mb interval on chromosome 3B. Minor QTL were identified on chromosomes 2A, 2D, 4A, and 5A that synergistically enhanced the expression of SSt1 to increase stem-solidness. These results suggest breeding for improved stem-solidness is possible by combining SSt1 with favorable alleles at minor loci. Finally, we investigated gene expression and structural variation within the SSt1 interval. This showed that in addition to structural variation between genome assemblies, the SSt1 locus has also undergone a series of functional gene duplication/expansion events. One gene encoding a Dof transcription factor (TraesCS3B01G60880) was consistently up-regulated across solid-stemmed cultivars. Further investigation revealed that solid-stemmed cultivars carry multiple copies of TraesCS3B01G60880. Screening of a mutant population identified two mutant lines with a hollow-stemmed phenotype that either have a deletion, or reduced expression of TraesCS3B01G60880. Taken together, this research provides new insights into the phenotypic and genetic expression of SSt1 in wheat, and will provide an important foundation for future experiments that will help breeders improve resistance to the WSS

A Novel Agonist of the TRIF Pathway Induces a Cellular State Refractory to Replication of Zika, Chikungunya, and Dengue Viruses.

The ongoing concurrent outbreaks of Zika, Chikungunya, and dengue viruses in Latin America and the Caribbean highlight the need for development of broad-spectrum antiviral treatments. The type I interferon (IFN) system has evolved in vertebrates to generate tissue responses that actively block replication of multiple known and potentially zoonotic viruses. As such, its control and activation through pharmacological agents may represent a novel therapeutic strategy for simultaneously impairing growth of multiple virus types and rendering host populations resistant to virus spread. In light of this strategy\u27s potential, we undertook a screen to identify novel interferon-activating small molecules. Here, we describe 1-(2-fluorophenyl)-2-(5-isopropyl-1,3,4-thiadiazol-2-yl)-1,2-dihydrochromeno[2,3

Search for single top quarks in the tau+jets channel using 4.8 fb−1^{-1} of ppˉp\bar{p} collision data

We present the first direct search for single top quark production using tau leptons. The search is based on 4.8 fb$^{-1}$ of integrated luminosity collected in $p\bar{p}$ collisions at $\sqrt{s}$=1.96 TeV with the D0 detector at the Fermilab Tevatron Collider. We select events with a final state including an isolated tau lepton, missing transverse energy, two or three jets, one or two of them $b$ tagged. We use a multivariate technique to discriminate signal from background. The number of events observed in data in this final state is consistent with the signal plus background expectation. We set in the tau+jets channel an upper limit on the single top quark cross section of \TauLimObs pb at the 95% C.L. This measurement allows a gain of 4% in expected sensitivity for the observation of single top production when combining it with electron+jets and muon+jets channels already published by the D0 collaboration with 2.3 fb$^{-1}$ of data. We measure a combined cross section of \SuperCombineXSall pb, which is the most precise measurement to date.Comment: 12 pages, 5 figure

b-Jet Identification in the D0 Experiment

Algorithms distinguishing jets originating from b quarks from other jet flavors are important tools in the physics program of the D0 experiment at the Fermilab Tevatron p-pbar collider. This article describes the methods that have been used to identify b-quark jets, exploiting in particular the long lifetimes of b-flavored hadrons, and the calibration of the performance of these algorithms based on collider data.Comment: submitted to Nuclear Instruments and Methods in Physics Research

Measurement of the dijet invariant mass cross section in proton anti-proton collisions at sqrt{s} = 1.96 TeV

The inclusive dijet production double differential cross section as a function of the dijet invariant mass and of the largest absolute rapidity of the two jets with the largest transverse momentum in an event is measured in proton anti-proton collisions at sqrt{s} = 1.96 TeV using 0.7 fb^{-1} integrated luminosity collected with the D0 detector at the Fermilab Tevatron Collider. The measurement is performed in six rapidity regions up to a maximum rapidity of 2.4. Next-to-leading order perturbative QCD predictions are found to be in agreement with the data.Comment: Published in Phys. Lett. B, 693, (2010), 531-538, 8 pages, 2 figures, 6 table

Measurement of Z/gamma*+jet+X angular distributions in ppbar collisions at sqrt{s}=1.96 TeV

We present the first measurements at a hadron collider of differential cross sections for Z+jet+X production in delta phi(Z, jet), |delta y(Z, jet)| and |y_boost(Z, jet)|. Vector boson production in association with jets is an excellent probe of QCD and constitutes the main background to many small cross section processes, such as associated Higgs production. These measurements are crucial tests of the predictions of perturbative QCD and current event generators, which have varied success in describing the data. Using these measurements as inputs in tuning event generators will increase the experimental sensitivity to rare signals.Comment: Published in Physics Letters B 682 (2010), pp. 370-380. 15 pages, 6 figure

Search for the standard model Higgs boson in tau final states

We present a search for the standard model Higgs boson using hadronically decaying tau leptons, in 1 inverse femtobarn of data collected with the D0 detector at the Fermilab Tevatron ppbar collider. We select two final states: tau plus missing transverse energy and b jets, and tau+ tau- plus jets. These final states are sensitive to a combination of associated W/Z boson plus Higgs boson, vector boson fusion and gluon-gluon fusion production processes. The observed ratio of the combined limit on the Higgs production cross section at the 95% C.L. to the standard model expectation is 29 for a Higgs boson mass of 115 GeV.Comment: publication versio

Search for new fermions ("quirks") at the Fermilab Tevatron Collider

We report results of a search for particles with anomalously high ionization in events with a high transverse energy jet and large missing transverse energy in $2.4$ fb$^{-1}$ of integrated luminosity collected by the D0 experiment at the Fermilab Tevatron $p\bar{p}$ collider. Production of such particles (quirks) is expected in scenarios with extra QCD-like {\it SU(N)} sectors, and this study is the first dedicated search for such signatures. We find no evidence of a signal and set a lower mass limit of 107 ~GeV for the mass of a charged quirk with strong dynamics scale $\Lambda$ in the range from 10 keV to 1 MeV.Comment: submitted to Phys. Rev. Letter