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Forecasting invasive-pathogen dynamics is paramount to anticipate eradication and containment strategies. Such predictions can be obtained using a model grounded on partial differential equations (PDE; often exploited to model invasions) and fitted to surveillance data. This framework allows the construction of phenomenological but concise models relying on mechanistic hypotheses and real observations. However, it may lead to models with overly rigid behavior and possible data-model mismatches. Hence, to avoid drawing a forecast grounded on a single PDE-based model that would be prone to errors, we propose to apply Bayesian model averaging (BMA), which allows us to account for both parameter and model uncertainties. Thus, we propose a set of different competing PDE-based models for representing the pathogen dynamics, we use an adaptive multiple importance sampling algorithm (AMIS) to estimate parameters of each competing model from surveillance data in a mechanistic-statistical framework, we evaluate the posterior probabilities of models by comparing different approaches proposed in the literature, and we apply BMA to draw posterior distributions of parameters and a posterior forecast of the pathogen dynamics. This approach is applied to predict the extent of Xylella fastidiosa in South Corsica, France, a phytopathogenic bacterium detected in situ in Europe less than 10 years ago (Italy 2013, France 2015). Separating data into training and validation sets, we show that the BMA forecast outperforms competing forecast approaches.

[Introduction] Sunflower breeding for resistance to the parasitic plant sunflower broomrape (Orobanche cumana Wallr.) requires the identification of novel resistance genes. In this research, we conducted a genome-wide association study (GWAS) to identify QTLs associated with broomrape resistance., [Methods] The marker-trait associations were examined across a germplasm set composed of 104 sunflower accessions. They were genotyped with a 600k AXIOM® genome-wide array and evaluated for resistance to three populations of the parasite with varying levels of virulence (races EFR, FGV, and GTK) in two environments., [Results and Discussion] The analysis of the genetic structure of the germplasm set revealed the presence of two main groups. The application of optimized treatments based on the general linear model (GLM) and the mixed linear model (MLM) allowed the detection of 14 SNP markers significantly associated with broomrape resistance. The highest number of marker-trait associations were identified on chromosome 3, clustered in two different genomic regions of this chromosome. Other associations were identified on chromosomes 5, 10, 13, and 16. Candidate genes for the main genomic regions associated with broomrape resistance were studied and discussed. Particularly, two significant SNPs on chromosome 3 associated with races EFR and FGV were found at two tightly linked SWEET sugar transporter genes. The results of this study have confirmed the role of some QTL on resistance to sunflower broomrape and have revealed new ones that may play an important role in the development of durable resistance to this parasitic weed in sunflower.

Crop multi-model ensembles (MME) have proven to be effective in increasing the accuracy of simulations in modelling experiments. However, the ability of MME to capture crop responses to changes in sowing dates and densities has not yet been investigated. These management interventions are some of the main levers for adapting cropping systems to climate change. Here, we explore the performance of a MME of 29 wheat crop models to predict the effect of changing sowing dates and rates on yield and yield components, on two sites located in a high-yielding environment in New Zealand. The experiment was conducted for 6 years and provided 50 combinations of sowing date, sowing density and growing season. We show that the MME simulates seasonal growth of wheat well under standard sowing conditions, but fails under early sowing and high sowing rates. The comparison between observed and simulated in-season fraction of intercepted photosynthetically active radiation (FIPAR) for early sown wheat shows that the MME does not capture the decrease of crop above ground biomass during winter months due to senescence. Models need to better account for tiller competition for light, nutrients, and water during vegetative growth, and early tiller senescence and tiller mortality, which are exacerbated by early sowing, high sowing densities, and warmer winter temperatures.

Respiration chambers are the gold standard technique for measuring methane in ruminants provided that their gas recovery rates are close to 100%. The determination of the gas recovery rate of respiration chamber facilities is a central prerequisite to assess the accuracy of the methane emission quantification. However, data of recovery tests are seldom reported. This paper presents data from gas recovery tests applied to an experimental facility of four open-circuit respiration chambers designed to measure methane emissions from goats. The experimental facility is located at Thiverval-Grignon, France. The recovery test was assessed by placing a known source of methane emission at six locations in each chamber successively. For each chamber, the gas from the chamber and the ambient air were continuously sampled by a Multi-Gas Analyser 3500 gas analyser provided with a multiport unit that switches the sampling between the pipe from chamber and from the ambient air every 90 s. The analyser determines the concentration (ppm) of methane by infrared. The data were further imported in an R script for calculation of the methane recovery percentage. These data are useful resources for illustrating the protocol to assess the accuracy of respiration chambers.

Analysing temporal patterns in plant communities is extremely important to quantify the extent and the consequences of ecological changes, especially considering the current biodiversity crisis. Long-term data collected through the regular sampling of permanent plots represent the most accurate resource to study ecological succession, analyse the stability of a community over time and understand the mechanisms driving vegetation change. We hereby present the LOng-Term Vegetation Sampling (LOTVS) initiative, a global collection of vegetation time-series derived from the regular monitoring of plant species in permanent plots. With 79 data sets from five continents and 7,789 vegetation time-series monitored for at least 6 years and mostly on an annual basis, LOTVS possibly represents the largest collection of temporally fine-grained vegetation time-series derived from permanent plots and made accessible to the research community. As such, it has an outstanding potential to support innovative research in the fields of vegetation science, plant ecology and temporal ecology.

The poverty of disease resistance gene reservoirs limits the breeding of crops for durable resistance against evolutionary dynamic pathogens. Zymoseptoria tritici which causes Septoria tritici blotch (STB), represents one of the most genetically diverse and devastating wheat pathogens worldwide. No fully virulent Z. tritici isolates against synthetic wheats carrying the major resistant gene Stb16q have been identified. Here, we use comparative genomics, mutagenesis and complementation to identify Stb16q, which confers broad-spectrum resistance against Z. tritici. The Stb16q gene encodes a plasma membrane cysteine-rich receptor-like kinase that was recently introduced into cultivated wheat and which considerably slows penetration and intercellular growth of the pathogen.

