Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Background Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.

Association study of resistance to Soilborne wheat mosaic virus in U.S. winter wheat

Soilborne wheat mosaic virus (SBWMV) is one of the most important winter wheat pathogens worldwide. To identify genes for resistance to the virus in U.S. winter wheat, association study was conducted using a selected panel of 205 elite experimental lines and cultivars from U.S. hard and soft winter wheat breeding programs. Virus symptoms were evaluated twice in virus-infected fields for the panel at Manhattan, KS in spring 2010 and 2011 and for a subpanel of 137 hard winter wheat accessions at Stillwater, OK in spring 2008. At the two locations, 69.8 and 79.5% of cultivars were resistant or moderately resistant to the disease, respectively. After 282 simple-sequence repeat markers covering all wheat chromosome arms were scanned for association in the panel, marker Xgwm469 on the long arm of chromosome 5D (5DL) showed a significant association with the disease rating. Three alleles (Xgwm469-165bp, -167bp, and -169bp) were associated with resistance and the null allele was associated with susceptibility. Correlations between the marker and the disease rating were highly significant (0.80 in Manhattan at P < 0.0001 and 0.63 in Stillwater at P < 0.0001). The alleles Xgwm469-165bp and Xgwm469-169bp were present mainly in the hard winter wheat group, whereas allele Xgwm469-167bp was predominant in the soft winter wheat. The 169 bp allele can be traced back to 'Newton', and the 165 bp allele to Aegilops tauschii. In addition, a novel locus on the short arm of chromosome 4D (4DS) was also identified to associate with the disease rating. Marker Xgwm469-5DL is closely linked to SBWMV resistance and highly polymorphic across the winter wheat accessions sampled in the study and, thus, should be useful in marker-assisted selection in U.S. winter wheat.

Incidental task sequence learning: perceptual rather than conceptual?

In four experiments we investigated whether incidental task sequence learning occurs when no instructional task cues are available (i.e. with univalent stimuli). We manipulated task sequence by presenting three simple binary-choice tasks (colour, form or letter case decisions) in regular repeated or random order. Participants were required to use the same two response keys for each of the tasks. We manipulated response sequence by ordering the stimuli so as to produce either a regular or a random order of left versus right-hand key presses. When sequencing in both, or either, separate stream (i.e. task sequence and/or response sequence) was changed to random, only those participants who had processed both sequences together showed evidence of sequence learning in terms of significant response time disruption (Experiments 1-3). This effect disappeared when the sequences were uncorrelated (Experiment 4). The results indicate that only the correlated integration of task sequence and response sequence produced a reliable incidental learning effect. As this effect depends on the predictable ordering of stimulus categories, it suggests that task sequence learning is perceptual rather than conceptual in nature.

The HCP5 single-nucleotide polymorphism: a simple screening tool for prediction of hypersensitivity reaction to abacavir

The HLA-B 5701 allele is predictive of hypersensitivity reaction to abacavir, a response herein termed "ABC-HSR." This study of 1,103 individuals infected with human immunodeficiency virus assessed the usefulness of genotyping a HCP5 single-nucleotide polymorphism (SNP), rs2395029, in relation to ABC-HSR. In populations with European ancestry, rs2395029 is in linkage disequilibrium with HLA-B 5701. The HCP5 SNP was present in all 98 HLA-B 5701-positive individuals and was absent in 999 of 1005 HLA-B 5701-negative individuals. rs2395029 was overrepresented in 25 individuals with clinically likely ABC-HSR, compared with its frequency in 175 ABC-tolerant individuals (80% vs. 2%, respectively; P < .0001). Therefore, HCP5 genotyping could serve as a simple screening tool for ABC-HSR, particularly in settings where sequence-based HLA typing is not available.

Implicit task sequence learning

Implicit task sequence learning (TSL) can be considered as an extension of implicit sequence learning which is typically tested with the classical serial reaction time task (SRTT). By design, in the SRTT there is a correlation between the sequence of stimuli to which participants must attend and the sequence of motor movements/key presses with which participants must respond. The TSL paradigm allows to disentangle this correlation and to separately manipulate the presences/absence of a sequence of tasks, a sequence of responses, and even other streams of information such as stimulus locations or stimulus-response mappings. Here I review the state of TSL research which seems to point at the critical role of the presence of correlated streams of information in implicit sequence learning. On a more general level, I propose that beyond correlated streams of information, a simple statistical learning mechanism may also be involved in implicit sequence learning, and that the relative contribution of these two explanations differ according to task requirements. With this differentiation, conflicting results can be integrated into a coherent framework.

Constraining porewater chemistry in a 250m thick argillaceous rock sequence

The geochemistry of an argillaceous rock sequence from a deep borehole in NE-Switzerland was investigated. The focus was to constrain the porewater chemistry in low permeability Jurassic rocks comprising the Liassic, the Opalinus Clay formation, the 'Brown Dogger' unit and the Effingen Member (Malm). A multi-method approach including mineralogical analysis, aqueous and Ni-ethylenediamine extraction, squeezing tests and pCO(2) measurements as well as geochemical modelling was applied for this purpose. A consistent dataset was obtained with regard to the main solutes in the porewaters. A fairly constant anion-accessible porosity of similar to 50% of the total porosity was deduced for all analysed samples which displayed variable clay-mineral contents. Sulphate concentrations were shown to be constrained by a sulphate-bearing phase, presumably by celestite or a Sr-Ba sulphate. Application of a simple equilibrium model, including cation exchange reactions, calcite and celestite equilibrium showed good agreement with squeezing data, indicating the suitability of the modelling approach to simulate porewater chemistry in the studied argillaceous rocks. The modelling highlighted the importance of correct determination of the exchangeable cation population. The analysis corroborates that squeezing of the studied rocks is a viable and efficient way to sample porewater.