Institut National de la Recherche Agronomique du Niger

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Although research on human-mediated exchanges of species has substantially intensified during the last centuries, we know surprisingly little about temporal dynamics of alien species accumulations across regions and taxa. Using a novel database of 45,813 first records of 16,926 established alien species, we show that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970-2014). Inter-continental and inter-taxonomic variation can be largely attributed to the diaspora of European settlers in the nineteenth century and to the acceleration in trade in the twentieth century. For all taxonomic groups, the increase in numbers of alien species does not show any sign of saturation and most taxa even show increases in the rate of first records over time. This highlights that past efforts to mitigate invasions have not been effective enough to keep up with increasing globalization.

Amazon forests are a key but poorly understood component of the global carbon cycle. If, as anticipated, they dry this century, they might accelerate climate change through carbon losses and changed surface energy balances. We used records from multiple long-term monitoring plots across Amazonia to assess forest responses to the intense 2005 drought, a possible analog of future events. Affected forest lost biomass, reversing a large long-term carbon sink, with the greatest impacts observed where the dry season was unusually intense. Relative to pre-2005 conditions, forest subjected to a 100-millimeter increase in water deficit lost 5.3 megagrams of aboveground biomass of carbon per hectare. The drought had a total biomass carbon impact of 1.2 to 1.6 petagrams (1.2 x 10(15) to 1.6 x 10(15) grams). Amazon forests therefore appear vulnerable to increasing moisture stress, with the potential for large carbon losses to exert feedback on climate change.

Bad News for Bees Neonicotinoid insecticides were introduced in the early 1990s and have become one of the most widely used crop pesticides in the world. These compounds act on the insect central nervous system, and they have been shown to be persistent in the environment and in plant tissues. Recently, there have been controversial connections made between neonicotinoids and pollinator deaths, but the mechanisms underlying these potential deaths have remained unknown. Whitehorn et al. (p. 351 , published online 29 March) exposed developing colonies of bumble bees to low levels of the neonicotinoid imidacloprid and then released them to forage under natural conditions. Treated colonies displayed reduced colony growth and less reproductive success, and they produced significantly fewer queens to found subsequent generations. Henry et al. (p. 348 , published online 29 March) documented the effects of low-dose, nonlethal intoxication of another widely used neonicotinoid, thiamethoxam, on wild foraging honey bees. Radio-frequency identification tags were used to determine navigation success of treated foragers, which suggested that their homing success was much reduced relative to untreated foragers.

Plants can recognize pathogens through the action of disease resistance (R) genes, which confer resistance to pathogens expressing unique corresponding avirulence (avr) genes. The molecular basis of this gene-for-gene specificity is unknown. The Arabidopsis thaliana RPM1 gene enables dual specificity to pathogens expressing either of two unrelated Pseudomonas syringae avr genes. Despite this function, RPM1 encodes a protein sharing molecular features with recently described single-specificity R genes. Surprisingly, RPM1 is lacking from naturally occurring, disease-susceptible Arabidopsis accessions.

Belclare and Cambridge are prolific sheep breeds, the origins of which involved selecting ewes with exceptionally high litter size records from commercial flocks. The variation in ovulation rate in both breeds is consistent with segregation of a gene (or genes) with a large effect on this trait. Sterile ewes, due to a failure of normal ovarian follicle development, occur in both breeds. New naturally occurring mutations in genes for the oocyte-derived growth factors growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) are described. These mutations are associated with increased ovulation rate in heterozygous carriers and sterility in homozygous carriers in both breeds. This is the first time that a mutation in the gene for GDF9 has been found that causes increased ovulation rate and infertility in a manner similar to inactivating mutations in BMP15, and shows that GDF9 is essential for normal folliculogenesis in sheep. Furthermore, it is shown, for the first time in any species, that individuals with mutations in both GDF9 and BMP15 have a greater ovulation rate than sheep with either of the mutations separately.