Individuals' distribution across habitats may depend on their personality. Human activities and infrastructures are critical elements of the landscape that may impact the habitat selection process. However, depending on their personality, individuals may respond differently to these unnatural elements. In the present study, we first investigated whether some human infrastructures (buildings, roads and paths) shaped Montagu's harrier nest spatial distribution in the landscape according to female personality (boldness). Second, we tested if the reproductive success of females depended on their boldness and nest location regarding infrastructures. Using a long-term (19 years) dataset, we calculated, for each infrastructure type, the distance from each nest to the nearest infrastructure and the infrastructure density around the nest. We tested the effects of female boldness (bold vs. shy) and its interaction with egg-laying date on these six metrics. Nest location in the landscape depended on female personality and on some human infrastructures: the building density was smaller around nests from shy females than from bold ones. Nest distribution related to other infrastructure metrics did not depend on female boldness. The pattern related to building density is consistent with some habitat choice hypotheses, which are discussed. Path density around nests negatively affected reproductive success regardless of female boldness, and late breeders nested further away from paths than early breeders. Human activities on paths (more common later in the season) could lead to disturbance and a decrease in parental care, reducing reproductive success. Increasing human presence in farmlands implies a need to better understand its impact on population composition, in terms of personality. Our results suggest that individual behavioural differences should be taken into account in studies assessing the effects of human disturbance on animal populations, to propose more appropriate con

[EN] Model-based accuracy, defined as the theoretical correlation between true and estimated breeding value, can be obtained for each individual as a function of its prediction error variance (PEV) and inbreeding coefficient F, in BLUP, GBLUP and SSGBLUP genetic evaluations. However, for computational convenience, inbreeding is often ignored in two places. First, in the computation of reliability = 1-PEV/(1 + F). Second, in the set-up, using Henderson's rules, of the inverse of the pedigree-based relationship matrix A. Both approximations have an effect in the computation of model-based accuracy and result in wrong values. In this work, first we present a reminder of the theory and extend it to SSGBLUP. Second, we quantify the error of ignoring inbreeding with real data in three scenarios: BLUP evaluation and SSGBLUP in Uruguayan dairy cattle, and BLUP evaluations in a line of rabbit closed for >40 generations with steady increase of inbreeding up to an average of 0.30. We show that ignoring inbreeding in the set-up of the A-inverse is equivalent to assume that non-inbred animals are actually inbred. This results in an increase of apparent PEV that is negligible for dairy cattle but considerable for rabbit. Ignoring inbreeding in reliability = 1-PEV/(1 + F) leads to underestimation of reliability for BLUP evaluations, and this underestimation is very large for rabbit. For SSGBLUP in dairy cattle, it leads to both underestimation and overestimation of reliability, both for genotyped and non-genotyped animals. We strongly recommend to include inbreeding both in the set-up of A-inverse and in the computation of reliability from PEVs.

Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.

In tissue engineering, biological, physical, and chemical inputs have to be combined to properly mimic cellular environments and successfully build artificial tissues which can be designed to fulfill different biomedical needs such as the shortage of organ donors or the development of in vitro disease models for drug testing. Inclusion body-like protein nanoparticles (pNPs) can simultaneously provide such physical and biochemical stimuli to cells when attached to surfaces. However, this attachment has only been made by physisorption. To provide a stable anchoring, a covalent binding of lactic acid bacteria (LAB) produced pNPs, which lack the innate pyrogenic impurities of Gram-negative bacteria like Escherichia coli, is presented. The reported micropatterns feature a robust nanoscale topography with an unprecedented mechanical stability. In addition, they are denser and more capable of influencing cell morphology and orientation. The increased stability and the absence of pyrogenic impurities represent a step forward towards the translation of this material to a clinical setting.

Lactic acid bacteria (LAB) encompasses industrially relevant bacteria involved in food fermentations as well as health-promoting members of our autochthonous microbiota. In the last years, we have witnessed major progresses in the knowledge of the biology of their cell wall, the outermost macrostructure of a Gram-positive cell, which is crucial for survival. Sophisticated biochemical analyses combined with mutation strategies have been applied to unravel biosynthetic routes that sustain the inter- and intra-species cell wall diversity within LAB. Interplay with global cell metabolism has been deciphered that improved our fundamental understanding of the plasticity of the cell wall during growth. The cell wall is also decisive for the antimicrobial activity of many bacteriocins, for bacteriophage infection and for the interactions with the external environment. Therefore, genetic circuits involved in monitoring cell wall damage have been described in LAB, together with a plethora of defence mechanisms that help them to cope with external threats and adapt to harsh conditions. Since the cell wall plays a pivotal role in several technological and health-promoting traits of LAB, we anticipate that this knowledge will pave the way for the future development and extended applications of LAB.

Watermelon mosaic virus (WMV; genus Potyvirus, family Potyviridae) is responsible for serious cucurbit yield losses worldwide. Different WMV genetic groups have been characterized so far. Among these, the "classical" (CL) group has been present in the Mediterranean basin for 40 years, whereas the "emergent" (EM) group includes isolates that are associated with more-severe symptoms observed since 2000. Information on the spatial and temporal evolution of WMV isolates in Italy is currently sparse. In this study, 39 WMV isolates samples collected in different regions over the last two decades were analysed at two different genomic regions that are known to be highly variable and contain recombination breakpoints. Most of the isolates collected between 2002 and 2009 were found to belong to the CL group, whereas the isolates from 2012 onwards were classified as EM, indicating that EM isolates have progressively displaced the CL population in Italy. Although genetic variability was observed within both CL and EM groups and recombinant isolates were detected, no positive selection or haplotype geographic structure were inferred. This suggest that the shift from CL to EM populations was likely due to multiple introductions of EM isolates in different regions of Italy rather than from genetic differentiation of local populations. The progressive increase in prevalence of the highly virulent EM populations is a serious concern because of their symptom severity, and the presence of multiple EM variants that include recombinants necessitates new efforts to develop durable control strategies.

