Registration of ‘Alba’ Barley

'Alba' (Reg. No. [CV-355, PI 672535]) is a winter, six-row barley released by the Oregon Agricultural Experiment Station in 2012. The name “Alba” was chosen due to the bright and attractive appearance of the crop at maturity. In high rainfall environments, it has a notable yield advantage over check varieties and maintains excellent test weight and kernel plumpness. These advantages are, in part, attributable to resistance to barley stripe rust (incited by Puccinia striiformis f. sp. hordei) and scald (incited by Rhynchosporium commune). The principal end-use of Alba grain is as feed, but it could also be used for food (after pearling) and preliminary tests show that it can be successfully malted and used in craft brewing.This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the Crop Science Society of America, Inc. and can be found at: https://dl.sciencesocieties.org/publications/jpr,The ‘Alba’ (Reg. No. CV-355, PI 672535) is the registration number that has been assigned to this winter, six-row barley (Hordeum vulgare L.) cultivar. The registration number for ‘Alba’ (Reg. No. CV-355, PI 672535) was assigned after the authors' final manuscript was accepted for publication and may be lacking in the version that appears here

Ginzburg-Landau-Gor'kov Theory of Magnetic oscillations in a type-II 2-dimensional Superconductor

We investigate de Haas-van Alphen (dHvA) oscillations in the mixed state of a type-II two-dimensional superconductor within a self-consistent Gor'kov perturbation scheme. Assuming that the order parameter forms a vortex lattice we can calculate the expansion coefficients exactly to any order. We have tested the results of the perturbation theory to fourth and eight order against an exact numerical solution of the corresponding Bogoliubov-de Gennes equations. The perturbation theory is found to describe the onset of superconductivity well close to the transition point $H_{c2}$. Contrary to earlier calculations by other authors we do not find that the perturbative scheme predicts any maximum of the dHvA-oscillations below $H_{c2}$. Instead we obtain a substantial damping of the magnetic oscillations in the mixed state as compared to the normal state. We have examined the effect of an oscillatory chemical potential due to particle conservation and the effect of a finite Zeeman splitting. Furthermore we have investigated the recently debated issue of a possibility of a sign change of the fundamental harmonic of the magnetic oscillations. Our theory is compared with experiment and we have found good agreement.Comment: 39 pages, 8 figures. This is a replacement of supr-con/9608004. Several sections changed or added, including a section on the effect of spin and the effect of a conserved number of particles. To be published in Phys. Rev.

Theory of de Haas-van Alphen Effect in Type-II Superconductors

Theory of quasiparticle spectra and the de Haas-van Alphen (dHvA) oscillation in type-II superconductors are developed based on the Bogoliubov-de Gennes equations for vortex-lattice states. As the pair potential grows through the superconducting transition, each degenerate Landau level in the normal state splits into quasiparticle bands in the magnetic Brillouin zone. This brings Landau-level broadening, which in turn leads to the extra dHvA oscillation damping in the vortex state. We perform extensive numerical calculations for three-dimensional systems with various gap structures. It is thereby shown that (i) this Landau-level broadening is directly connected with the average gap at H=0 along each Fermi-surface orbit perpendicular to the field H; (ii) the extra dHvA oscillation attenuation is caused by the broadening around each extremal orbit. These results imply that the dHvA experiment can be a unique probe to detect band- and/or angle-dependent gap amplitudes. We derive an analytic expression for the extra damping based on the second-order perturbation with respect to the pair potential for the Luttinger-Ward thermodynamic potential. This formula reproduces all our numerical results excellently, and is used to estimate band-specific gap amplitudes from available data on NbSe_2, Nb_3Sn, and YNi_2B_2C. The obtained value for YNi_2B_2C is fairly different from the one through a specific-heat measurement, indicating presence of gap anisotropy in this material. C programs to solve the two-dimensional Bogoliubov-de Gennes equations are available at http://phys.sci.hokudai.ac.jp/~kita/index-e.html .Comment: 16 pages, 11 figure

