A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.).
BACKGROUND
Many plant species have been investigated in the last years for the identification and characterization of the corresponding miRNAs, nevertheless extensive studies are not yet available on barley (at the time of this writing). To extend and to update information on miRNAs and their targets in barley and to identify candidate polymorphisms at miRNA target sites, the features of previously known plant miRNAs have been used to systematically search for barley miRNA homologues and targets in the publicly available ESTs database. Matching sequences have then been related to Unigene clusters on which most of this study was based.


RESULTS
One hundred-fifty-six microRNA mature sequences belonging to 50 miRNA families have been found to significantly match at least one EST sequence in barley. As expected on the basis of phylogenetic relations, miRNAs putatively orthologous to those of Triticum are significantly over-represented inside the set of identified barley microRNA mature sequences. Many previously known and several putatively new miRNA/target pairs have been identified. When the predicted microRNA targets were grouped into functional categories, biological processes previously known to be regulated by miRNAs, such as development and response to biotic and abiotic stress, have been highlighted and most of the target molecular functions were related to transcription regulation. Candidate microRNA coding genes have been reported and genetic variation (SNPs/indels) both in functional regions of putative miRNAs (mature sequence) and at miRNA target sites has been found.


CONCLUSIONS
This study has provided an update of the information on barley miRNAs and their targets representing a foundation for future studies. Many of previously known plant microRNAs have homologues in barley with expected important roles during development, nutrient deprivation, biotic and abiotic stress response and other important physiological processes. Putative polymorphisms at miRNA target sites have been identified and they can represent an interesting source for the identification of functional genetic variability.
Colaiacovo
Moreno
M
CRA-Genomics Research Centre, via S,Protaso 302, I-29107 Fiorenzuola d'Arda (Pc), Italy. moreno.colaiacovo@entecra.it
Subacchi
Annalisa
A
Bagnaresi
Paolo
P
Lamontanara
Antonella
A
Cattivelli
Luigi
L
Faccioli
Primetta
P
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D020224:Expressed Sequence Tags; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D001467:Hordeum / Q000235:genetics*; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D009690:Nucleic Acid Conformation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D016415:Sequence Alignment
D035683:MicroRNAs; D012322:RNA Precursors; D018749:RNA, Plant