Identifying FHB Resistance Genes in Wheat Using a Next-Generation Sequencing Approach

Fusarium Head Blight (FHB) is a disease caused by the fungal pathogen Fusarium graminearum that affects wheat and other small grains and can lead to yield loss. The Fhb1 QTL on wheat chromosome 3BS confers type II resistance to FHB, resistance to the spread of infection on the spike. To gain a better genetic understanding of the Fhb1 QTL locus, a near-isogenic line (NIL) pair carrying the resistant and susceptible alleles for Fhb1 was subjected to SNP genotyping and gene expression analysis. We genotyped the NIL pair with 9,000 SNPs and found the lines to be 98% identical with 40% of the SNP differences that could be mapped found on chromosome 3BS. We established three experiments to examine gene expression in the NIL pair and to identify candidates for the Fhb1 gene. We used next-generation sequencing of RNA from the following experiments to obtain the gene expression data: (1) point inoculation of spikelets with F. graminearum and sampling the inoculated spikelets at 96 hours after inoculation; (2) point inoculation of deoxynivalenol (DON) or sterile water and sampling the inoculated spikelets at 12 hours after inoculation; and (3) point inoculation of F. graminearum and sampling of the rachis at 96 hours after inoculation. For all experiments at least 100 million sequencing reads were obtained for each genotype. For all analyses differential expression is defined with at least a 2-fold change in expression and a q-value less than 0.05. For experiment #1 we identified 5,973 sequences that showed differential expression between the two genotypes. For experiment #2, we identified 2,210 sequences that showed differential expression between the two genotypes when DON inoculated and 866 sequences that showed differential expression when water inoculated. For experiment #3, we identified 4,771 sequences that showed differential expression between the two genotypes. In addition, we mapped the sequencing reads from experiments #1 and #3 to the F. graminearum genome to identify genes that are expressed by the fungus during infection. For experiment #1, we identified 137 transcripts that showed differential expression between the two genotypes. For experiment #3, we identified 419 transcripts that showed differential expression between the two genotypes. Results of the differentially expressed genes will be presented.