The discovery of the first non-cellular infectious agent, later determined to be tobacco mosaic virus, paved the way for the field of virology. In the ensuing decades, research focused on discovering and eliminating viral threats to plant and animal health. However, recent conceptual and methodological revolutions have made it clear that viruses are not merely agents of destruction but essential components of global ecosystems. As plants make up over 80% of the biomass on Earth, plant viruses likely have a larger impact on ecosystem stability and function than viruses of other kingdoms. Besides preventing overgrowth of genetically homogeneous plant populations such as crop plants, some plant viruses might also promote the adaptation of their hosts to changing environments. However, estimates of the extent and frequencies of such mutualistic interactions remain controversial. In this Review, we focus on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors. We also identify currently unknown aspects of plant virus ecology and evolution that are of practical importance and that should be resolvable in the near future through viral metagenomics.

Orobanche cumana (sunflower broomrape) is an obligate parasitic plant that infects sunflower roots, causing yield losses. Here, by using a map-based cloning strategy, we identified HaOr7—a gene that confers resistance to O. cumana race F—which was found to encode a leucine-rich repeat receptor-like kinase. The complete HAOR7 protein is present in resistant lines of sunflower and prevents O. cumana from connecting to the vascular system of sunflower roots, whereas susceptible lines encode a truncated protein that lacks transmembrane and kinase domains.

Efforts to limit global warming to below 2°C in relation to the pre‐industrial level are under way, in accordance with the 2015 Paris Agreement. However, most impact research on agriculture to date has focused on impacts of warming >2°C on mean crop yields, and many previous studies did not focus sufficiently on extreme events and yield interannual variability. Here, with the latest climate scenarios from the Half a degree Additional warming, Prognosis and Projected Impacts (HAPPI) project, we evaluated the impacts of the 2015 Paris Agreement range of global warming (1.5 and 2.0°C warming above the pre‐industrial period) on global wheat production and local yield variability. A multi‐crop and multi‐climate model ensemble over a global network of sites developed by the Agricultural Model Intercomparison and Improvement Project (AgMIP) for Wheat was used to represent major rainfed and irrigated wheat cropping systems. Results show that projected global wheat production will change by −2.3% to 7.0% under the 1.5°C scenario and −2.4% to 10.5% under the 2.0°C scenario, compared to a baseline of 1980–2010, when considering changes in local temperature, rainfall, and global atmospheric CO2 concentration, but no changes in management or wheat cultivars. The projected impact on wheat production varies spatially; a larger increase is projected for temperate high rainfall regions than for moderate hot low rainfall and irrigated regions. Grain yields in warmer regions are more likely to be reduced than in cooler regions. Despite mostly positive impacts on global average grain yields, the frequency of extremely low yields (bottom 5 percentile of baseline distribution) and yield inter‐annual variability will increase under both warming scenarios for some of the hot growing locations, including locations from the second largest global wheat producer—India, which supplies more than 14% of global wheat. The projected global impact of warming <2°C on wheat production is therefore not

Wheat grain protein concentration is an important determinant of wheat quality for human nutrition that is often overlooked in efforts to improve crop production. We tested and applied a 32‐multi‐model ensemble to simulate global wheat yield and quality in a changing climate. Potential benefits of elevated atmospheric CO2 concentration by 2050 on global wheat grain and protein yield are likely to be negated by impacts from rising temperature and changes in rainfall, but with considerable disparities between regions. Grain and protein yields are expected to be lower and more variable in most low‐rainfall regions, with nitrogen availability limiting growth stimulus from elevated CO2. Introducing genotypes adapted to warmer temperatures (and also considering changes in CO2 and rainfall) could boost global wheat yield by 7% and protein yield by 2%, but grain protein concentration would be reduced by −1.1 percentage points, representing a relative change of −8.6%. Climate change adaptations that benefit grain yield are not always positive for grain quality, putting additional pressure on global wheat production.

The gut microbiota has been evolving with its host along the time creating a symbiotic relationship. In this study, we assess the role of the host genome in the modulation of the microbiota composition in pigs. Gut microbiota compositions were estimated through sequencing the V3-V4 region of the 16S rRNA gene from rectal contents of 285 pigs. A total of 1,261 operational taxonomic units were obtained and grouped in 18 phyla and 101 genera. Firmicutes (45.36%) and Bacteroidetes (37.47%) were the two major phyla obtained, whereas at genus level Prevotella (7.03%) and Treponema (6.29%) were the most abundant. Pigs were also genotyped with a high-throughput method for 45,508 single nucleotide polymorphisms that covered the entire pig genome. Subsequently, genome-wide association studies were made among the genotypes of these pigs and their gut microbiota composition. A total of 52 single-nucleotide polymorphisms distributed in 17 regions along the pig genome were associated with the relative abundance of six genera; Akkermansia, CF231, Phascolarctobacterium, Prevotella, SMB53, and Streptococcus. Our results suggest 39 candidate genes that may be modulating the microbiota composition and manifest the association between host genome and gut microbiota in pigs.

