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Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.

Jujube is widely cultivated in the semi-arid region of the Loess Plateau in Northwest China due to its high water deficit tolerance. In such an ecologically vulnerable area, it is critical to explore the water consumption processes of key tree species and their responses to driving factors. Sap flow data gathered during a two-year field study in a jujube plantation were analyzed as a surrogate for transpiration measurements. The measured sap flows were related to changes in the soil water content, meteorological factors (the vapor pressure deficit and the level of photosynthetically active radiation), and plant physiological factors (the sap wood area, leaf area and leaf area index). The factors that govern sap flow were found to vary depending on the growing season, and on hourly and daily timescales. The plants' drought tolerance could be predicted based on their peak sap flows and the variation in their sap flow rates at different soil water levels. The sap flow was most strongly affected by the water content of the topmost (0-20 cm) soil layer. Of the studied meteorological factors, the photosynthetically active radiation had a greater effect on sap flow than the vapor pressure deficit. The correlation we found could be applied to predict jujube tree water consumption and assist the design of irrigation scheme.

Previous data showed that the parasitoid wasp Aphelinus asychis was more successful on Sitobion avenae clones artificially infected with different strains of Regiella insecticola compared to the same clones lacking facultative symbionts. To test whether this resulted from a specific interaction between the aphid and symbiont genotype, we used new clonal lines from a different genotype of S. avenae (Linyi) infected with the same R. insecticola strains. The parasitism rate of A. asychis was higher on the two Linyi lines infected with R. insecticola than on the uninfected control line, while the emergence rate was lower due to higher mortality during development. However, a different wasp species, Aphidius gifuensis, showed no difference in the parasitism rate and emergence rate between the three Linyi lines, suggesting that the increase in parasitism rate could be wasp species-dependent. The mortality of A. asychis during development in the presence of R. insecticola may be linked to (i) a direct toxic or metabolic effect since the weight of the emerged wasps was also reduced and (ii) a general effect on the aphid fitness since the survival and fecundity of infected aphids having survived A. asychis attack were clearly reduced compared to the control, while those surviving A. gifuensis attack had only a slight increase in their survival rate. Our data therefore enriched the panel of phenotypic effects that R. insecticola could contribute to the aphid and emphasized the potential implications of symbionts on biological pest control.

There has been considerable complaint regarding the character of the vinegar that is being sold as pure cider vinegar. Merchants complain that they purchase fancy price products, guaranteed to be pure cider vinegar, but which do not in their estimation give tests such as cider vinegar should. Several of these vinesrars have...

Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2x = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.

Diagnosis of African animal trypanosomosis is vital to controlling this severe disease which hampers development across 10 million km(2) of Africa endemic to tsetse flies. Diagnosis at the point of treatment is currently dependent on parasite detection which is unreliable, and on clinical signs, which are common to several other prevalent bovine diseases. the repeat sequence of the GM6 antigen of Trypanosoma vivax (TvGM6), a flagellar-associated protein, was analysed from several isolates of T. vivax and found to be almost identical despite the fact that T. vivax is known to have high genetic variation. The TvGM6 repeat was recombinantly expressed in E. coli and purified. An indirect ELISA for bovine sera based on this antigen was developed. The TvGM6 indirect ELISA had a sensitivity of 91.4% (95% CI: 91.3 to 91.6) in the period following 10 days post experimental infection with T. vivax, which decreased ten-fold to 9.1% (95% CI: 7.3 to 10.9) one month post treatment. With field sera from cattle infected with T. vivax from two locations in East and West Africa, 91.5% (95% CI: 83.2 to 99.5) sensitivity and 91.3% (95% CI: 78.9 to 93.1) specificity was obtained for the TvGM6 ELISA using the whole trypanosome lysate ELISA as a reference. For heterologous T. congolense field infections, the TvGM6 ELISA had a sensitivity of 85.1% (95% CI: 76.8 to 94.4). this study is the first to analyse the GM6 antigen of T. vivax and the first to test the GM6 antigen on a large collection of sera from experimentally and naturally infected cattle. This study demonstrates that the TvGM6 is an excellent candidate antigen for the development of a point-of-treatment test for diagnosis of T. vivax, and to a lesser extent T. congolense, African animal trypanosomosis in cattle.