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of these tocochromanol forms in barley, seven of which were within 2 cM of sequences homologous to cloned genes associated with tocochromanol production in barley and/or other plants. These associations confirmed a prior report based on bi-parental QTL mapping. This knowledge will aid future efforts to better understand the role of tocochromanols in barley, with specific reference to abiotic stress resistance. It will also be useful in developing barley varieties with higher tocochromanol concentrations, although at current recommended daily consumption amounts, barley would not be an effective sole source of vitamin E. However, it could be an important contributor in the context of whole grains in a balanced diet

ThesisData.tar.gz

This thesis consists of three manuscripts addressing separate components of barley breeding, plus an introduction and a conclusion summarizing the status of barley in the Pacific Northwest, plus the implications of the research presented in this thesis. In the first manuscript, a package written for the statistical software "R" that is designed to identify subsets of plant accessions that would be favorable for rare-trait discovery and genome-wide association studies is presented. In the second manuscript, genome-wide association scanning is used to identify thirteen single-nucleotide polymorphism markers that are significantly associated with tocochromanol concentration in a set of elite, spring barley accessions. In the third manuscript, the barley variety "Alba" was described in a germplasm release

GraebnerRyanC2015.pdf

This thesis consists of three manuscripts addressing separate components of barley breeding, plus an introduction and a conclusion summarizing the status of barley in the Pacific Northwest, plus the implications of the research presented in this thesis. In the first manuscript, a package written for the statistical software "R" that is designed to identify subsets of plant accessions that would be favorable for rare-trait discovery and genome-wide association studies is presented. In the second manuscript, genome-wide association scanning is used to identify thirteen single-nucleotide polymorphism markers that are significantly associated with tocochromanol concentration in a set of elite, spring barley accessions. In the third manuscript, the barley variety "Alba" was described in a germplasm release

Breeding qualitative and quantitative traits for potatoes in the Columbia Basin

The cultivated potato (Solanum tuberosum L.) is one of the world’s most important staple crops, ranked fourth after maize, rice, and wheat. While the potato’s success is due largely to its high yield, it also benefits from its broad global acceptance, and its ability to be used by the consumer without prior processing. However, the potato’s success as a crop comes despite an array of pathogens that can cause extreme yield losses, and quality defects that can make the potato essentially unmarketable. While they can be costly and at times devastating, the presence of these pathogens creates an enormous opportunity for the genetic improvement of the potato. For every major pathogen in potato, multiple sources of resistance have been identified in landraces or wild potato species that if combined in a suitable potato cultivar, could reduce or eliminate the damage caused by that pathogen. While the utilization of genes from exotic germplasm is far from trivial, advances in genetics, genomics, and phenomics will certainly accelerate this process. In addition to improved biotic and abiotic stress resistance, a major feat in potato breeding would be to identify an improved system for developing potato clones with superior quantitative traits. The current strategy used to develop new cultivars, which involves planting tens of thousands of seedlings each year from intercrossed heterozygous clones, may be the best strategy for developing new varieties. However, the difficulty of producing superior potato clones using this strategy has prompted some breeding programs to explore how alternative breeding methods might be applied. Nine wild potato species were evaluated for their resistance to Meloidogyne chitwoodi (the Columbia root-knot nematode, CRKN), which can cause serious damage in potato production systems. Greenhouse screening identified fifteen clones from S. hougasii, one clone from S. bulbocastanum, and one clone from S. stenophyllidium, with moderate to high levels of resistance against three isolates of M. chitwoodi. Geographical mapping showed that these newly identified resistance sources are clustered in the states of Jalisco and Michoacán in west-central Mexico. Further, we screened seedlings from nine potato species for their response to Verticillium wilt (Verticillium dahliae), a major soil-borne pathogen of potatoes in many regions of the world. Greenhouse screenings identified two clones from Solanum andreanum and one clone from S. bulbocastanum that had resistance equal to or greater than ‘Ranger Russet’, the moderately resistant check. These new V. dahliae resistance sources have different taxonomic origins from previous V. dahliae sources and will expand our V. dahliae resistant potato germplasm. ‘Castle Russet’ is a newly released variety from the Northwest potato variety development program with improved agronomic performance and resistance to Potato virus Y (PVY) and Corky ringspot (CRS). A mapping population was developed to study segregation of resistance to PVY and CRS and identify single nucleotide polymorphism (SNP) markers linked to these resistances. SNP genotyping identified that the population phenotyped is in fact a mix of two populations. Molecular mapping of the real population of 49 clones identified 31 SNPs linked to PVY resistance, in addition to the markers STM0003 and YES3-3B, which were previously shown to be linked to Rysto. A single marker association analysis for CRS identified a major peak in chromosome 9 and two minor peaks in chromosomes 1 and 10. The identified linked SNPs for PVY and CRS need to be validated in a larger population for effective use in marker assisted breeding. Finally, we investigated crosses between “Russet” and “Chipper” type potato clones (Russet-Chipper crosses), as well as between elite long- day adapted tetraploid clones and clones from an improved population of diploid potatoes derived from Group Phureja and Group Stenotomum (4x-2x crosses) were investigated. In our trials, clones derived from Russet-Chipper crosses had few notable benefits when compared to clones derived from crosses made within the Russet and Chipper groups in our trial. On the other hand, many of the clones derived from 4x-2x crosses clearly out-yielded the highest yielding clones from crosses between elite long-day adapted tetraploid potato clones. While every favorable quality trait measured was present in at least several clones derived from 4x-2x crosses, the frequency of many of these favorable quality traits was lower than was observed in crosses between elite long-day adapted tetraploid potato clones. Therefore, continued selection of parental clones in 4x and 2x populations would likely be required before a high yielding clone with acceptable or superior quality characteristics could be expected from these 4x-2x crosses. When evaluating the 4x-2x crosses, we found that 61.5% of the resulting clones were triploid, compared to a previously reported frequency of 0.0-7.6%. Tubers of these triploids are generally intermediate between the two parental groups, indicating that there are no pronounced tuber characteristics associated with triploid potato clones. This finding opens the possibility of using triploid potatoes in potato variety development programs and in genetic and genomic studies