Sunflower broomrape (Orobanche cumana Wallr.) is a holoparasitic plant that causes major yield losses to sunflower crops in the Old World. Efforts to understand how this parasitic weed recognizes and interacts with sunflowers are important for developing long-term genetic resistance strategies. However, such studies are hampered by the lack of genetic tools for O. cumana. The objectives of this research were to construct a genetic linkage map of this species using SSR and SNP markers, and mapping the Pg locus that is involved in plant pigmentation. The genetic map was developed from the progenies of a cross between the O. cumana inbred lines EK-12 and EK-A1, which originated from populations belonging to two distant and geographically separated gene pools identified in Spain. The inbred lines also differed in plant pigmentation, with EK-A1 lacking anthocyanin pigmentation (pgpg genotype). A genetic map comprising 26 SSR and 701 SNP markers was constructed, which displayed 19 linkage groups (LGs), corresponding to the 19 chromosome pairs of O. cumana. The total length of the map was 1795.7 cM, with an average distance between two adjacent positions of 2.5 cM and a maximum map distance of 41.9 cM. The Pg locus mapped to LG19 between the SNP markers OS02468 and OS01653 at 7.5 and 3.4 cM, respectively. This study constitutes the first linkage map and trait mapping study in Orobanche spp., laying a key foundation for further genome characterization and providing a basis for mapping additional traits such as those having a key role in parasitism.

Temporal aroma compound release during eating is a function of the physicochemical properties of the food matrix, aroma compounds, and oral physiology of individuals. However, the influence of each parameter on the release of each aroma component should be clarified. Two flavored lipoprotein matrices varying in composition were chewed in a chewing simulator that reproduced most of the physiological functions of the mouth. Aroma compound releases (butanoic acid, 2-heptanone, ethyl butyrate, 3-octanone, and 2-nonanone) were followed in real time by direct connection of the device to APCI-MS (atmospheric pressure chemical ionization mass spectrometry). Each oral parameter was controlled and decoupled using the in vitro device. The food matrix composition had only a low impact on aroma compound release, but the controlled oral parameters had significantly different influences on the release of aroma compounds according to their physicochemical characteristics. The release of certain compounds seemed more sensitive to bite force, while others seemed more sensitive to the shearing angle. The salivary flow rate primarily influenced the more hydrophobic compounds. Significant interactions were also observed between shear angle, salivary flow rate, and lipoprotein matrix composition, mainly for the release of the more hydrophobic volatile compounds; this needs further investigations to be clarified.

[EN] Chitin, a major component of fungal cell walls, is a well-known pathogen-associated molecular pattern (PAMP) that triggers defense responses in several mammal and plant species. Here, we show that two chitooligosaccharides, chitin and chitosan, act as PAMPs in grapevine (Vitis vinifera) as they elicit immune signalling events, defense gene expression and resistance against fungal diseases. To identify their cognate receptors, the grapevine family of LysM receptor kinases (LysM-RKs) was annotated and their gene expression profiles were characterized. Phylogenetic analysis clearly distinguished three V. vinifera LysM-RKs (VvLYKs) located in the same clade as the Arabidopsis CHITIN ELICITOR RECEPTOR KINASE1 (AtCERK1), which mediates chitin-induced immune responses. The Arabidopsis mutant Atcerk1, impaired in chitin perception, was transformed with these three putative orthologous genes encoding VvLYK1-1, -2, or -3 to determine if they would complement the loss of AtCERK1 function. Our results provide evidence that VvLYK1-1 and VvLYK1-2, but not VvLYK1-3, functionally complement the Atcerk1 mutant by restoring chitooligosaccharide-induced MAPK activation and immune gene expression. Moreover, expression of VvLYK1-1 in Atcerk1 restored penetration resistance to the non-adapted grapevine powdery mildew (Erysiphe necator). On the whole, our results indicate that the grapevine VvLYK1-1 and VvLYK1-2 participate in chitin- and chitosan-triggered immunity and that VvLYK1-1 plays an important role in basal resistance against E. necator.

[EN] This study aims to determine the digestibility of milk by the young rabbit (21-25 d old), taking into account the increment of digesta content and urine excretion. Nineteen litters of 9 young rabbits 21 to 25 d old were used: 12 litters (S group) fed exclusively with milk using controlled suckling, and 7 litters (Control group) with free suckling and access to the pelleted feed of the doe. The faecal digestibility of milk dry matter (DM) was measured between 21 and 25 d of age, for S litters housed from 15 d of age in a metabolism cage separately from their mother. Between 21 and 25 d, the milk intake, faeces and urine excretion were controlled daily, and the mean increment in digesta content was measured by comparing digesta weight of the whole tract at 21 and 25 d of age (one kit per litter). The increment in digesta content from 21 to 25 d averaged 77% (+8.5 g), sourcing mainly from stomach and caecum contents increase (+57 and +120% respectively). The mean increase for the dry content of the gut (from 21 to 25 d) was 1.75 g DM/kit, and was considered as non-digested to calculate the digestibility coefficient of the milk. The milk intake averaged 30 g/d/kit (7.9 g DM/d kit). No faecal excretion was recorded between 21 and 25 d. From the milk intake and increment in digesta content, the corrected digestibility of the milk dry matter reached 94% (minimum=92.9%, maximum=95.6%). The daily urine excretion averaged 5.1 mL/kit, corresponding to 1.2 g DM/kit. Therefore, the corrected DM retention coefficient of the milk was 79.5%. The quantity of nitrogen excreted in urine was low (0.06 g/d kits), thus the corrected nitrogen retention coefficient for milk reached 82% and the nitrogen retained (corrected) reached 0.44 g/d kit. Accordingly, the amount in metabolisable protein for the milk was 90 g/kg (fresh). The corrected energy retention coefficient was estimated to 95.8%, for a crude energy concentration estimated at 28.14 MJ/kg DM for the milk. Thus, the energy re

In this study, we used BovineSNP50 Genotyping BeadChip data to estimate the structure, putative ancestral origin as well as to identify regions with selective sweeps that may have had an important role in the adaptation to tropical conditions of the ‘Charolais de Cuba’ (CHCU) breed. According to a principal component analysis, CHCU samples cluster together with taurine breeds with an estimated 93% of taurus ancestral alleles. Despite the short period since importation, we detected differentiation (Fst = 0.049) between the French Charolaise (CHA) and CHCU. However, CHA breed was the closest breed to CHCU followed by other hybrids breed with a clear CHA origin. Linkage disequilibrium (r2) decay tends to be lower in CHCU compared to CHA probably due to a less intense artificial selection programs of CHCU. Signals of recent adaptation to tropical conditions between CHCU and CHA were identified. Genes mapping within those regions reflect different functions related to immunity, metabolic changes and heat tolerance (CHCU) and muscle development and meat quality (CHA) that may have had an important role in the phenotypic differentiation of these breeds. Further studies will expand our knowledge on the molecular basis of adaptation of cattle to tropical conditions and molecular process associated with meat quality traits.

