title: Exploring the interaction between small RNAs and R genes during Brachypodium response to Fusarium culmorum infection.
abstract: 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.
authors.affiliation: Sabanci University, Faculty of Engineering & Natural Sciences, Istanbul, Turkey.
authors.forename: Stuart James
authors.initials: SJ
authors.lastname: Lucas
authors.affiliation: Selçuk University, Department of Plant Protection, Konya, Turkey.
authors.forename: Kubilay
authors.initials: K
authors.lastname: Baştaş
authors.affiliation: Sabanci University, Faculty of Engineering & Natural Sciences, Istanbul, Turkey. Electronic address: budak@sabanciuniv.edu.
authors.forename: Hikmet
authors.initials: H
authors.lastname: Budak
mesh_terms: D001483:Base Sequence; D058431:Brachypodium / Q000235:genetics* / Q000382:microbiology; D019295:Computational Biology / Q000379:methods; D060585:Fusariosis / Q000235:genetics* / Q000382:microbiology; D005670:Fusarium; D016334:Genes, vpr / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering
keywords: 5-bromo-4-chloro-3-indolyl β-D-galactopyranoside; ABA; ANOVA; Abscisic Acid; Analysis of Variance; BLAST; Basic Local Alignment Search Tool; Brachypodium distachyon; CDS; Coding Sequence; DCL; DNA; DNA complementary to RNA; DNase; Deoxyribonuclease; Dicer-Like (nuclease); EST; ET; Ethylene; Expressed sequence Tag; FHB; Fusarium head blight; GSS; Genomic Survey Sequence; HR; Hypersensitive Response; IPTG; JA; Jasmonic Acid; L-Amp; LRR; Leucine Rich Repeat; Luria-Bertani Agar supplemented with Ampicillin; NBS; NBS-LRRs; Nucleotide Binding Site; PCR; Plant disease; Plant miRNAs; Polymerase Chain Reaction; R genes; RISC; RNA; RNA-induced silencing combplex; RNase; RT; RT-qPCR; Resistance genes; Reverse Transcriptase-quantitative PCR; Ribonuclease; Ribonucleic Acid; SA; Salicylic Acid; Tm; UTR; X-Gal; base pairs; bp; cDNA; deoxyribonucleic acid; double-stranded; ds; gDNA; genomic DNA; isopropyl β-D-thiogalactopyranoside; mRNA; mature miRNA complementary sequence; melting temperature; messenger RNA; miRCB; miRNA; miRNA Candidate Brachypodium; miRNA*; microRNA; nt; nucleotides; pre-miRNA; precursor miRNA; pri-miRNA; primary microRNA; rRNA; reverse transcriptase; ribosomal RNA; siRNA; small interfering RNA; untranslated region