1. There is increasing evidence that species diversity enhances the temporal stability (TS) of community productivity in different ecosystems, although its effect at the population and tree levels seems to be negative or neutral. Asynchrony in species responses to environmental conditions was found to be one of the main drivers of this stabilizing process. However, the effect of species mixing on the stability of productivity, and the relative importance of the associated mechanisms, remain poorly understood in forest communities.2. We investigated the way mixing species influenced the TS of productivity in Pinus sylvestris L. and Fagus sylvatica L. forests, and attempted to determine the main drivers among overyielding, asynchrony between species annual growth responses to environmental conditions, and temporal shifts in species interactions. We used a network of 93 experimental plots distributed across Europe to compare the TS of basal area growth over a 15-year period (1999-2013) in mixed and monospecific forest stands at different organizational levels, namely the community, population and individual tree levels.3. Mixed stands showed a higher TS of basal area growth than monospecific stands at the community level, but not at the population or individual tree levels. The TS at the community level was related to asynchrony between species growth in mixtures, but not to overyielding nor to asynchrony between species growth in monospecific stands. Temporal shifts in species interactions were also related to asynchrony and to the mixing effect on the TS.4. Synthesis. Our findings confirm that species mixing can stabilize productivity at the community level, whereas there is a neutral or negative effect on stability at the population and individual tree levels. The contrasting findings regarding the relationships between the temporal stability and asynchrony in species growth in mixed and monospecific stands suggest that the main driver in the stabilizing process may be the temporal niche complementarity between species rather than differences in species' intrinsic responses to environmental conditions.

Doc number: 25 Abstract Background: Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora . A broad, large-effect quantitative trait locus (QTL) for fire blight resistance has been reported on linkage group 3 of Malus 'Robusta 5'. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. Results: When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with 'Robusta 5' as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand 'Malling 9' X 'Robusta 5' population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1 ) and a closely linked class 3 peroxidase gene. While the QTL detected in the German 'Idared' X 'Robusta 5' population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90 ). In the US 'Otawa3' X 'Robusta5' population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with fire blight resistance. However, this QTL was not observed in the New Zealand or German populations. Conclusions: The results suggest that the upper region of 'Robusta 5' linkage group 3 contains multiple genes contributing to fire blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative fire blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of fire blight resistance.

The current study aims to examine, the response of contrasted recombinant inbred lines of common bean to the application of phosphorus, to identify the bean recombinant inbred lines which were efficient in phosphorus utilization when dependent on nitrogen fixation as a source of nitrogen. The experiment was conducted at the experimental farm of Agricultural Research Station of the Nubaria district, Behera, Egypt, during the winter seasons of 2008-2009. Three levels of mineral phosphorus fertilizers were applied (0, 45 and 90 kg ha(-1) phosphorus pentoxide). Nodulation, plant growth parameters, leaf area, soil Olsen phosphorus, pH, and phosphorus and nitrogen of shoots, nodules and seeds were measured. The results have shown that the recombinant inbred lines responded positively to P application levels. The best values were observed in recombinant inbred lines 75, 83 and 34. Vegetative growth parameters were significantly enhanced by increasing levels of phosphorus. The highest level of phosphorus, i.e., 90 kg ha(-1) phosphorus pentoxide gave the optimal values of growth parameters for all common bean recombinant inbred lines while control plants obtained the lowest values. An increase of Olsen-P and a decrease of soil pH were also observed with increases in phosphorus. These results led to the conclusions that phosphorus applied to Nubaria soil: (1) improved the soil fertility; (2) enhanced the ability of root nodules of common bean recombinant inbred lines to fix atmospheric nitrogen; and (3) increased the release of hydrogen by roots, thus decreasing soil pH and reducing the immobilization of phosphorus in the soil solution and transforming it into available form for the plant.