Bacillus subtilis bacteriophage SPP1 is a lytic siphovirus first described 50 years ago. Its complete DNA sequence was reported in 1997. Here we present an updated annotation of the 44,016 bp SPP1 genome and its correlation to different steps of the viral multiplication process. Five early polycistronic transcriptional units encode phage DNA replication proteins and lysis functions together with less characterized, mostly non-essential, functions. Late transcription drives synthesis of proteins necessary for SPP1 viral particles assembly and for cell lysis, together with a short set of proteins of unknown function. The extensive genetic, biochemical and structural biology studies on the molecular mechanisms of SPP1 DNA replication and phage particle assembly rendered it a model system for tailed phages research. We propose SPP1 as the reference species for a new SPP1-like viruses genus of the Siphoviridae family.

Humanity faces the challenge of having to increase food production to feed an exponentially growing world population, while crop diseases reduce yields to levels that we can no longer afford. Besides, a significant amount of waste is produced after fruit harvest. Fruit decay due to diseases at a post-harvest level can claim up to 50% of the total production worldwide. Currently, the most effective means of disease control is the use of pesticides. However, their use post-harvest is extremely limited due to toxicity. The last few decades have witnessed the development of safer methods of disease control post-harvest. They have all been included in programs with the aim of achieving integrated pest (and disease) management (IPM) to reduce pesticide use to a minimum. Unfortunately, these approaches have failed to provide robust solutions. Therefore, it is necessary to develop alternative strategies that would result in effective control. Exploiting the immune capacity of plants has been described as a plausible route to prevent diseases post-harvest. Post-harvest-induced resistance (IR) through the use of safer chemicals from biological origin, biocontrol, and physical means has also been reported. In this review, we summarize the successful activity of these different strategies and explore the mechanisms behind. We further explore the concept of priming, and how its long-lasting and broad-spectrum nature could contribute to fruit resistance.

Agriculture contributes to a significant proportion of global emissions of greenhouse gases (GHG) but can also participate in climate change mitigation. The introduction of legumes in crop rotations reduces the dependence on N fertilizers and may mitigate the carbon (C) footprint of cropping systems. The aim of this study was to quantify the C footprint of six low-input arable cropping systems resulting from the combination of three levels of grain legumes introduction in a 3-yr rotation (GL0: no grain legumes, GL1: 1 grain legume, GL2: 2 grain legumes) and the use of cover crops (CC) or bare fallow (BF) between cash crops, covering two rotation cycles (6 years). The approach considered external emissions, on-site emissions and soil organic carbon (SOC) stock changes, and prioritized (i) field observations and (ii) simulation of non-measured variables with the STICS model, rather than default emission factors. As expected, fertilizers accounted for 80–90% of external emissions, being reduced by 50% and 102% with grain legumes introduction in GL1-BF and GL2-BF, compared to the cereal-based rotation (GL0-BF). Cover crops management increased machinery emissions by 24–35% compared to BF. Soil nitrous oxide (N2O) emissions were low, ranging between 205 and 333 kg CO2 eq. ha−1 yr−1 in GL1-BF and GL0-BF, respectively. Nitrate leaching represented the indirect emission of 11.6 to 27.2 kg CO2 eq. ha−1 yr−1 in the BF treatments and 8.2 to 10.7 kg CO2 eq. ha−1 yr−1 in the CC treatments. Indirect emissions due to ammonia volatilization ranged between 8.4 and 41.8 kg CO2 eq. ha−1 yr−1. The introduction of grain legumes strongly influenced SOC changes and, consequently, the C footprint. In the BF systems, grain legumes introduction in the rotations led to a significant increase in the C footprint, because of higher SOC losses. Contrarily, the use of cover crops mitigated SOC losses, and lowered the C footprint. These results indicated the need of CC when increasing the number of

Monoclonal antibodies (mAbs) have significantly improved the treatment of certain cancers. However, in general mAbs alone have limited therapeutic activity. One of their main mechanisms of action is to induce antibody-dependent cell-mediated cytotoxicity (ADCC), which is mediated by natural killer (NK) cells. Unfortunately, most cancer patients have severe immune dysfunctions affecting NK activity. This can be circumvented by the injection of allogeneic, expanded NK cells, which is safe. Nevertheless, despite their strong cytolytic potential against different tumors, clinical results have been poor. Methods: We combined allogeneic NK cells and mAbs to improve cancer treatment. We generated expanded NK cells (e-NK) with strong in vitro and in vivo ADCC responses against different tumors and using different therapeutic mAbs, namely rituximab, obinutuzumab, daratumumab, cetuximab and trastuzumab. Results: Remarkably, e-NK cells can be stored frozen and, after thawing, armed with mAbs. They mediate ADCC through degranulation-dependent and -independent mechanisms. Furthermore, they overcome certain anti-apoptotic mechanisms found in leukemic cells. Conclusion: We have established a new protocol for activation/expansion of NK cells with high ADCC activity. The use of mAbs in combination with e-NK cells could potentially improve cancer treatment.

