Promocijas darbs

Elektroniskā versija nesatur pielikumusPromocijas darba tiek analizeti divi BJR notiekošie parmainu procesi: integracija un regionalizacija. Darba tika izvirzitas divas hipotezes. Pirmkart, BJR starpvalstu sadarbiba atbilst regionalizacijas, nevis integracijas pazimem. Otrkart, integracijas un regionalizacijas pazimes BJR pec 2004. gada ES paplašinašanas ir kluvušas vajakas. Lai noskaidrotu integracijas un regionalizacijas procesu attiecibas BR ietvaros, tika izpetiti tris gadijumi: Baltijas juras valstu padome, Ziemelu dimensija un Kaliningradas apgabals. Pirma hipoteze neapstiprinajas, tomer kopuma var apgalvot, ka BJR valstu sadarbiba vairak liecina par regionalizaciju, nevis integraciju. Otra hipoteze apstiprinajas, jo izpetes gaita atklajas, ka BJR valstu sadarbiba kopš 2004. gada ir vajinajusies.The Doctoral Thesis INTEGRATION AND REGIONALIZATION IN THE BALTIC SEA REGION (BSR) discusses the manifestations of two change processes – integration and regionalization – in the BSR. Two hypotheses were established. First, regional cooperation in the BSR resembles the pattern of regionalization, not integration. Second, patterns of regionalization and integration have become weaker since the 2004 EU enlargement. Three cases were analyzed to explore the relationship between integration and regionalization: Council of the Baltic Sea States, Kaliningrad Oblast, and the Northern Dimension. Although the first hypothesis was not confirmed, the main conclusion is that regional cooperation resembles regionalization. The second hypothesis was confirmed because cooperation in the BSR has indeed become weaker since 2004

Genome-wide and Mla locus-specific characterisation of Latvian barley varieties

Genetic diversity in locally adapted germplasm forms the basis for crop improvement through breeding. While single loci have been routinely used for studies of genetic diversity, the highthroughput genotyping platforms that have recently become available for large genome cro plants offer an unbiased view on genetic diversity on a genome-wide scale. We assessed genetic diversity in Latvian barley varieties and some progenitors using DArT markers and studied the extent of linkage disequilibrium in Latvian germplasm. Further, genetic diversity at three loci flanking the barley powdery mildew Mla locus conferring race-specific resistance was studied in Latvian barley germplasm. The Mla locus encompasses several closely related resistance gene homologues with a complex evolutionary history, which complicates the design of molecular markers for different Mla genes. We observed significant linkage disequilibrium between the single nucleotide polymorphisms (SNPs) at the three loci, 206i20_T7, ABC15612, and 538P8, flanking the Mla locus. SNP haplotypes were largely in agreement with known phenotypic data and, thus, may be potentially diagnostic for Mla resistance genes in hybrids.publishersversionPeer reviewe

Development and Validation of a Reversed-Phase Liquid Chromatography Method for the Simultaneous Determination of Indole-3-Acetic Acid, Indole-3-Pyruvic Acid, and Abscisic Acid in Barley (Hordeum vulgare L.)

A simple, sensitive, precise, and specific reverse HPLC method was developed and validated for the determination of plant hormones in barley (Hordeum vulgare L.). The method includes extraction in aqueous organic solvent followed by solid-phase extraction, sample evaporation, and reversed-phase HPLC analysis in a general purpose UV-visible (abscisic acid (ABA)) and fluorescence detection (indole-3-acetic acid (IAA) and indole-3-pyruvic acid (IPA)), high-performance liquid chromatography system. The separation was carried out on Zorbax Eclipse XDB C8 column (150  ×  4.6  mm I.D) with a mobile phase composed of methanol and 1% acetic acid (60 : 40 v/v) in isocratic mode at a flow rate of 1 ml min−1. The detection was monitored at 270 nm (ABA) and at 282 nm (Ex) and 360 nm (Em) (IAA, IPA). The developed method was validated in terms of accuracy, precision, linearity, limit of detection, limit of quantification, and robustness. The determined validation parameters are in the commonly acceptable ranges for that kind of analysis

