Response of dark respiration to temperature in Eriophorum vaginatum from a 30-year-old transplant experiment in Alaska

Background: In the Arctic region, temperature increases are expected to be greater under anticipated climate change than the global average. Understanding how dark respiration (

Carbon respiration from subsurface peat accelerated by climate warming in the subarctic.

Among the largest uncertainties in current projections of future climate is the feedback between the terrestrial carbon cycle and climate. Northern peatlands contain one-third of the worlds soil organic carbon, equivalent to more than half the amount of carbon in the atmosphere. Climate-warming-induced acceleration of carbon dioxide (CO 2) emissions through enhanced respiration of thick peat deposits, centuries to millennia old, may form a strong positive carbon cycle-climate feedback. The long-term temperature sensitivity of carbon in peatlands, especially at depth, remains uncertain, however, because of the short duration or correlative nature of field studies and the disturbance associated with respiration measurements below the surface in situ or during laboratory incubations. Here we combine non-disturbing in situ measurements of CO 2 respiration rates and isotopic (13 C) composition of respired CO 2 in two whole-ecosystem climate-manipulation experiments in a subarctic peatland. We show that approximately 1 °C warming accelerated total ecosystem respiration rates on average by 60% in spring and by 52% in summer and that this effect was sustained for at least eight years. While warming stimulated both short-term (plant-related) and longer-term (peat soil-related) carbon respiration processes, we find that at least 69% of the increase in respiration rate originated from carbon in peat towards the bottom (25-50 cm) of the active layer above the permafrost. Climate warming therefore accelerates respiration of the extensive, subsurface carbon reservoirs in peatlands to a much larger extent than was previously thought. Assuming that our data from a single site are indicative of the direct response to warming of northern peatland soils on a global scale, we estimate that climate warming of about 1 °C over the next few decades could induce a global increase in heterotrophic respiration of 38-100 megatonnes of C per year. Our findings suggest a large, long-lasting, positive feedback of carbon stored in northern peatlands to the global climate system. © 2009 Macmillan Publishers Limited

Pan-Arctic modelling of net ecosystem exchange of CO2

Net ecosystem exchange (NEE) of C varies greatly among Arctic ecosystems. Here, we show that approximately 75 per cent of this variation can be accounted for in a single regression model that predicts NEE as a function of leaf area index (LAI), air temperature and photosynthetically active radiation (PAR). The model was developed in concert with a survey of the light response of NEE in Arctic and subarctic tundras in Alaska, Greenland, Svalbard and Sweden. Model parametrizations based on data collected in one part of the Arctic can be used to predict NEE in other parts of the Arctic with accuracy similar to that of predictions based on data collected in the same site where NEE is predicted. The principal requirement for the dataset is that it should contain a sufficiently wide range of measurements of NEE at both high and low values of LAI, air temperature and PAR, to properly constrain the estimates of model parameters. Canopy N content can also be substituted for leaf area in predicting NEE, with equal or greater accuracy, but substitution of soil temperature for air temperature does not improve predictions. Overall, the results suggest a remarkable convergence in regulation of NEE in diverse ecosystem types throughout the Arctic

Gross Primary Productivity of a High Elevation Tropical Montane Cloud Forest

For decades, the productivity of tropical montane cloud forests (TMCF) has been assumed to be lower than in tropical lowland forests due to nutrient limitation, lower temperatures, and frequent cloud immersion, although actual estimates of gross primary productivity (GPP) are very scarce. Here, we present the results of a process-based modeling estimate of GPP, using a soil-plant-atmosphere model, of a high elevation Peruvian TMCF. The model was parameterized with field-measured physiological and structural vegetation variables, and driven with meteorological data from the site. Modeled transpiration corroborated well with measured sap flow, and simulated GPP added up to 16.2 ± SE 1.6 Mg C h

Nutrient limitation in rainforests and cloud forests along a 3,000-m elevation gradient in the Peruvian Andes.

We report results from a large-scale nutrient fertilization experiment along a "megadiverse" (154 unique species were included in the study) 3,000-m elevation transect in the Peruvian Andes and adjacent lowland Amazonia. Our objectives were to test if nitrogen (N) and phosphorus (P) limitation shift along this elevation gradient, and to determine how an alleviation of nutrient limitation would manifest in ecosystem changes. Tree height decreased with increasing elevation, but leaf area index (LAI) and diameter at breast height (DBH) did not vary with elevation. Leaf N:P decreased with increasing elevation (from 24 at 200 m to 11 at 3,000 m), suggesting increased N limitation and decreased P limitation with increasing elevation. After 4 years of fertilization (N, P, N + P), plots at the lowland site (200 m) fertilized with N + P showed greater relative growth rates in DBH than did the control plots; no significant differences were evident at the 1,000 m site, and plots fertilized with N at the highest elevation sites (1,500, 3,000 m) showed greater relative growth rates in DBH than did the control plots, again suggesting increased N constraint with elevation. Across elevations in general N fertilization led to an increase in microbial respiration, while P and N + P addition led to an increase in root respiration and corresponding decrease in hyphal respiration. There was no significant canopy response (LAI, leaf nutrients) to fertilization, suggesting that photosynthetic capacity was not N or P limited in these ecosystems. In sum, our study significantly advances ecological understanding of nutrient cycling and ecosystem response in a region where our collective knowledge and data are sparse: we demonstrate N limitation in high elevation tropical montane forests, N and P co-limitation in lowland Amazonia, and a nutrient limitation response manifested not in canopy changes, but rather in stem and belowground changes. © 2012 Springer-Verlag Berlin Heidelberg

ASSIsT: an automatic SNP scoring tool for in- and outbreeding species

ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio® (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux

Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16

Apple (Malus×domestica Borkh) is among the main sources of phenolic compounds in the human diet. The genetic basis of the quantitative variations of these potentially beneficial phenolic compounds was investigated. A segregating F(1) population was used to map metabolite quantitative trait loci (mQTLs). Untargeted metabolic profiling of peel and flesh tissues of ripe fruits was performed using liquid chromatography-mass spectrometry (LC-MS), resulting in the detection of 418 metabolites in peel and 254 in flesh. In mQTL mapping using MetaNetwork, 669 significant mQTLs were detected: 488 in the peel and 181 in the flesh. Four linkage groups (LGs), LG1, LG8, LG13, and LG16, were found to contain mQTL hotspots, mainly regulating metabolites that belong to the phenylpropanoid pathway. The genetics of annotated metabolites was studied in more detail using MapQTL(®). A number of quercetin conjugates had mQTLs on LG1 or LG13. The most important mQTL hotspot with the largest number of metabolites was detected on LG16: mQTLs for 33 peel-related and 17 flesh-related phenolic compounds. Structural genes involved in the phenylpropanoid biosynthetic pathway were located, using the apple genome sequence. The structural gene leucoanthocyanidin reductase (LAR1) was in the mQTL hotspot on LG16, as were seven transcription factor genes. The authors believe that this is the first time that a QTL analysis was performed on such a high number of metabolites in an outbreeding plant species

Silencing the major apple allergen Mal d 1 by using the RNA interference approach

BACKGROUND: Apple allergy is dominated by IgE antibodies against Mal d 1 in areas where birch pollen is endemic. Apples with significantly decreased levels of Mal d 1 would allow most patients in these areas to eat apples without allergic reactions. OBJECTIVE: The aim of this study was to inhibit the expression of Mal d 1 in apple plants by RNA interference. METHODS: In vitro -grown apple plantlets were transformed with a construct coding for an intron-spliced hairpin RNA containing a Mal d 1-specific inverted repeat sequence separated by a Mal d 1-specific intron sequence. The presence of the construct in transformants was checked by PCR. Expression of Mal d 1 in leaves was monitored by prick-to-prick skin testing in 3 patients allergic to apples and by immunoblotting with a Mal d 1-reactive mAb and with IgE antibodies against Mal d 1. RESULTS: After transformation, plantlets were selected on the basis of having a normal phenotype and growth rate. With PCR, in 6 of 9 selected plantlets, the presence of the gene-silencing construct was demonstrated. By skin prick test it was shown that a wild-type plantlet had significantly ( P <.05) higher allergenicity than 5 of the transformants. Reduction of expression of Mal d 1 was confirmed by immunoblotting. In wild-type and unsuccessful transformants, a strong band was detected with Mal d 1-reactive mAb 5H8 at the expected apparent M r of 17 kDa. This band was virtually absent in the transformants that carried the gene-silencing construct. With human IgE antibodies, the same observations were made. CONCLUSIONS: Mal d 1 expression was successfully reduced by RNA interference. This translated into significantly reduced in vivo allergenicity. These observations support the feasibility of the production by gene silencing of apples hypoallergenic for Mal d

Review of Fruit Genetics and Breeding Programmes and a New European Initiative to Increase Fruit Breeding Efficiency

none18siThe European fruit industry is facing economic challenges imposed by increasingly fierce international competition and decreasing fruit consumption, societal demand for a more sustainable production, and biological problems caused by climate changes. Releasing new cultivars that meet these challenges is a major goal of all European breeding programmes. However, addressing them has been slow due to the nature of fruit tree breeding: long term, low efficiency and high cost. For the past 15 years, efficient networks of fruit geneticists and genomicists have progressively been built thanks in particular to EU-funded projects. Europe has thus become a leader in research on fruit genetics aimed at enhancing fruit quality traits as well as resistance to biotic stresses. European teams working on fruit genetics have developed up-to-date tools and skills covering most of the “omics” fields as well as statistics and software development. Although fruit breeding is very active in Europe, very few breeding programmes are really using the output of the fruit genetics/genomics research. A few bottlenecks can explain this situation. To solve that, a new European initiative has been set up by the FruitBreedomic. This large collaborative project, has the strategic goal of improving the efficiency of current fruit breeding programmes by bridging the existing gap between molecular genetics research and application in breeding.noneF. Laurens; M.J. Aranzana; P. Arús; D. Bassi; J. Bonany; L. Corelli; C.E. Durel; J. Mes; T. Pascal; A. Patocchi; A. Peil; B. Quilot; S. Salvi; S. Tartarini; M. Troggio; A. Vecchietti; R. Velasco; E. van de WegF. Laurens; M.J. Aranzana; P. Arús; D. Bassi; J. Bonany; L. Corelli; C.E. Durel; J. Mes; T. Pascal; A. Patocchi; A. Peil; B. Quilot; S. Salvi; S. Tartarini; M. Troggio; A. Vecchietti; R. Velasco; E. van de We

The new EU project FruitBreedomics: an integrated approach for increasing breeding efficiency in fruit tree crops

An international consortium gathering European and non European teams has designed FruitBreedomics to bridge the gap between scientific genetics research and application in breeding. The project will focus on apple and peach, two major fruits in Europe, but the tools and the knowledge gained will also benefit other species of the Rosaceae family. The aim of FruitBreedomics is to provide the European fruit tree sector with cutting-edge breeding tools for the efficient and accelerated creation of new apple and peach varieties with excellent fruit quality characteristics, improved resistances to diseases and pests, and that can be grown in sustainable agriculture systems in the context of climate change. This poster presents the aims, structure and participants of the projec