Looking for the needle in a downsized haystack: Whole-exome sequencing unravels genomic signals of climatic adaptation in Douglas-fir (Pseudotsuga menziesii).

Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.A 40-year-old common garden experiment comprising 16 Douglas-fir (Pseudotsuga menziesii) provenances from a north-to-south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs.We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas-fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera. Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well-known coastal and interior varieties of Douglas-fir.

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release.

BACKGROUND: Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. RESULTS: The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. CONCLUSION: In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.

Transcriptomic changes in wind-exposed poplar leaves are dependent on developmental stage.

Responses of plant tissue to environmental challenges can vary among different plant parts and among plants of different ages. Investment into defense has been proposed to be influenced by fitness value and/or allocation of available resources. Here we show at first time at transcriptome level that plant defense is non-linear. On very young, expanding, adult and old leaves of Populus nigra plants exposed to air perturbation, we studied the ontogenic trajectory of gene expression changes to such a low-dose factor similar to wind. Although plant responses to mechanical sensation (wind, touch) are described and summarized as thigmomorphogenesis, the knowledge on the molecular background of plant responses to wind is largely incomplete. Our data describe which genes are activated during a ubiquitous and continuous environmental factor such as wind, and based on existing knowledge complement the picture on ongoing processes.

Effects of transgenic glufosinate-tolerant oilseed rape (Brassica napus) and the associated herbicide application on eubacterial and Pseudomonas communities in the rhizosphere.

A containment experiment was carried out in order to evaluate possible shifts in eubacterial and Pseudomonas rhizosphere community structures due to the release of genetically modified Basta-tolerant oilseed rape and the associated herbicide application. Treatments included cultivation of the transgenic plant as well as of the wild-type cultivar in combination with mechanical removal of weeds and the application of the herbicides Basta (active ingredient: glufosinate) and Butisan S (active ingredient: metazachlor). Rhizosphere soil was sampled from early and late flowering plants as well as from senescent plants. A culture-independent approach was chosen to characterize microbial communities based on denaturing gradient gel electrophoresis of 16S rRNA gene fragments amplified from rhizosphere DNA using eubacterial and Pseudomonas-specific PCR primers. Dominant pseudomonads in the rhizosphere were analyzed by sequence analysis. Whole community and Pseudomonas electrophoresis fingerprints revealed slightly altered microbial communities in the rhizosphere of transgenic plants; however, effects were minor as compared to the plant developmental stage-dependent shifts. Both herbicides caused transient changes in the eubacterial and Pseudomonas population structure, whereas differences due to the genetic modification were still detected at the senescent growth stage. The observed differences between transgenic and wild-type lines were most likely due to unintentionally modified plant characteristics such as altered root exudation.