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.

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

BACKGROUND: 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. RESULTS: 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 P. abies individuals sampled across Austria and in an additional screening population of 96 P. abies 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. CONCLUSIONS: 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.

Microsatellite markers in the tree peony, Paeonia suffruticosa (Paeoniaceae).

PREMISE OF THE STUDY: Microsatellite primers were developed in the tree peony, Paeonia suffruticosa, to perform paternity tests as well as assignment to variety in special Austrian collections. • METHODS AND RESULTS: Using SSR-enriched libraries and EST-mining, 8 polymorphic primer sets were identified in Austrian collections of Paeonia sect. Moutan DC. The primers amplified di- and trinucleotide repeats with 2-6 alleles per locus. All primers also amplified in P. ostii, P. pontaninii var. trolloides, P. delavayi, and P. lutea, and in the herbaceous species P. peregrina and P. tenuifolia (Paeonia sect. Paeon). • CONCLUSIONS: These results show the usefulness of primers in P. suffruticosa for population genetic studies and their ability to cross amplify in related taxa across the genus.