Impacts of climate change are likely to be marked in areas with steep climatic transitions. Species turnover, spread of invasive species, altered productivity, and modified processes such as fire regimes can all spread rapidly along ecotones, which challenge the current paradigms of ecosystem management. We conducted a literature review at a continental-wide scale of South-Western European forests, where the drier and warmer conditions of the Mediterranean have been widely used as examples of what is expected in more temperate areas. Results from the literature point to: (a) an expansion of slow-growing evergreen hardwood trees; (b) increased dieback and mortality episodes in forests (both natural and planted) mostly related to competition and droughts, and mainly affecting conifers; and (c) an increase in emergent diseases and pests of keystone-trees used in agroforestry zones. There is no consensus in the literature that fire regimes are directly increasing due to climate change, but available satellite data of fire intensity in the last 17 years has been lower in zones where agroforestry practices are dominant compared to unmanaged forests. In contrast, there is agreement in the literature that the current spread of fire events is probably related to land abandonment patterns. The practice of agroforestry, common in all Mediterranean countries, emerges as a frequent recommendation in the literature to cope with drought, reduce fire risk, and maintain biodiverse landscapes and rural jobs. However, it is unknown the extent to which the open vegetation resulting from agroforestry is of interest to forest managers in temperate areas used to exploiting closed forest vegetation. Hence, many transitional areas surrounding the Mediterranean Basin may be left unmanaged with potentially higher climate-change risks, which require active monitoring in order to understand and help ongoing natural adaptation processes.

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.

The tomato red spider mite, Tetranychus evansi, is an emerging pest of solanaceous crops. Two distinct genetic lineages (I and II) have been identified, lineage I having a much wider geographic distribution than lineage II. This has been attributed to differences in cold hardiness that make lineage I better adapted to colonize the coldest parts of the invaded area. However, other factors such as the ability to exploit different hosts may also be involved. In this work, we compared the performance of the Nice (lineage I) and Perpignan (lineage II) strains of T. evansi on two frequent host plants for this species: black nightshade, Solanum nigrum, and cultivated tomato, S. lycopersicum. In general, Nice strain mites performed better (higher fecundity, lower offspring mortality, bigger egg size and lower percentage of males) than Perpignan strain mites when both: (1) they were reared and tested on the same host plant (S. lycopersicum or S. nigrum); and (2) when shifted from S. nigrum to S. lycopersicum and vice versa. Digestive proteases showed also higher expression in Nice strain mites than in Perpignan strain mites, independently of their plant host, potentially reflecting a more efficient proteolytic digestion of plant proteins. However, no differences in detoxification enzyme (P450, esterases and glutathione S-transferases) activities were found when the two strains were compared. In conclusion, our results demonstrate that Nice strain mites exhibited life history traits leading to higher fitness on two different hosts, which may be related with the higher invasive potential and outbreak risks of mites from lineage I.

Ecological transitions between different lifestyles, such as pathogenicity, mutualism and saprophytism, have been very frequent in the course of microbial evolution, and often driven by horizontal gene transfer. Yet, how genomes achieve the ecological transition initiated by the transfer of complex biological traits remains poorly known. Here, we used experimental evolution, genomics, transcriptomics and high-resolution phenotyping to analyze the evolution of the plant pathogen Ralstonia solanacearum into legume symbionts, following the transfer of a natural plasmid encoding the essential mutualistic genes. We show that a regulatory pathway of the recipient R. solanacearum genome involved in extracellular infection of natural hosts was reused to improve intracellular symbiosis with the Mimosa pudica legume. Optimization of intracellular infection capacity was gained through mutations affecting two components of a new regulatory pathway, the transcriptional regulator efpR and a region upstream from the RSc0965–0967 genes of unknown functions. Adaptive mutations caused the downregulation of efpR and the over-expression of a downstream regulatory module, the three unknown genes RSc3146–3148, two of which encoding proteins likely associated to the membrane. This over-expression led to important metabolic and transcriptomic changes and a drastic qualitative and quantitative improvement of nodule intracellular infection. In addition, these adaptive mutations decreased the virulence of the original pathogen. The complete efpR/RSc3146–3148 pathway could only be identified in the genomes of the pathogenic R. solanacearum species complex. Our findings illustrate how the rewiring of a genetic network regulating virulence allows a radically different type of symbiotic interaction and contributes to ecological transitions and trade-offs.

The vast amount of sequence data generated to analyze complex traits is posing new challenges in terms of the analysis and interpretation of the results. Although simulation is a fundamental tool to investigate the reliability of genomic analyses and to optimize experimental design, existing software cannot realistically simulate complete genomes. To remedy this, we have developed a new strategy (Sequence-Based Virtual Breeding, SBVB) that uses real sequence data and simulates new offspring genomes and phenotypes in a very efficient and flexible manner. Using this tool, we studied the efficiency of full sequence in genomic prediction compared to SNP arrays. We used real porcine sequences from three breeds as founder genomes of a 2500-animal pedigree and two genetic architectures: “neutral” and “selective.” In the neutral architecture, frequencies and allele effects were sampled independently whereas, in the selective case, SNPs were sites putatively under selection after domestication and a negative correlation between effect and frequency was induced. We compared the effectiveness of different genotyping strategies for genomic selection, including the use of full sequence commercial arrays or randomly chosen SNP sets in both outbred and crossbred experimental designs. We found that accuracy increases using sequence instead of commercial chips but modestly, perhaps by ≤ 4%. This result was robust to extreme genetic architectures. We conclude that full sequence is unlikely to offset commercial arrays for predicting genetic value when the number of loci is relatively large and the prior given to each SNP is uniform. Using sequence to improve selection thus requires optimized prior information and, likely, increased population sizes. The code and manual for SBVB are available at https://github.com/mperezenciso/sbvb0.

