3 for the former change and 1. 3 for the latter suggesting that some SNPs can stabilize destabilize pre miRNA structure. No target gene has been reported in literature for miR1137. In plants most of the miRNA based regulation relies on the cleavage of target mRNAs that normally occurs at the tenth nucleotide of the complementary region and numerous studies on miRNA target interaction have www.selleckchem.com/products/CAL-101.html highlighted the importance of positions 2 to 12, more frequently 10 and 11. Although most of the putative polymorphisms highlighted in this work are outside those critical positions, several examples of putative functionally relevant polymorphisms have been detected. Table 6 reports the putative polymorphisms detected after comparison among EST sequences inside Unigene clusters, without any selection against false positives.

Some of these nucleotide variation could be due to sequencing errors or related to very similar genes belonging to a specific family, nevertheless when the SNPs indels rely on two or more copies of independent sequences it can be considered a good candidate for a true positive polymorphic target site. For example, a polymorphism in miRNA 408 target site detected by AutoSNP in contig 2094 is based on sequences from two different cultivars report ing the same allelic variant as part of a haplotype where a SSR polymorphism is located upstream the target sequence. Some polymorphisms also showed an evolutionary conserved position, the nucleotide variation identified in Hv. 2498 has also been found in the ortho logous gene of Arabidopsis in the same position by Ehrenreich and Purugganan.

The Squamosa promoter Binding Protein is a known target family for miR156. Many plant transcription factors involved in the regulation of the transition from the vegetative to the reproductive phase belong to this family and it has been shown that overexpressing SBP genes can lead to increased leaf initiation, decreased apical dominance and delayed flowering time. The increase of the activity of some miRNAs is part of the infection strategy performed by the Turnip mosaic virus in Arabidopsis. miR156 performs a critical function in mediating developmental processes and it is also related to the response to biotic stress. The screening of barley databases has identified two SBP genes targeted by miR156 for which two nucleotide variations occur in critical positions.

If these SNPs will be experimentally confirmed, they could have the effect of destabilizing the interaction between the miRNA and the mRNA, which could consequently avoids cleavage and lead to phenotypical variations in developmental features or in the resistance to viral infection. A SNP also occurs in a crucial point of the experimen tally confirmed NAC1 GSK-3 target for miR164. NAC1 is a tran scription factor involved in shoot apical meristem formation and auxin mediated lateral root formation. Guo et al.