Germplasm design, gene discovery, and variety release: breeding barley for the Pacific Northwest

This thesis consists of three manuscripts addressing separate components of barley breeding, plus an introduction and a conclusion summarizing the status of barley in the Pacific Northwest, plus the implications of the research presented in this thesis. In the first manuscript, a package written for the statistical software "R" that is designed to identify subsets of plant accessions that would be favorable for rare-trait discovery and genome-wide association studies is presented. In the second manuscript, genome-wide association scanning is used to identify thirteen single-nucleotide polymorphism markers that are significantly associated with tocochromanol concentration in a set of elite, spring barley accessions. In the third manuscript, the barley variety "Alba" was described in a germplasm release

Data from: Variable competitive effects of fungicide resistance in field experiments with a plant pathogenic fungus

Classic evolutionary theory suggests that mutations associated with antimicrobial and pesticide resistance result in a fitness cost in the absence of the selective antimicrobial agent or pesticide. There is experimental evidence to support fitness costs associated with resistance to anti-microbial compounds and pesticides across many biological disciplines, including human pathology, entomology, plant sciences, and plant pathology. However, researchers have also found examples of neutral and increased fitness associated with resistance, where the effect of a given resistance mutation depends on environmental and biological factors. We used Zymoseptoria tritici, a model evolutionary plant pathogenic fungus, to compare the competitive ability of fungicide-resistant isolates to fungicide-sensitive isolates. We conducted four large-scale inoculated winter wheat experiments at Oregon State University agriculture experiment stations. We found a significant change in the frequency of fungicide resistance over time in all four experiments. The direction and magnitude of these changes, however, differed by experimental location, year of experiment, and inoculum resistance treatment (fungicide-resistant, resistant/sensitive mixture, and fungicide-sensitive). These results suggest that the competitive ability of resistant isolates relative to sensitive isolates varied depending upon environmental conditions, including the initial frequency of resistant individuals in the population