The grapevine reference genome was published by Jaillon et al. [1]. The sequence for the first version of the genome, called the 8X version, was obtained using a whole genome shotgun strategy and the Sanger sequencing technology and was assembled from reads representing 8X coverage. Soon after, the assembly was improved through the addition of 4X of additional coverage, including more Bacterial Artificial Chromosome end sequences that greatly improved the scaffolding of the sequence contigs [2], [3]. The corresponding scaffolds and raw sequences were deposited in European Molecular Biology Laboratory (EMBL) archives (FN594950-FN597014, 2065 entries, release 102). A new chromosome assembly was also developed, based on an improved version of the maps used for the 8X genome version [2], [3], [4], [5] and was also archived at EMBL (FN597015-FN597047, 33 entries, release 102): it is referenced in the grapevine community as the 12X.v0 version of the grapevine reference genome. The chromosome sequence scaffolding of this version still necessitated improvements as around 9% of the sequence was not anchored to chromosomes (with the corresponding scaffolds stacked in the “Unknown” chromosome) and 3.5% of the sequence could be assigned to a chromosome but without certain placement and orientation within the chromosome (stacked in additional “random” chromosomes).

[Background] Parasitic weeds are widespread and cause significant losses in important crops. Their germination requires the detection of crop‐derived molecules such as strigolactones. Strigolactone mimics are germination‐inducing molecules with the potential to apply a suicidal germination strategy for seed bank control of parasitic weeds., [Results] The D‐ring, which is instrumental in the germination process of seeds of parasitic weeds, was attached to gibberellin (GA3) and kaurenoic acid as the scaffold. It was shown that indeed strigolactone mimics prepared from GA3 and kaurenoic acid are active as stimulants when a D‐ring is present; some of the mimics are as active as GR24., [Conclusions] The starting molecules were plant hormones that had previous growth‐regulating activity in other organisms and the products showed enhanced activity towards parasitic weeds. The information generated may contribute to a better understanding of the germination biochemistry of the weed species used. Further research is required in this area but it is clear that the results are promising. © 2017 Society of Chemical Industry.

A direct comparison of cow and goat performance and milk fatty acid (FA) responses to diets known to induce milk fat depression in the bovine has suggested interspecies differences in rumen and mammary lipid metabolism. Thus, this study was conducted to infer some potential mechanisms responsible for the differences in mammary lipogenesis due to diet and ruminant species. To meet this objective, 12 cows and 15 goats were fed a basal diet (control), a similar diet supplemented with 2.2% fish oil (FO), or a diet containing 5.3% sunflower oil and additional starch (+38%; SOS) according to a 3 × 3 Latin square design with 26-d experimental periods. Milk yield, milk composition, FA profile, and FA secretion were measured. On the last day of each period, the mRNA abundance of 19 key genes in mammary metabolism or the enzyme activity or both were measured in mammary tissue sampled by biopsy or at slaughter or both. The results show significant differences in the response of cows and goats to the dietary treatments. In cows, milk fat content and yield were lowered by FO and SOS (−31%), whereas only FO decreased milk fat content in goats (−21%) compared with the control. In cows and to a lesser extent in goats, FO and SOS decreased the secretion of C16 FA output (mmol/kg of BW). However, SOS increased the secretion of >C16 FA in goats. These changes in milk fat content and FA secretion were not associated with modifications in mammary expression or the activity of 19 proteins involved in the major lipogenic pathways. This absence of variation may be attributable to posttranscriptional regulation for these genes or related to the time of sampling of the mammary tissue relative to the previous meal and milking. Otherwise, the abundances of 15 mRNA among the 19 encoding for genes involved in lipid metabolism in the mammary gland were different among species, with 9 more abundant in cows (FASN, FADS1, SCD1, GPD1, LALBA, SREBF1, LXRA, PPARA, and P

Increasing the accuracy of crop productivity estimates is a key element in planning adaptation strategies to ensure global food security under climate change. Process-based crop models are effective means to project climate impact on crop yield, but have large uncertainty in yield simulations. Here, we show that variations in the mathematical functions currently used to simulate temperature responses of physiological processes in 29 wheat models account for >50% of uncertainty in simulated grain yields for mean growing season temperatures from 14 °C to 33 °C. We derived a set of new temperature response functions that when substituted in four wheat models reduced the error in grain yield simulations across seven global sites with different temperature regimes by 19% to 50% (42% average). We anticipate the improved temperature responses to be a key step to improve modelling of crops under rising temperature and climate change, leading to higher skill of crop yield projections.

Revista oficial de la Asociación Española de Teledetección, [EN] Land surface phenology from time series of satellite data are expected to contribute to improve the represen-tation of vegetation phenology in earth system models. We characterized the baseline phenology of the vegetation at the global scale from GEOCLIM-LAI, a global climatology of leaf area index (LAI) derived from 1-km SPOT VEGETATION time series for 1999-2010. The calibration with ground measurements showed that the start and end of season were best identified using respectively 30% and 40% threshold of LAI amplitude values. The satellite-derived phenology was spatially consistent with the global distributions of climatic drivers and biome land cover. The accuracy of the derived phenological metrics, evaluated using available ground observations for birch forests in Europe, cherry in Asia and lilac shrubs in North America showed an overall root mean square error lower than 19 days for the start, end and length of season, and good agreement between the latitudinal gradients of VEGETATION LAI phenology and ground data, [ES] La teledetección debe contribuir a mejorar la representación de la fenología en los modelos climáticos. En este estudio se ha caracterizado la fenología típica de la vegetación a escala global mediante GEOCLIM-LAI, una climatología del índice de área foliar (LAI) calculada a partir de series temporales en el periodo 1999-2010 de datos SPOT VEGETATION a 1-km de resolución espacial. A partir de la calibración con observaciones in situ, el inicio y fin de la estación de crecimiento se han definido como la fecha para la cual el LAI alcanza, respectivamente, el 30% y 40% de la amplitud de su ciclo anual. Los patrones espaciales de la fenología de satélite muestran una gran consistencia con la distribución espacial de cubiertas vegetales y factores climáticos. La comparación con medidas in situ para las fe-nofases correspondientes al inicio, fin y duración de la estación de crecimiento de abedul común en Europa, cerezo en Asia y lilo en Norte América muestra errores medios menores de 19 días, y un gran acuerdo en el gradiente latitudinal de la fenología observada in situ y estimada a partir de series temporales LAI VEGETATION.

