Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine

Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9) using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.     

Chiral Discrimination of Ammonium Neurotransmitters by C3‐Symmetric Enantiopure Hemicryptophane Hosts

Enantiopure hemicryptophanes efficiently discriminate chiral ammonium neurotransmitters. The ephedrine and norephedrine molecules associate with hemicryptophane hosts to form 1:1 and 1:2 host‐guest complexes. Binding constants are determined by fitting the ¹H nuclear magnetic resonance (NMR) titration curves to give β₁ and β₂ values, which are used to characterize the diastereomeric and enantiomeric discriminating potentials of the hosts. Chirality 25:47–479, 2013. © 2013 Wiley Periodicals, Inc.     

Study of response of Swiss Webster mice to light subunit of mushroom tyrosinase

The light subunit of mushroom, Agaricus bisporus, tyrosinase (LSMT), has been identified as an extrinsic component of the enzyme. Its function is unknown, but it can cross an epithelial cell layer, which suggests that it can be absorbed by the intestine. A similar capability has been demonstrated for the HA-33 component of the progenitor toxin from Clostridium botulinum, which is the closest structural homolog of LSMT. Unlike HA-33, LSMT appears to be non-immunogenic as shown by preliminary tests in Swiss Webster mice. We investigated the immunogenicity and histopathology of LSMT in mice to determine its safety in vivo. LSMT did not evoke generation of antibodies after prolonged periods of intraperitoneal administration. Histopathological observations confirmed the absence of responses in organs after twelve weekly administrations of LSMT. We found that LSMT is not toxic and is less immunogenic than the C. botulinum HA-33 protein, which supports further research and development for pharmaceutical application.     

Carrageenan oligosaccharides enhance stress-induced microspore embryogenesis in Brassica oleracea var. italica

Embryogenic induction in cultures of isolated microspores is a stress-dependent process, which can be triggered by heat shock, sucrose or nitrogen starvation or by anti-microtubular drugs. As they are known to mimic biotic stress, oligosaccharides were tested as an alternative source of compounds to induce microspore embryogenesis in Brassica oleracea var. italica. Among the eight oligosaccharide series that were investigated and the corresponding polysaccharides, namely pectin, alginate, fucan, laminarin, agar and κ-, ι-, and λ-carrageenans, only the carrageenan oligomers displayed significant effects on microspore induction. When supplied in combination to heat stress, they markedly enhanced the final yields of microspore-derived embryos, with a two-fold increase in the most reactive treatment, i.e. in the presence of λ-carrageenan oligosaccharides. A 30 min treatment was enough to stimulate embryogenesis, and two optimal concentrations were observed, 170 nM and 34 μM.     

Photosynthetic innovation broadens the niche within a single species

Adaptation to changing environments often requires novel traits, but how such traits directly affect the ecological niche remains poorly understood. Multiple plant lineages have evolved C₄ photosynthesis, a combination of anatomical and biochemical novelties predicted to increase productivity in warm and arid conditions. Here, we infer the dispersal history across geographical and environmental space in the only known species with both C₄ and non‐C₄ genotypes, the grass Alloteropsis semialata. While non‐C₄ individuals remained confined to a limited geographic area and restricted ecological conditions, C₄ individuals dispersed across three continents and into an expanded range of environments, encompassing the ancestral one. This first intraspecific investigation of C₄ evolutionary ecology shows that, in otherwise similar plants, C₄ photosynthesis does not shift the ecological niche, but broadens it, allowing dispersal into diverse conditions and over long distances. Over macroevolutionary timescales, this immediate effect can be blurred by subsequent specialisation towards more extreme niches.