MiSolRNA: A tomato micro RNA relational database.

Ariel A Bazzini,Alisdair R Fernie,Ramón Asís,Sebastián Bassi,Mariana Conte,Virginia González,Marcelo Soria,Sebastián Asurmendi,Fernando Carrari

doi:10.1186/1471-2229-10-240

Abstract

BackgroundThe economic importance of Solanaceae plant species is well documented and tomato has become a model for functional genomics studies. In plants, important processes are regulated by microRNAs (miRNA).DescriptionWe describe here a data base integrating genetic map positions of miRNA-targeted genes, their expression profiles and their relations with quantitative fruit metabolic loci and yield associated traits. miSolRNA provides a metadata source to facilitate the construction of hypothesis aimed at defining physiological modes of action of regulatory process underlying the metabolism of the tomato fruit.ConclusionsThe MiSolRNA database allows the simple extraction of metadata for the proposal of new hypothesis concerning possible roles of miRNAs in the regulation of tomato fruit metabolism. It permits i) to map miRNAs and their predicted target sites both on expressed (SGN-UNIGENES) and newly annotated sequences (BAC sequences released), ii) to co-locate any predicted miRNA-target interaction with metabolic QTL found in tomato fruits, iii) to retrieve expression data of target genes in tomato fruit along their developmental period and iv) to design further experiments for unresolved questions in complex trait biology based on the use of genetic materials that have been proven to be a useful tools for map-based cloning experiments in Solanaceae plant species.

Highlights

The economic importance of Solanaceae plant species is well documented and tomato has become a model for functional genomics studies
Target sites found in genomic clones were annotated by using two gene prediction softwares (Augustus; [20] and GenomeThreader; [21]) and aligned against S. lycopersicom unigenes and Arabidopsis thaliana peptide sequences and mapped onto the respective BINs of the introgression lines (ILs) population using the molecular markers of two genetic maps (Tomato EXPEN2000 and Tomato EXPEN1992, http://www.solgenomics.net)
Retrieved information can be set by the user in the following fields: i) quantitative trait loci (QTL), indicates those metabolites and yield associated traits showing significant variations associated to the genomic regions where a miRNA target was found; ii) target localization, indicates the genetic BIN where the target was localized; iii) hit definition, shows annotations of the Unigene and/or the predicted products for the cases of target found onto genomic regions and iv) alignment, shows the alignments between the miRNA and the target site

Summary

Conclusions

MiSolRNA database allows the simple extraction of metadata favoring the proposal of new hypotheses about possible roles of miRNAs in the regulation of tomato fruit metabolism. MiSolRNA together with the previously released Tomato small RNAs database (http:// ted.bti.cornell.edu/cgi-bin/TFGD/sRNA/home.cgi[43]), provides an insight into putative miRNA target sites within specific regions of the tomato genome and of individual genes. It displays how these putative target genes are expressed in fruits and the colocation of these target sites with QTL for fruit metabolism. Additional file 1: Primer sequences and PCR amplification conditions The file contains primer sequences and PCR amplification conditions used for the “proof of concept example” described in figure 3

Background