ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata

<p>Abstract</p> <p>Background</p> <p>The guppy, <it>Poecilia reticulata</it>, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available.</p> <p>Results</p> <p>With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags (ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST-linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes.</p> <p>Conclusion</p> <p>Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy.</p

Superconductor strip with transport current: Magneto-optical study of current distribution and its relaxation

The dynamics of magnetic flux distributions across a YBaCuO strip carrying transport current is measured using magneto-optical imaging at 20 K. The current is applied in pulses of 40-5000 ms duration and magnitude close to the critical one, 5.5 A. During the pulse some extra flux usually penetrates the strip, so the local field increases in magnitude. When the strip is initially penetrated by flux, the local field either increases or decreases depending both on the spatial coordinate and the current magnitude. Meanwhile, the current density always tends to redistribute more uniformly. Despite the relaxation, all distributions remain qualitatively similar to the Bean model predictions.Comment: RevTeX, 9 pages, 9 figures, submitted to Supercond. Sci. Technol. Revision: MO image and more refs are adde

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 × 10−9 base substitutions per site per generation, the majority of which are G:C→A:T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light–induced mutagenesis

Red lists for cultivated species: why we need it and suggestions for the way forward

The world's food basket is today shrinking at an alarming rate and most concerning is the reduction in the number of species and varieties used by humankind for food and nutrition, which raises serious concerns about the sustainability of feeding the world today and in the future. Yet, whereas we deploy consistent efforts in monitoring the status of wild biodiversity, very limited is the research in monitoring diversity of plants used by farmers, assess threats of genetic erosion, understand how diversity is helping farmers in coping with climate change, etc. Documenting and monitoring agrobiodiversity on farm is fundamental for enhancing its sustainable use and prevent losses of both genetic diversity and indigenous knowledge to happen before it is too late. This poster explains why a Red List for Cultivated Species is needed and a proposed approach to creating one

Global diversity of the Brachypodium species complex as a resource for genome-wide association studies demonstrated for agronomic traits in response to climate

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.We are grateful for funding and support from the Australian Research Council Centre of Excellence in Plant Energy Biology (CE140100008). Australian Plant Phenomics Facility is supported under the National Collaborative Research Infrastructure Strategy of the Australian Government. The research was undertaken with the assistance of resources from the National Computational Infrastructure (NCI), which is supported by the Australian Government

Evidences of vortex curvature and anisotropic pinning in superconducting films by quantitative magneto-optics

We present the experimental observation of magnetic field line curvature at the surface of a superconducting film by local quantitative magneto-optics. In addition to the knowledge of the full induction field at the superconductor surface yielding the quantitative observation of the flux line curvature, our analysis method allows also local value measurements of the electrical current density inside the sample. Thus, we study the interplay between the electrodynamic constraints dictated by the film geometry and the pinning properties of the superconductor. In particular, we investigate the anisotropic vortex-pinning, due to columnar defects introduced by heavy ion irradiation, as revealed in the local current density dependence on the vortex curvature during magnetic flux diffusion inside the superconducting film.Comment: 12 pages, 11 figures, to be submitted to Phys. Rev.

A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon

The recalcitrance of secondary plant cell walls to digestion constrains biomass use for the production of sustainable bioproducts and for animal feed. We screened a population of Brachypodium recombinant inbred lines (RILs) for cell wall digestibility using commercial cellulases and detected a quantitative trait locus (QTL) associated with this trait. Examination of the chromosomal region associated with this QTL revealed a candidate gene that encodes a putative glycosyl transferase family (GT) 43 protein, orthologue of IRX14 in Arabidopsis, and hence predicted to be involved in the biosynthesis of xylan. Arabinoxylans form the major matrix polysaccharides in cell walls of grasses, such as Brachypodium. The parental lines of the RIL population carry alternative nonsynonymous polymorphisms in the BdGT43A gene, which were inherited in the RIL progeny in a manner compatible with a causative role in the variation in straw digestibility. In order to validate the implied role of our candidate gene in affecting straw digestibility, we used RNA interference to lower the expression levels of the BdGT43A gene in Brachypodium. The biomass of the silenced lines showed higher digestibility supporting a causative role of the BdGT43A gene, suggesting that it might form a good target for improving straw digestibility in crops

Autoimmune Response as a Mechanism for a Dobzhansky-Muller-Type Incompatibility Syndrome in Plants

Epistatic interactions between genes are a major factor in evolution. Hybrid necrosis is an example of a deleterious phenotype caused by epistatic interactions that is observed in many intra- and interspecific plant hybrids. A large number of hybrid necrosis cases share phenotypic similarities, suggesting a common underlying mechanism across a wide range of plant species. Here, we report that approximately 2% of intraspecific crosses in Arabidopsis thaliana yield F1 progeny that express necrosis when grown under conditions typical of their natural habitats. We show that several independent cases result from epistatic interactions that trigger autoimmune-like responses. In at least one case, an allele of an NB-LRR disease resistance gene homolog is both necessary and sufficient for the induction of hybrid necrosis, when combined with a specific allele at a second locus. The A. thaliana cases provide insights into the molecular causes of hybrid necrosis, and serve as a model for further investigation of intra- and interspecific incompatibilities caused by a simple epistatic interaction. Moreover, our finding that plant immune-system genes are involved in hybrid necrosis suggests that selective pressures related to host–pathogen conflict might cause the evolution of gene flow barriers in plants

Local-Scale Patterns of Genetic Variability, Outcrossing, and Spatial Structure in Natural Stands of Arabidopsis thaliana

As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local “outcrossing hotspots” appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions