Characterization of variable EST SSR markers for Norway spruce (Picea abies L.)

<p>Abstract</p> <p>Background</p> <p>Norway spruce is widely distributed across Europe and the predominant tree of the Alpine region. Fast growth and the fact that timber can be harvested cost-effectively in relatively young populations define its status as one of the economically most important tree species of Northern Europe. In this study, EST derived simple sequence repeat (SSR) markers were developed for the assessment of putative functional diversity in Austrian Norway spruce stands.</p> <p>Results</p> <p>SSR sequences were identified by analyzing 14,022 publicly available EST sequences. Tri-nucleotide repeat motifs were most abundant in the data set followed by penta- and hexa-nucleotide repeats. Specific primer pairs were designed for sixty loci. Among these, 27 displayed polymorphism in a testing population of 16 <it>P. abies </it>individuals sampled across Austria and in an additional screening population of 96 <it>P. abies </it>individuals from two geographically distinct Austrian populations. Allele numbers per locus ranged from two to 17 with observed heterozygosity ranging from 0.075 to 0.99.</p> <p>Conclusions</p> <p>We have characterized variable EST SSR markers for Norway spruce detected in expressed genes. Due to their moderate to high degree of variability in the two tested screening populations, these newly developed SSR markers are well suited for the analysis of stress related functional variation present in Norway spruce populations.</p

Genetic and geographic influence on phenotypic variation in European sarcoidosis patients

IntroductionSarcoidosis is a highly variable disease in terms of organ involvement, type of onset and course. Associations of genetic polymorphisms with sarcoidosis phenotypes have been observed and suggest genetic signatures.MethodsAfter obtaining a positive vote of the competent ethics committee we genotyped 1909 patients of the deeply phenotyped Genetic-Phenotype Relationship in Sarcoidosis (GenPhenReSa) cohort of 31 European centers in 12 countries with 116 potentially disease-relevant single-nucleotide polymorphisms (SNPs). Using a meta-analysis, we investigated the association of relevant phenotypes (acute vs. sub-acute onset, phenotypes of organ involvement, specific organ involvements, and specific symptoms) with genetic markers. Subgroups were built on the basis of geographical, clinical and hospital provision considerations.ResultsIn the meta-analysis of the full cohort, there was no significant genetic association with any considered phenotype after correcting for multiple testing. In the largest sub-cohort (Serbia), we confirmed the known association of acute onset with TNF and reported a new association of acute onset an HLA polymorphism. Multi-locus models with sets of three SNPs in different genes showed strong associations with the acute onset phenotype in Serbia and Lublin (Poland) demonstrating potential region-specific genetic links with clinical features, including recently described phenotypes of organ involvement.DiscussionThe observed associations between genetic variants and sarcoidosis phenotypes in subgroups suggest that gene–environment-interactions may influence the clinical phenotype. In addition, we show that two different sets of genetic variants are permissive for the same phenotype of acute disease only in two geographic subcohorts pointing to interactions of genetic signatures with different local environmental factors. Our results represent an important step towards understanding the genetic architecture of sarcoidosis

