Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage

There has been much excitement about the possibility that exposure to specific environments can induce an ecological memory in the form of whole-sale, genome-wide epigenetic changes that are maintained over many generations. In the model plant Arabidopsis thaliana, numerous heritable DNA methylation differences have been identified in greenhouse-grown isogenic lines, but it remains unknown how natural, highly variable environments affect the rate and spectrum of such changes. Here we present detailed methylome analyses in a geographically dispersed A. thaliana population that constitutes a collection of near-isogenic lines, diverged for at least a century from a common ancestor. Methylome variation largely reflected genetic distance, and was in many aspects similar to that of lines raised in uniform conditions. Thus, even when plants are grown in varying and diverse natural sites, genome-wide epigenetic variation accumulates mostly in a clock-like manner, and epigenetic divergence thus parallels the pattern of genome-wide DNA sequence divergence.     

Mapping-by-Sequencing Identifies HvPHYTOCHROME C as a Candidate Gene for the early maturity 5 Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley

Phytochromes play an important role in light signaling and photoperiodic control of flowering time in plants. Here we propose that the red/far-red light photoreceptor HvPHYTOCHROME C (HvPHYC), carrying a mutation in a conserved region of the GAF domain, is a candidate underlying the early maturity 5 locus in barley (Hordeum vulgare L.). We fine mapped the gene using a mapping-by-sequencing approach applied on the whole-exome capture data from bulked early flowering segregants derived from a backcross of the Bowman(eam5) introgression line. We demonstrate that eam5 disrupts circadian expression of clock genes. Moreover, it interacts with the major photoperiod response gene Ppd-H1 to accelerate flowering under noninductive short days. Our results suggest that HvPHYC participates in transmission of light signals to the circadian clock and thus modulates light-dependent processes such as photoperiodic regulation of flowering.     

Simulating mycorrhiza contribution to forest C- and N cycling-the MYCOFON model

Although mycorrhiza has been identified to be of major importance for plant nutrition and ecosystem stability, existing C- and N- simulation models on the ecosystem scale do not explicitly consider the feedbacks between ectomycorrhizal fungi and plants. We present a simple dynamic feedback model which allows estimating the main C- and N- flows between ectomycorrhizal fungi and tree roots in order to test the sensitivity of the system fungus-tree to environmental parameters and to assess the fungal contribution to plant N nutrition. Sensitivity tests carried out showed that the model responses to variations of model parameters, particularly with regard to N availability, are in agreement with published results from field and laboratory studies. However, there are still some processes and parameters which are not well constrained. Fungal N uptake rates and the ratio between mycelium, hartig net, and mantle biomass are parameters which significantly affect model results but for which published data are scarce or missing. Nevertheless, the model is already providing a platform to test our understanding of the importance of mycorrhiza for forest stand nutrition. Future coupling to a mechanistic ecosystem model will allow simulating the importance of mycorrhization for e.g. stand growth and C and N retention.     

Sensitivity of volatile monoterpene emission to changes in canopy structure: a model-based exercise with a process-based emission model

This paper investigates the dependence of monoterpene emissions at the canopy scale on total leaf area and leaf distribution. Simulations were carried out for a range of hypothetical but realistic forest canopies of the evergreen Quercus ilex (holm oak). Two emission models were applied that either did (SIM-BIM2) or did not (G93) account for cumulative responses to temperature and light. Both were embedded into a canopy model that considered spatial and temporal variations of foliage properties. This canopy model was coupled to a canopy climate model (CANOAK) to determine the micrometeorological conditions at the leaf scale. Structural properties considerably impacted monoterpene emission. The sensitivities to changes in total leaf area and to leaf area distribution were found to be of similar magnitude. The two different models performed similarly on a whole-year basis but showed clear differences during certain episodes. The analysis showed that structural indices have to be carefully evaluated for proper scaling of emission from leaves to canopy. Further research is encouraged on seasonal dynamics of emission potentials.