Comparative RNA-Seq Transcriptome Analysis of Wheat and Brachypodium after Fungal Infection

Difficulties in understanding the molecular basis of resistance to necrotrophic pathogens of cereals arise from the highly quantitative nature of resistance, further compounded by host genomic complexity. The aim of this project is to develop Brachypodium distachyon, the genetic model for Pooid grasses, as a pathosystem to study the host molecular response during infection by Fusarium pseudograminearum (Fp), the predominant cause of Fusarium crown rot, costing the Australian wheat industry A$79 million/annum. A transcriptomic approach using RNAseq (Illumina HiSeq2000) was adopted to comparatively analyse global gene expression in wheat and Brachypodium seedlings three days after inoculation with Fp. Four biological replicates of two treatments (Fp and mock-inoculated), each consisting of 16 and 32 plants for wheat and Brachypodium respectively, were sequenced and differential gene expression was assessed using the Tuxedo Suite bioinformatics package. Approximately 10% of annotated canonical transcripts showed differential expression in both species with 2234 wheat genes (1521 up- and 713 down-regulated) and 2292 Brachypodium genes (1316 up- and 976 down-regulated) differentially expressed during infection. Shared responses activated during pathogen challenge include expression of defence proteins, production of phytoalexins, mycotoxin detoxification and systemic defence signalling pathway activation. Comparative analysis of wheat and Brachypodium transcriptomes reveal close functional overlap between the gene sets and reveal a high degree of sequence identity for homologous of differentially expressed genes between species, highlighting the suitability of Brachypodium as a model for this system. Further work will exploit established transformational and mutant resources to characterize Brachypodium genes of interest emerging from this study.