Stress gene based diversity of Austrian oak populations

Die durch den vorhergesagten Klimawandel ausgelöste Temperaturerhöhung und die resultierende Wasserknappheit werden langlebige Waldbäume zunehmend unter Druck setzen. Sowohl inter- als auch intraspezifische Variation stellen ein Schlüsselelement für die Anpassung an die veränderten Umweltbedingungen und die Trockenheitstoleranz dar. In der vorliegenden Studie wurde eine parallelisierte Hochdurchsatz-Sequenziermethode (Roche 454 FLX) und eine eigens entwickelte Bioinformatik-Pipeline verwendet, um Einzelnukleotid-Polymorphismen und allelische Sequenzen in Kandidatengenen zu identifizieren. Diese Gene finden sich in Individuen der Stieleiche (Quercus robur) und Traubeneiche (Q. petraea) und sind bekannt dafür, auf Trockenheit bzw. osmotischen Stress zu reagieren. Insgesamt wurden acht Gene von 336 österreichischen Individuen untersucht und 158 Polymorphismen entdeckt. Basierend auf den erhaltenen Daten wurde die Diversität, die Korrelation zwischen Allelfrequenzen und Klima sowie eventuelles Abweichen von neutralen Entwicklungsmodellen analysiert. Des Weiteren wurden grundlegende genetische Parameter berechnet und die Populationsstruktur mittels Differenzierungsindizes und Bayesschem Clustering analysiert. Signifikante Werte der Populationsdifferenzierung sowie eine starke Korrelation zwischen lokalen Verhältnissen betreffend Temperatur/Niederschlag und Allelfrequenzen zeigen ein höheres Anpassungsvermögen von Q. petraea an wasserarme Bedingungen. Die Ergebnisse der Arbeit bieten eine gute Basis für weiterführende Studien in einem größeren geografischen Umfang und können für die Entwicklung von molekularen Marken für Trockenheits-Resistenz verwendet werden.Rise of temperatures and shortening of available water as result of predicted climate change will impose significant pressure on long-lived forest tree species. Inter- as well as intraspecific diversity is the key element of a plants potential to adapt to a changing environment and tolerance towards drought stress. In the present study, we have used Roche 454 sequencing and developed a bioinformatic pipeline to process multiplexed tagged amplicons in order to identify single nucleotide polymorphisms and allelic sequences of candidate genes related to drought/osmotic stress from pedunculate oak (Quercus robur) and sessile oak (Q. petraea) individuals. Out of these, eight genes of 336 oak individuals growing in Austria have been detected with a total number of 158 polymorphic sites. Nucleotide diversity, correlations to environmental conditions, and deviations from standard neutral models were examined, baseline genetic parameters were calculated and population structure was investigated using differentiation indices and Bayesian clustering. Significant differentiation and strong correlations between the local temperature-precipitation regime and the allele frequencies point towards a higher adaptive potential of Q. petraea under arid conditions. These results can serve as basis for future studies in larger geographic scale and may be used for the development of molecular markers for drought tolerance.vorgelegt von Andreas HomolkaAbweichender Titel laut Übersetzung der Verfasserin/des VerfassersZsfassung in dt. SpracheWien, Univ. für Bodenkultur, Diss., 2013OeBB(VLID)193116

Data from: Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing

BACKGROUND: Rise of temperatures and shortening of available water as result of predicted climate change will impose significant pressure on long-lived forest tree species. Discovering allelic variation present in drought related genes of two Austrian oak species can be the key to understand mechanisms of natural selection and provide forestry with key tools to cope with future challenges. RESULTS: In the present study we have used Roche 454 sequencing and developed a bioinformatic pipeline to process multiplexed tagged amplicons in order to identify single nucleotide polymorphisms and allelic sequences of ten candidate genes related to drought/osmotic stress from sessile oak (Quercus robur) and pedunculate oak (Q. petraea) individuals. Out of these, eight genes of 336 oak individuals growing in Austria have been detected with a total number of 158 polymorphic sites. Allele numbers ranged from ten to 52 with observed heterozygosity ranging from 0.115 to 0.640. All loci deviated from Hardy-Weinberg equilibrium and linkage disequilibrium was found among six combinations of loci. CONCLUSIONS: We have characterized 183 alleles of drought related genes from oak species and detected first evidences of natural selection. Beside the potential for marker development, we have created an expandable bioinformatic pipeline for the analysis of next generation sequencing data

Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing

BACKGROUND: Rise of temperatures and shortening of available water as result of predicted climate change will impose significant pressure on long-lived forest tree species. Discovering allelic variation present in drought related genes of two Austrian oak species can be the key to understand mechanisms of natural selection and provide forestry with key tools to cope with future challenges. RESULTS: In the present study we have used Roche 454 sequencing and developed a bioinformatic pipeline to process multiplexed tagged amplicons in order to identify single nucleotide polymorphisms and allelic sequences of ten candidate genes related to drought/osmotic stress from sessile oak (Quercus robur) and sessile oak (Q. petraea) individuals. Out of these, eight genes of 336 oak individuals growing in Austria have been detected with a total number of 158 polymorphic sites. Allele numbers ranged from ten to 52 with observed heterozygosity ranging from 0.115 to 0.640. All loci deviated from Hardy-Weinberg equilibrium and linkage disequilibrium was found among six combinations of loci. CONCLUSIONS: We have characterized 183 alleles of drought related genes from oak species and detected first evidences of natural selection. Beside the potential for marker development, we have created an expandable bioinformatic pipeline for the analysis of next generation sequencing data

OAK Sequencing Pool 6

OAK Sequencing Pool

OAK_454_barcodes

Association list of hexanuceotide barcodes with Quercus spp. for each sequencing poo