Evolutionary trees are often estimated from DNA or RNA sequence data. How much confidence should we have in the estimated trees? In 1985, Felsenstein [Felsenstein, J. (1985) Evolution 39, 783-791] suggested the use of the bootstrap to answer this question. Felsenstein's method, which in concept is a straightforward application of the bootstrap, is widely used, but has been criticized as biased in the genetics literature. This paper concerns the use of the bootstrap in the tree problem. We show that Felsenstein's method is not biased, but that it can be corrected to better agree with standard ideas of confidence levels and hypothesis testing. These corrections can be made by using the more elaborate bootstrap method presented here, at the expense of considerably more computation.

*The rich ecology of tropical forests is intimately tied to their moisture status. Multi-site syntheses can provide a macro-scale view of these linkages and their susceptibility to changing climates. Here, we report pan-tropical and regional-scale analyses of tree vulnerability to drought. *We assembled available data on tropical forest tree stem mortality before, during, and after recent drought events, from 119 monitoring plots in 10 countries concentrated in Amazonia and Borneo. *In most sites, larger trees are disproportionately at risk. At least within Amazonia, low wood density trees are also at greater risk of drought-associated mortality, independent of size. For comparable drought intensities, trees in Borneo are more vulnerable than trees in the Amazon. There is some evidence for lagged impacts of drought, with mortality rates remaining elevated 2 yr after the meteorological event is over. *These findings indicate that repeated droughts would shift the functional composition of tropical forests toward smaller, denser-wooded trees. At very high drought intensities, the linear relationship between tree mortality and moisture stress apparently breaks down, suggesting the existence of moisture stress thresholds beyond which some tropical forests would suffer catastrophic tree mortality.

Mycotoxins are secondary metabolites produced by fungi especially those belonging to the genus Aspergillus, Penicillum and Fusarium. Mycotoxin contamination can occur in all agricultural commodities in the field and/or during storage, if conditions are favourable to fungal growth. Regarding animal feed, five mycotoxins (aflatoxins, deoxynivalenol, zearalenone, fumonisins and ochratoxin A) are covered by EU legislation (regulation or recommendation). Transgressions of these limits are rarely observed in official monitoring programs. However, low level contamination by Fusarium toxins is very common (e.g., deoxynivalenol (DON) is typically found in more than 50% of the samples) and co-contamination is frequently observed. Multi-mycotoxin studies reported 75%-100% of the samples to contain more than one mycotoxin which could impact animal health at already low doses. Co-occurrence of mycotoxins is likely to arise for at least three different reasons (i) most fungi are able to simultaneously produce a number of mycotoxins, (ii) commodities can be contaminated by several fungi, and (iii) completed feed is made from various commodities. In the present paper, we reviewed the data published since 2004 concerning the contamination of animal feed with single or combinations of mycotoxins and highlighted the occurrence of these co-contaminations.

Kinzig, A. P., P. Ryan, M. Etienne, H. Allison, T. Elmqvist, and B. H. Walker. 2006. Resilience and regime shifts: assessing cascading effects. Ecology and Society 11(1): 20. https://doi.org/10.5751/ES-01678-110120

Phylogenetic signal is the tendency for closely related species to display similar trait values as a consequence of their phylogenetic proximity. Ecologists and evolutionary biologists are becoming increasingly interested in studying the phylogenetic signal and the processes which drive patterns of trait values in the phylogeny. Here, we present a new R package, phylosignal which provides a collection of tools to explore the phylogenetic signal for continuous biological traits. These tools are mainly based on the concept of autocorrelation and have been first developed in the field of spatial statistics. To illustrate the use of the package, we analyze the phylogenetic signal in pollution sensitivity for 17 species of diatoms.

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.

