FINDING WHEAT CHROMOSOME 4D miRNA PRODUCTION SITES AND TARGET GENES ACROSS THE WHOLE GENOME THROUGH A COMPUTATIONAL APPROACH

CRESCENTE J. M.; VANZETTI L. S.; GONZALEZ S.; GUIDOBALDI F.; RIVAROLA M.; VALARIK M.; SIMKOVA H.; DOLEZEL J.; TRANQUILLI G.; PANIEGO N.; ECHENIQUE V.; HELGUERA M.

Congreso; 11th International Plant Molecular Biology Congress; 2015

Plant microRNAs (miRNAs) play important roles in post-transcriptional gene regulation by targeting mRNAs for cleavage or repressing translation emerging as important players in biotic and abiotic stress responses for crops. We developed a bioinformatic pipeline capable to detect 21bp miRNA putative production sites from the wheat chromosome-4D and putative target genes located across the whole wheat genome. As result, 2732 miRNAs were detected from a 290588 21bp-miRNA library, which, were likely originated from 1740 short DNA regions (200-300bp) located within 1472 4D scaffolds. Also 709 of 1740 short DNA regions were defined as hotspots (including ≥4 different miRNA). The 70% of detected hotspots showed homology with transposable-elementsts (TE), mostly MITEs-ClassII, Mariner. The remaining 30% would be putative not-described TEs or low repetitive DNA regions including genes. On the other hand, 1031 short DNA regions originating 3 or less different miRNA each, were detected, including 53% with high homology with TEs (mostly ClassI, Gypsy). As before, the remaining 47% were either not, described TEs or low repetitive DNA region including genes. In a second analysis step, the pipeline challenged the IWGSC gene/transcript annotation against the 2732 miRNAs from chromosome-4D, and we observed that 1595 miRNAs as candidates for regulation of 560 genes across the 21 wheat chromosomes. The chromosome 2D showed the highest number of target genes-(50) and the 3B showed the lowest value on target genes-(6). As conclusion the developed pipeline was an efficient tool to detect miRNA producing regions and explore putative target genes across the whole wheat genome.