Regulation of NBS-LRR genes by MicroRNAs in wheat: Computational identification of candidate MIR-2118 genes and evidence of flexibility

Abstract

Plant microRNAs are crucial for post-transcriptional regulation of gene expression, with some of them particularly involved in regulating several disease resistance (R) genes. This study is a computational screening for microRNAs potentially involved in the regulation of disease resistance in bread wheat Triticum aestivum, through the genome and transcriptome of this crop species. We used plant miRNAs of the superfamily miR-482/2118 to find complementarities with the expressed sequence tags (ESTs) coding NBS-LRR proteins of the bread wheat. This analysis revealed a vast recognition potential, highlighting highly variable miRNA-mRNA hybridization schemes. Precursors of miR-2118/482 sequences that showed a potential for recognizing wheat NBS-LRR ESTs were used as input for similarity search in the T. aestivum transcriptome shotgun assemblies (TSA) database, enabling the identification of a couple of wheat TSA sequences (JV952948.1 and JV851699.1) that were predicted to adopt a stable miRNA/miRNA∗ duplex structure. The genomic regions corresponding to both predicted tae-miR-2118 genes were determined on wheat chromosomes 2DL and 5AS. The findings of the present study will contribute to a better understanding of R gene expression regulation in wheat.