Differential disease resistance response in the barley necrotic mutant nec1

<p>Abstract</p> <p>Background</p> <p>Although ion fluxes are considered to be an integral part of signal transduction during responses to pathogens, only a few ion channels are known to participate in the plant response to infection. CNGC4 is a disease resistance-related cyclic nucleotide-gated ion channel. <it>Arabidopsis thaliana </it>CNGC4 mutants <it>hlm1 </it>and <it>dnd2 </it>display an impaired hypersensitive response (HR), retarded growth, a constitutively active salicylic acid (SA)-mediated pathogenesis-related response and elevated resistance against bacterial pathogens. Barley CNGC4 shares 67% aa identity with AtCNGC4. The barley mutant <it>nec1 </it>comprising of a frame-shift mutation of CNGC4 displays a necrotic phenotype and constitutively over-expresses <it>PR-1</it>, yet it is not known what effect the <it>nec1 </it>mutation has on barley resistance against different types of pathogens.</p> <p>Results</p> <p><it>nec1 </it>mutant accumulated high amount of SA and hydrogen peroxide compared to parental cv. Parkland. Experiments investigating <it>nec1 </it>disease resistance demonstrated positive effect of <it>nec1 </it>mutation on non-host resistance against <it>Pseudomonas syringae </it>pv. <it>tomato </it>(<it>Pst</it>) at high inoculum density, whereas at normal <it>Pst </it>inoculum concentration <it>nec1 </it>resistance did not differ from wt. In contrast to augmented <it>P. syringae </it>resistance, penetration resistance against biotrophic fungus <it>Blumeria graminis </it>f. sp. <it>hordei </it>(<it>Bgh</it>), the causal agent of powdery mildew, was not altered in <it>nec1</it>. The <it>nec1 </it>mutant significantly over-expressed race non-specific <it>Bgh </it>resistance-related genes <it>BI-1 </it>and <it>MLO</it>. Induction of <it>BI-1 </it>and <it>MLO </it>suggested putative involvement of <it>nec1 </it>in race non-specific <it>Bgh </it>resistance, therefore the effect of <it>nec1</it>on <it>mlo-5</it>-mediated <it>Bgh </it>resistance was assessed. The <it>nec1</it>/<it>mlo-5 </it>double mutant was as resistant to <it>Bgh </it>as <it>Nec1</it>/<it>mlo-5 </it>plants, suggesting that <it>nec1 </it>did not impair <it>mlo-5 </it>race non-specific <it>Bgh </it>resistance.</p> <p>Conclusions</p> <p>Together, the results suggest that <it>nec1 </it>mutation alters activation of systemic acquired resistance-related physiological markers and non-host resistance in barley, while not changing rapid localized response during compatible interaction with host pathogen. Increased resistance of <it>nec1 </it>against non-host pathogen <it>Pst </it>suggests that <it>nec1 </it>mutation may affect certain aspects of barley disease resistance, while it remains to be determined, if the effect on disease resistance is a direct response to changes in SA signaling.</p

Development of metabolic engineering approaches to regulate the content of total phenolics, antiradical activity and organic acids in callus cultures of the highbush blueberry (Vaccinium corymbosum L.)

Blueberry (Vaccinium corymbosum L.) is increasingly cultivated to produce high quality berries for consumption and potential applications in medicine, nutrition and as industrial precursors. Seasonal availability sets limitations on chemical compound isolation from cultivated plants. Biotechnological solutions, such as tissue cultures and metabolic engineering, can provide sufficient amounts of plant material with reasonably high metabolite levels, which may be adjusted by different strategies. Here, we describe our approach to modifying total phenolic content (TPC), antiradical activity (ARA) and amounts of selected organic acids in in vitro cultures of two varieties of V. corymbosum by varying the growth media. TPC, ARA and acid levels were determined in mature leaves of field-grown plants and in stable callus cultures derived from leaves of varieties ‘Bluecrop’ and ‘Duke’ grown on Murashige-Skoog (MS) and Woody plant (WP) media supplemented with varying concentrations and combinations of different plant growth hormones. TPC varied from 83 mg g -1 dry weight (DW) to 142 mg g -1 DW in leaves of ‘Bluecrop’ and ‘Duke’, respectively, and correlated with their ARA with ‘Duke’ at the lead. For callus cultures the highest ARA, as well as the highest TPC of 94 mg g -1 DW was observed in ‘Bluecrop’ grown on WP medium with 2,4-dichlorophenoxyacetic acid (2,4-D). High level of quinic acid was found in the mature leaves of all tested varieties, while callus cultures exhibited relative increase in amounts of malic, succinic and citric acids instead. Oxalic acid was found only in callus cultures

Single-feature polymorphism discovery in the barley transcriptome

A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes

Towards whole genome association genetic scans in barley

In crop plants, the potential of association mapping, with the objective of estimating the position of genes conferring a specific trait or phenotype using linkage disequilibrium (LD) between alleles of genetically mapped markers, has recently become a focus of considerable interest. One major attraction of association genetics is the potential to locate genes responsible for a wide range of traits in a single sample population using pre-existing phenotypic data that has been collected during crop improvement and cultivar registration programs. This study testify to the potential of exploiting whole genome LD-scans to locate genes controlling key biological traits in cultivated barley. We are currently increasing the density of markers, particularly those with a MAF >0.1, by developing two further pilot OPAs, which in due course will be compressed into two commercially available platforms for high throughput low cost genotyping in cultivated barley. In the immediate future these will be used in large association genetic studies in the UK and US involving approximately 4000 barley genotypes with the aim of realising the potential for whole genome association genetic scans in cultivated barley

Development and Evaluation of a Barley 50k iSelect SNP Array

High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1 and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al., 2012) and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segregating population derived from a Golden Promise × Morex cross (Liu et al., 2014) and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions. Manual adjustment of the cluster files used by the interpreting software for genotype scoring improved results substantially, but migration of cluster files between sites led to a deterioration of results, suggesting that local adjustment of cluster files is required on a site-per-site basis. Information relating to the markers on the chip is available online at https://ics.hutton.ac.uk/50k