Recommendations for riparian ecosystem management based on the general frame defined in EUFORGEN and results from EUROPOP

International audienc

In Vitro vs In Silico Detected SNPs for the Development of a Genotyping Array: What Can We Learn from a Non-Model Species?

Background: There is considerable interest in the high-throughput discovery and genotyping of single nucleotide polymorphisms (SNPs) to accelerate genetic mapping and enable association studies. This study provides an assessment of EST-derived and resequencing-derived SNP quality in maritime pine (Pinus pinaster Ait.), a conifer characterized by a huge genome size (~23.8 Gb/C). [br/] Methodology/Principal Findings: A 384-SNPs GoldenGate genotyping array was built from i/ 184 SNPs originally detected in a set of 40 re-sequenced candidate genes (in vitro SNPs), chosen on the basis of functionality scores, presence of neighboring polymorphisms, minor allele frequencies and linkage disequilibrium and ii/ 200 SNPs screened from ESTs (in silico SNPs) selected based on the number of ESTs used for SNP detection, the SNP minor allele frequency and the quality of SNP flanking sequences. The global success rate of the assay was 66.9%, and a conversion rate (considering only polymorphic SNPs) of 51% was achieved. In vitro SNPs showed significantly higher genotyping-success and conversion rates than in silico SNPs (+11.5% and +18.5%, respectively). The reproducibility was 100%, and the genotyping error rate very low (0.54%, dropping down to 0.06% when removing four SNPs showing elevated error rates). [br/] Conclusions/Significance: This study demonstrates that ESTs provide a resource for SNP identification in non-model species, which do not require any additional bench work and little bio-informatics analysis. However, the time and cost benefits of in silico SNPs are counterbalanced by a lower conversion rate than in vitro SNPs. This drawback is acceptable for population-based experiments, but could be dramatic in experiments involving samples from narrow genetic backgrounds. In addition, we showed that both the visual inspection of genotyping clusters and the estimation of a per SNP error rate should help identify markers that are not suitable to the GoldenGate technology in species characterized by a large and complex genome

Characterisation and natural variation of a dehydrin gene in Quercus petraea (Matt.) Liebl.

For the first time in sessile oak [Quercus petraea (Matt.) Liebl.], the isolation and characterisation of a full-length dehydrin gene and its promoter region, as well as its allelic variation in natural populations, is reported. Dehydrins (Dhn) are stress-related genes important for the survival of perennial plants in a seasonal climate. A full-length dehydrin gene (Dhn3) was characterised at the nucleotide level and the protein structure was modelled. Additionally, the allelic variation was analysed in five natural populations of Quercus petraea (Matt.) Liebl. sampled along an altitudinal gradient in the French Pyrenees. The analysed sequences contain typical domains of the K n class of dehydrins in the coding region. Also, the 5′untranslated region (promoter) of the gene was amplified, which shows typical motifs essential for drought- and cold-responsive gene expression. Single nucleotide substitutions and indels (insertions/deletions) within the coding region determine large biochemical differences at the protein level. However, only low levels of genetic differentiation between populations from different altitudes were detectable. © 2011 German Botanical Society and The Royal Botanical Society of the Netherlands

<em>Diplodia sapinea</em> infection reprograms foliar traits of its pine (<em>Pinus sylvestris </em>L.) host to death.

Infection with the necrotrophic fungus Diplodia sapinea is among the economically and ecologically most devastating diseases of conifers in the northern hemisphere accelerated by global climate change. The present study aims to characterize the changes mediated by D. sapinea infection on its pine host (Pinus sylvestris L.) that lead to the death of its needles. For this purpose, we performed an indoor infection experiment and inoculated shoot tips of pine seedlings with virulent D. sapinea. The consequences for foliar traits, including the phytohormone profile were characterized at both the metabolite and transcriptome level. Our results showed that D. sapinea infection strongly affected foliar levels of most phytohormones and impaired a multitude of other metabolic and structural foliar traits, such as ROS scavenging. Transcriptome analysis revealed that these changes are partially mediated via modified gene expression by fungal exposure. D. sapinea appears to overcome defense reactions of its pine host by reprogramming gene expression and post-transcriptional controls that determine essential foliar metabolic traits such as the phytohormone profile, cell wall composition and antioxidative system