Exploring the interaction between small RNAs and R genes during Brachypodium response to Fusarium culmorum infection

• Published in: Gene Vol. 536; no. 2; pp. 254 - 264
• Main Authors: Lucas, Stuart James, Baştaş, Kubilay, Budak, Hikmet
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 25.02.2014
• Subjects: Base Sequence; bioinformatics; Brachypodium - genetics; Brachypodium - microbiology; Brachypodium distachyon; Computational Biology - methods; DNA libraries; fungal diseases of plants; Fusariosis - genetics; Fusariosis - microbiology; Fusarium; Fusarium culmorum; gene expression; genes; Genes, vpr - genetics; genotype; grasses; microRNA; MicroRNAs - genetics; Molecular Sequence Data; NBS-LRRs; nucleotide sequences; Plant disease; plant hormones; Plant miRNAs; plant pathogenic fungi; Polymorphism, Genetic - genetics; prediction; R genes; RNA, Small Interfering - genetics; salicylic acid; Sequence Alignment; Sequence Analysis, DNA; small interfering RNA; ABA; FHB; RT; RNA; R genes; nt; Plant disease; DNase; HR; mRNA; LRR; bp; SA; ds; X-Gal; UTR; CDS; ANOVA; miRNA; Tm; cDNA; pri-miRNA; BLAST; RT-qPCR; NBS; gDNA; RNase; RISC; NBS-LRRs; miRCB; GSS; rRNA; EST; L-Amp; Plant miRNAs; siRNA; DCL; ET; Brachypodium distachyon; DNA; JA; IPTG; pre-miRNA; PCR; small interfering RNA; Basic Local Alignment Search Tool; Dicer-Like (nuclease); Salicylic Acid; ribosomal RNA; DNA complementary to RNA; mature miRNA complementary sequence; Fusarium head blight; genomic DNA; Luria-Bertani Agar supplemented with Ampicillin; reverse transcriptase; Reverse Transcriptase-quantitative PCR; untranslated region; Nucleotide Binding Site; base pairs; Analysis of Variance; isopropyl β-D-thiogalactopyranoside; Hypersensitive Response; nucleotides; Resistance genes; Ethylene; Ribonuclease; Jasmonic Acid; miRNA Candidate Brachypodium; precursor miRNA; deoxyribonucleic acid; messenger RNA; melting temperature; Polymerase Chain Reaction; Ribonucleic Acid; Expressed sequence Tag; 5-bromo-4-chloro-3-indolyl β-D-galactopyranoside; Deoxyribonuclease; Abscisic Acid; double-stranded; Leucine Rich Repeat; Genomic Survey Sequence; RNA-induced silencing combplex; primary microRNA; microRNA; Coding Sequence
• ISSN: 0378-1119; 1879-0038; 1879-0038
• DOI: 10.1016/j.gene.2013.12.025

The present study aims to investigate small RNA interactions with putative disease response genes in the model grass species Brachypodium distachyon. The fungal pathogen Fusarium culmorum (Fusarium herein) and phytohormone salicylic acid treatment were used to induce the disease response in Brachypodium. Initially, 121 different putative disease response genes were identified using bioinformatic and homology based approaches. Computational prediction was used to identify 33 candidate new miRNA coding sequences, of which 9 were verified by analysis of small RNA sequence libraries. Putative Brachypodium miRNA target sites were identified in the disease response genes, and a subset of which were screened for expression and possible miRNA interactions in 5 different Brachypodium lines infected with Fusarium. An NBS-LRR family gene, 1g34430, was polymorphic among the lines, forming two major genotypes, one of which has its miRNA target sites deleted, resulting in altered gene expression during infection. There were siRNAs putatively involved in regulation of this gene, indicating a role of small RNAs in the B. distachyon disease response. •We define a set of B. distachyon proteins predicted to be involved in disease responses•We identify 9 new B. distachyon putative microRNA coding sequences, and a further 24 miRNA candidates•Expression levels of 6 selected disease resistance genes are not subject to miRNA regulation•R gene 1g34430 is a target for numerous siRNAs which could bind a polymorphic region in its 3′ UTR•Putative miRNAs predicted to target this region are probably mis-identified siRNAs