Locally Epistatic Genomic Relationship Matrices for Genomic Association and Prediction

In plant and animal breeding studies a distinction is made between the genetic value (additive plus epistatic genetic effects) and the breeding value (additive genetic effects) of an individual since it is expected that some of the epistatic genetic effects will be lost due to recombination. In this article, we argue that the breeder can take advantage of the epistatic marker effects in regions of low recombination. The models introduced here aim to estimate local epistatic line heritability by using genetic map information and combining local additive and epistatic effects. To this end, we have used semiparametric mixed models with multiple local genomic relationship matrices with hierarchical designs. Elastic-net postprocessing was used to introduce sparsity. Our models produce good predictive performance along with useful explanatory information.     

Pollen flow in fragmented landscapes maintains genetic diversity following stand-replacing disturbance in a neotropical pioneer tree,Vochysia ferruginea Mart

In forests with gap disturbance regimes, pioneer tree regeneration is typically abundant following stand-replacing disturbances, whether natural or anthropogenic. Differences in pioneer tree density linked to disturbance regime can influence pollinator behaviour and impact on mating patterns and genetic diversity of pioneer populations. Such mating pattern shifts can manifest as higher selfing rates and lower pollen diversity in old growth forest populations. In secondary forest, where more closely related pollen donors occur, an increase in biparental inbreeding is a potential problem. Here, we investigate the consequences of secondary forest colonisation on the mating patterns and genetic diversity of open-pollinated progeny arrays for the long-lived, self-compatible pioneer tree, Vochysia ferruginea, at two Costa Rican sites. Five microsatellite loci were screened across adult and seed cohorts from old growth forest with lower density, secondary forest with higher density, and isolated individual trees in pasture. Progeny from both old growth and secondary forest contexts were predominantly outcrossed (t_m=1.00) and experienced low levels of biparental inbreeding (t_m−t_s=0.00–0.04). In contrast to predictions, our results indicated that the mating patterns of V. ferruginea are relatively robust to density differences between old growth and secondary forest stands. In addition, we observed that pollen-mediated gene flow possibly maintained the genetic diversity of open-pollinated progeny arrays in stands of secondary forest adults. As part of a natural resource management strategy, we suggest that primary forest remnants should be prioritised for conservation to promote restoration of genetic diversity during forest regeneration.     

Divergent phenotypic responses to predators and cyanobacteria in Daphnia lumholtzi

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Leadership of herd progressions in the Thornicroft's giraffe of Zambia

In cohesive social groups, travel progressions are often led by dominant or older individuals, but the leadership traits of individuals residing in flexible social systems are poorly known. Giraffe reside in herds characterized by fission–fusion dynamics frequently mediated by kinship. We analyzed 41 years (1971–2012) of longitudinal data collected from a community of Thornicroft's giraffe (Giraffa camelopardalis thornicrofti) living around South Luangwa National Park, Zambia, to assess the characteristics of herd leaders. Movement of giraffe in a single file progression was not associated with either season or time of day, but progressions were significantly more likely to occur when giraffe traveled in open areas. The oldest female in a herd was significantly more likely to be at the front position than expected, occupying the leadership niche on 79% of observations. We reason that matriarchal leadership in giraffe, as in African elephants, Loxodonta africana, is associated with resource learning. Giraffe societies are constructed on a heretofore unrecognized foundation that integrates relatedness and familiarity with matriarchal leadership in herd movement.     

The composition and function of all‐male herds of Thornicroft's giraffe,Giraffa camelopardalis thornicrofti,in Zambia

Temporary all‐male social groups are formed in a number of animal species. We examined 34 years of data collected from 36 male Thornicroft's giraffe in the Luangwa Valley, Zambia, to test a set of predictions related to five possible functions of all‐male herds (predator protection, practicing aggressive skills, prolonging life, nutritional demands and resource learning). We found that all‐male herds were significantly smaller than mixed‐sex herds, usually contained a mature bull, and were not dependent upon season or habitat. Dyadic associations between males in single sex herds were quite weak, with <25% of potential male dyads sighted together in an all‐male herd. Our data are best explained as a resource learning strategy adopted by males to obtain more extensive knowledge about the habitat, including both food and female distribution. However, other benefits in the form of predator protection, dietary intake and sharpening competitive skills for future contests over estrous females also seem to mediate formation of giraffe all‐male groups. We conclude that the primary advantage of roaming in all‐male herds changes during the life history of males.     

Phosphorus application and elevated CO2 enhance drought tolerance in field pea grown in a phosphorus-deficient vertisol

Background and Aims Benefits to crop productivity arising from increasing CO₂ fertilization may be offset by detrimental effects of global climate change, such as an increasing frequency of drought. Phosphorus (P) nutrition plays an important role in crop responses to water stress, but how elevated CO₂ (eCO₂) and P nutrition interact, especially in legumes, is unclear. This study aimed to elucidate whether P supply improves plant drought tolerance under eCO₂.Methods A soil-column experiment was conducted in a free air CO₂ enrichment (SoilFACE) system. Field pea (Pisum sativum) was grown in a P-deficient vertisol, supplied with 15 mg P kg⁻¹ (deficient) or 60 mg P kg⁻¹ (adequate for crop growth) and exposed to ambient CO₂ (aCO₂; 380–400 ppm) or eCO₂ (550–580 ppm). Drought treatments commenced at flowering. Measurements were taken of soil and leaf water content, photosynthesis, stomatal conductance, total soluble sugars and inorganic P content (Pi).Key Results Water-use efficiency was greatest under eCO₂ when the plants were supplied with adequate P compared with other treatments irrespective of drought treatment. Elevated CO₂ decreased stomatal conductance and transpiration rate, and increased the concentration of soluble sugars and relative water contents in leaves. Adequate P supply increased concentrations of soluble sugars and Pi in drought-stressed plants. Adequate P supply but not eCO₂ increased root length distribution in deeper soil layers.Conclusions Phosphorus application and eCO₂ interactively enhanced periodic drought tolerance in field pea as a result of decreased stomatal conductance, deeper rooting and high Pi availability for carbon assimilation in leaves.     

蜜粉源植物对天敌昆虫的作用及其在生物防治中的应用

寄生性和捕食性天敌昆虫成虫普遍存在通过取食蜜粉源植物补充营养的行为,这可不同程度地促进天敌昆虫性成熟、延长其寿命、提高其生殖力或寄生率,以及搜寻寄主效率和子代雌性比率,从而显著提高天敌昆虫在生物防治中的控害能力和效果。蜜粉源植物花的结构及植物对天敌昆虫产生的嗅觉、视觉信号和花蜜花粉对天敌昆虫产生的味觉信号又显著影响天敌昆虫选择蜜粉源植物的行为和结果。但是,蜜粉源植物也可成为害虫的补充营养植物,从而提高害虫的为害能力。因此,需深入研究不同蜜粉源植物对天敌昆虫及害虫的作用,趋利避害,才可能应用蜜粉源植物成功调控天敌与害虫的益害比,实现害虫的可持续控制。     

Key challenges for the creation and maintenance of specialist protein resources

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long‐term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value. Proteins 2015; 83:1005–1013. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

Purification and properties of diamine oxidase from pea epicotyls

Diamine oxidase (DAO) (EC 1.4.3.6) was purified from pea epicotyls to homogeneity by the criterion of polyacrylamide gel electrophoresis (PAGE). The pu