Large-scale bioinformatic analysis of the regulation of the disease resistance NBS gene family by microRNAs in Poaceae

Abstract

In the present study, we have screened 71, 713, 525, 119 and 241 mature miRNA variants from Hordeum vulgare, Oryza sativa, Brachypodium distachyon, Triticum aestivum, and Sorghum bicolor, respectively, and classified them with respect to their conservation status and expression levels. These Poaceae non-redundant miRNA species (1,669) were distributed over a total of 625 MIR families, among which only 54 were conserved across two or more plant species, confirming the relatively recent evolutionary differentiation of miRNAs in grasses. On the other hand, we have used 257 H. vulgare, 286T. aestivum, 119 B. distachyon, 269 O. sativa, and 139 S. bicolor NBS domains, which were either mined directly from the annotated proteomes, or predicted from whole genome sequence assemblies. The hybridization potential between miRNAs and their putative NBS genes targets was analyzed, revealing that at least 454 NBS genes from all five Poaceae were potentially regulated by 265 distinct miRNA species, most of them expressed in leaves and predominantly co-expressed in additional tissues. Based on gene ontology, we could assign these probable miRNA target genes to 16 functional groups, among which three conferring resistance to bacteria (Rpm1, Xa1 and Rps2), and 13 groups of resistance to fungi (Rpp8,13, Rp3, Tsn1, Lr10, Rps1-k-1, Pm3, Rpg5, and MLA1,6,10,12,13). The results of the present analysis provide a large-scale platform for a better understanding of biological control strategies of disease resistance genes in Poaceae, and will serve as an important starting point for enhancing crop disease resistance improvement by means of transgenic lines with artificial miRNAs.

Genome-wide identification, characterization, and evolutionary analysis of NBS-encoding resistance genes in barley

“…In plants, miRNAs regulate a number of fundamental functions, such as organogenesis, meristem development, seed development and germination, leaf and flower morphogenesis, signal transduction, hormone interaction and response to environmental stresses (Guo et al 2005;Nikovics et al 2006;Das et al 2015;Bai et al 2017). Disease resistance NBS gene family has been shown to be targeted by multiple, independent miRNA families (Zhai et al 2011;Zhu et al 2013;Li et al 2012;Habachi-Houimli et al 2016), and there is increasing evidence that small RNAs are involved in regulating plant immunity (Fei et al 2016). Because the expression profiles of plant R genes are often mediated by factors other than pathogen infection, such as tissue type, developmental stage, or environmental conditions (Collins et al 1999), miRNA-mediated spatiotemporal regulation of R gene expression greatly enhances the optimization of plant defense responses in terms of reducing fitness costs of defense signaling.…”

Expression Analysis of Pyrenophora teres f. maculata-Responsive Loci in Hordeum vulgare

“…Therefore, a large number of host genes may take part in resistance signaling and defense processes, and they may interact in a complex manner. In addition to resistance genes with cumulative effects, gene expression is often modulated, at the transcriptional level, by gene repressor/activator proteins that bind transcription factors, and, at the post-transcriptional level, by non coding microRNAs (miRNAs) that are able to modulate the expression in both normal and pathological conditions, by inhibiting translation or inducing degradation of transcripts [38][39][40]. Therefore, in order to efficiently develop resistant varieties, it is imperative to have a deeper knowledge of changes in the mRNA, protein, cellular metabolites and regulatory miRNAs after barley infection by P. teres.…”