In this review, we present the recent developments and future prospects of improving nitrogen use efficiency (NUE) in crops using various complementary approaches. These include conventional breeding and molecular genetics, in addition to alternative farming techniques based on no-till continuous cover cropping cultures and/or organic nitrogen (N) nutrition. Whatever the mode of N fertilization, an increased knowledge of the mechanisms controlling plant N economy is essential for improving NUE and for reducing excessive input of fertilizers, while maintaining an acceptable yield and sufficient profit margin for the farmers. Using plants grown under agronomic conditions, with different tillage conditions, in pure or associated cultures, at low and high N mineral fertilizer input, or using organic fertilization, it is now possible to develop further whole plant agronomic and physiological studies. These can be combined with gene, protein and metabolite profiling to build up a comprehensive picture depicting the different steps of N uptake, assimilation and recycling to produce either biomass in vegetative organs or proteins in storage organs. We provide a critical overview as to how our understanding of the agro-ecophysiological, physiological and molecular controls of N assimilation in crops, under varying environmental conditions, has been improved. We have used combined approaches, based on agronomic studies, whole plant physiology, quantitative genetics, forward and reverse genetics and the emerging systems biology. Long-term sustainability may require a gradual transition from synthetic N inputs to legume-based crop rotation, including continuous cover cropping systems, where these may be possible in certain areas of the world, depending on climatic conditions. Current knowledge and prospects for future agronomic development and application for breeding crops adapted to lower mineral fertilizer input and to alternative farming techniques are explored, whilst taking into account the constraints of both the current world economic situation and the environment.

Grape phenolics are structurally diverse, from simple molecules to oligomers and polymers that are usually designated “tannins,” referring to their ability to interact with proteins. Anthocyanin pigments and tannins are particularly important for red wine quality. Their extraction depends on their location in the berry and their solubility. All phenolic compounds are unstable and undergo numerous enzymatic and chemical reactions. Color and taste changes during red wine aging have been ascribed to anthocyanin-tannin reactions. The structures and properties of tannins and pigmented tannins from these reactions are often misunderstood. Current research on wine phenolic composition is reviewed, with emphasis on the following issues: (1) reactions of tannins yield both larger polymers and smaller species; (2) anthocyanin reactions can generate colorless species as well as polymeric and small various pigments; (3) some polymeric pigments undergo sulfite bleaching while some low molecular weight pigments do not; (4) polymers are both soluble and astringent, so the astringency loss during aging may involve cleavage rather than polymerization; and (5) sensory properties of anthocyanins and tannins are modulated by interactions with other wine components.

Abstract Estimates of carbon leaching losses from different land use systems are few and their contribution to the net ecosystem carbon balance is uncertain. We investigated leaching of dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), and dissolved methane (CH 4 ), at forests, grasslands, and croplands across Europe. Biogenic contributions to DIC were estimated by means of its δ 13 C signature. Leaching of biogenic DIC was 8.3±4.9 g m −2 yr −1 for forests, 24.1±7.2 g m −2 yr −1 for grasslands, and 14.6±4.8 g m −2 yr −1 for croplands. DOC leaching equalled 3.5±1.3 g m −2 yr −1 for forests, 5.3±2.0 g m −2 yr −1 for grasslands, and 4.1±1.3 g m −2 yr −1 for croplands. The average flux of total biogenic carbon across land use systems was 19.4±4.0 g C m −2 yr −1 . Production of DOC in topsoils was positively related to their C/N ratio and DOC retention in subsoils was inversely related to the ratio of organic carbon to iron plus aluminium (hydr)oxides. Partial pressures of CO 2 in soil air and soil pH determined DIC concentrations and fluxes, but soil solutions were often supersaturated with DIC relative to soil air CO 2 . Leaching losses of biogenic carbon (DOC plus biogenic DIC) from grasslands equalled 5–98% (median: 22%) of net ecosystem exchange (NEE) plus carbon inputs with fertilization minus carbon removal with harvest. Carbon leaching increased the net losses from cropland soils by 24–105% (median: 25%). For the majority of forest sites, leaching hardly affected actual net ecosystem carbon balances because of the small solubility of CO 2 in acidic forest soil solutions and large NEE. Leaching of CH 4 proved to be insignificant compared with other fluxes of carbon. Overall, our results show that leaching losses are particularly important for the carbon balance of agricultural systems.