We present ms2gs, a combined coalescence – gene dropping (i.e. backward–forward) simulator for complex traits. It therefore aims at combining the advantages of both approaches. It is primarily conceived for very short term, recent scenarios such as those that are of interest in animal and plant breeding. It is very flexible in terms of defining QTL architecture and SNP ascertainment bias, and it allows for easy modelling of alternative markers such as RADs. It can use real sequence or chip data or generate molecular polymorphisms via the coalescence. It can generate QTL conditional on extant molecular information, such as low-density genotyping. It models (simplistically) sequence, imputation or genotyping errors. It requires as input both genotypic data in plink or ms formats, and a pedigree that is used to perform the gene dropping. By default, it compares accuracy for BLUP, SNP ascertained data, sequence, and causal SNPs. It employs VanRaden's linear (GBLUP) and nonlinear method for incorporating molecular information. To illustrate the program, we present a small application in a half-sib population and a multiparental (MAGIC) cross. The program, manual and examples are available at https://github.com/mperezenciso/ms2gs.

Crop attack by parasitic weeds such as Striga and Orobanche occurs through developmental processes triggered by host chemodetection. Seeds of those weed species remain dormant in the soil until germination is triggered by host root exudates. The development of haustorium, a parasitic plant organ that invades the host to withdraw its nutrients, is also initiated in Orobanchaceae by host molecular cues. The induction of haustorium development by exogenous signals has previously been reported for Striga but not for Orobanche species. In this work, we demonstrate that sphaeropsidone and epi-sphaeropsidone, two phytotoxic cyclohexene oxides isolated from the fungus Diplodia cupressi, a causal agent of cypress canker, induce haustorium development in radicles of the parasitic weeds Striga hermonthica, Orobanche crenata, and Orobanche cumana. This is the first report of chemical stimulation of haustorium development in radicles of Orobanche in the absence of host. In addition, SAR studies were carried out by testing the haustorium-inducing activity of the natural cyclohexene oxides, seven already known and four new hemisynthetic derivatives, in O. cumana, O. crenata, and S. hermonthica, to find a molecular specificity model required for haustorium induction. The results suggested that the haustorium-inducing activity is due to the possibility to convert the natural sphaeropsidone and natural and hemisynthetic derivatives in the corresponding 3-methoxyquinone and that the stereochemistry at C-5 also seems to affect this activity.

Increasing water scarcity challenges crop sustainability in many regions. As a consequence, the enhancement of transpiration efficiency (TE)—that is, the biomass produced per unit of water transpired—has become crucial in breeding programs. This could be achieved by reducing plant transpiration through a better closure of the stomatal pores at the leaf surface. However, this strategy generally also lowers growth, as stomatal opening is necessary for the capture of atmospheric CO2 that feeds daytime photosynthesis. Here, we considered the reduction in transpiration rate at night (En) as a possible strategy to limit water use without altering growth. For this purpose, we carried out a genetic analysis for En and TE in grapevine, a major crop in drought-prone areas. Using recently developed phenotyping facilities, potted plants of a cross between Syrah and Grenache cultivars were screened for 2 y under well-watered and moderate soil water deficit scenarios. High genetic variability was found for En under both scenarios and was primarily associated with residual diffusion through the stomata. Five quantitative trait loci (QTLs) were detected that underlay genetic variability in En. Interestingly, four of them colocalized with QTLs for TE. Moreover, genotypes with favorable alleles on these common QTLs exhibited reduced En without altered growth. These results demonstrate the interest of breeding grapevine for lower water loss at night and pave the way to breeding other crops with this underexploited trait for higher TE.

Direct comparison of cow and goat performanceand milk fatty acid responses to diets known to inducemilk fat depression (MFD) in the bovine revealsrelevant species-by-diet interactions in ruminal lipidmetabolism. Thus, this study was conducted to inferpotential mechanisms responsible for differences in therumen microbial biohydrogenation (BH) due to dietand ruminant species. To meet this objective, 12 cowsand 15 goats were fed a basal diet (control), a similardiet supplemented with 2.2% fish oil (FO), or a dietcontaining 5.3% sunflower oil and additional starch(+38%; SOS) according to a 3 × 3 Latin square designwith 25-d experimental periods. On the last day of eachperiod, fatty acid composition (by gas chromatography)and bacterial community (by terminal-RFLP),as well as fermentation characteristics, were measuredin rumen fluid samples. Results showed significant differencesin the response of cows and goats to dietarytreatments, although variations in some fermentationparameters (e.g., decreases in the acetate-to-propionateratio due to FO or SOS) were similar in both species.Main alterations in ruminal BH pathways potentiallyresponsible for MFD on the SOS diet (i.e., the shiftfrom trans-11 to trans-10 18:1 and related increases intrans-10,cis-12 18:2) tended to be more pronounced incows, which is consistent with an associated MFD onlyin this species. However, changes linked to FO-inducedMFD (e.g., decreases in 18:0 and increases in totaltrans-18:1) were stronger in caprine rumen fluid, whichmay explain their unexpected susceptibility (althoughless marked than in bovine) to the negative effect ofFO on milk fat content. Altogether, these results suggestthat distinct ruminal mechanisms lead to eachtype of diet-induced MFD and confirm a pronouncedinteraction with species. With regard to microbiota,differences between cows and goats in the compositionof the rumen bacterial community might be behindthe disparity in the microorganisms affected by theexperimental diets (e.g.