ABSTRACT The effects of elevated atmospheric CO 2 concentration on growth of forest tree species are difficult to predict because practical limitations restrict experiments to much shorter than the average life‐span of a tree. Long‐term, process‐based computer models must be used to extrapolate from shorter‐term experiments. A key problem is to ensure a strong flow of information between experiments and models. In this study, meta‐analysis techniques were used to summarize a suite of photosynthetic model parameters obtained from 15 field‐based elevated [CO 2 ] experiments on European forest tree species. The parameters studied are commonly used in modelling photosynthesis, and include observed light‐saturated photosynthetic rates ( A max ), the potential electron transport rate ( J max ), the maximum Rubisco activity ( V cmax ) and leaf nitrogen concentration on mass ( N m ) and area ( N a ) bases. Across all experiments, light‐saturated photosynthesis was strongly stimulated by growth in elevated [CO 2 ]. However, significant down‐regulation of photosynthesis was also observed; when measured at the same CO 2 concentration, photosynthesis was reduced by 10–20%. The underlying biochemistry of photosynthesis was affected, as shown by a down‐regulation of the parameters J max and V cmax of the order of 10%. This reduction in J max and V cmax was linked to the effects of elevated [CO 2 ] on leaf nitrogen concentration. It was concluded that the current model is adequate to model photosynthesis in elevated [CO 2 ]. Tables of model parameter values for different European forest species are given.

In this paper the hedonic price technique is applied to Bordeaux wine. In the hedonic price function we include not only the ‘objective’ characteristics appearing on the label of the bottle, but also the sensory characteristics of the wine. Our data come from an experimental study in which juries have evaluated and graded a sample of Bordeaux wines. The estimation of the hedonic price equation shows that the market price is essentially determined by the objective characteristics. The estimation of a jury grade equation shows that quality, unlike the market price, is essentially determined by the sensory characteristics.

Jaynes' information theory formalism of statistical mechanics is applied to the stationary states of open, non-equilibrium systems. First, it is shown that the probability distribution pΓ of the underlying microscopic phase space trajectories Γ over a t

Turncoat Aphids Aphid color has consequences for the fate of the wearer: Coccinellid beetles prefer to eat red ones and parasitoid wasps attack green ones. What might happen if aphids could change color and outwit their predators? Tsuchida et al. (p. 1102 ) have found that a subpopulation of the pea aphid can do this, but not without help from a previously unknown species of bacterium that lives intimately with the aphid as an endosymbiont and makes red aphids turn green. The bacterium interferes with host pigment biosynthesis—itself borrowed from fungi long ago in evolution—to stimulate blue-green pigment production as the aphid larva matures, turning the red nymph into a green adult. The ecological consequences of this about-turn of color have yet to be tested, but other studies have shown a variety of effects on aphid behavior mediated by endosymbionts in response to adaptation to different food plants, temperature tolerance, and predator avoidance.

A consensus linkage map has been developed in the chicken that combines all of the genotyping data from the three available chicken mapping populations. Genotyping data were contributed by the laboratories that have been using the East Lansing and Compton reference populations and from the Animal Breeding and Genetics Group of the Wageningen University using the Wageningen/Euribrid population. The resulting linkage map of the chicken genome contains 1889 loci. A framework map is presented that contains 480 loci ordered on 50 linkage groups. Framework loci are defined as loci whose order relative to one another is supported by odds greater then 3. The possible positions of the remaining 1409 loci are indicated relative to these framework loci. The total map spans 3800 cM, which is considerably larger than previous estimates for the chicken genome. Furthermore, although the physical size of the chicken genome is threefold smaller then that of mammals, its genetic map is comparable in size to that of most mammals. The map contains 350 markers within expressed sequences, 235 of which represent identified genes or sequences that have significant sequence identity to known genes. This improves the contribution of the chicken linkage map to comparative gene mapping considerably and clearly shows the conservation of large syntenic regions between the human and chicken genomes. The compact physical size of the chicken genome, combined with the large size of its genetic map and the observed degree of conserved synteny, makes the chicken a valuable model organism in the genomics as well as the postgenomics era. The linkage maps, the two-point lod scores, and additional information about the loci are available at web sites in Wageningen (http://www.zod.wau.nl/vf/ research/chicken/frame_chicken.html) and East Lansing (http://poultry.mph.msu.edu/).