P0215Comparative Transcriptome Analysis of Leaf Sheath Blight Response in Rice
Austin Meier
,
Oregon State University, Corvallis, OR
Matthew Geniza
,
Oregon State University, Corvallis, OR
Yamid Sanabria
,
Louisiana State University, Baton Rouge, LA
James Oard
,
Louisiana State University Agricultural Center, Baton Rouge, LA
Pankaj Jaiswal
,
Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR
In rice,
Rhizoctonia solanii causes leaf sheath blight (SB) disease, which leads to widespread decline in yield in almost all US rice varieties. Therefore, we carried out a RNA-seq based transcriptome study on two rice varieties, Cocodrie (CCDR; rice sheath blight susceptible) and MCR10277 (MCR; rice sheath blight resistant), to profile the time-series wide genome-scale transcriptional differences in response to
R. solanii infection. The analysis was carried out on samples collected on the day of inoculation, day 0 (control), and on 1, 3, and 5 days post inoculation with 3 biological replicates per time point per variety. We will present the results of the study in our presentation on candidate genes within the major SB resistance QTL region in chromosome 9 that show significant expression and carry novel SNPs that were not part of the earlier study with 21 loci within the major QTL.
Bioinformatics workflows, were used to identify variety specific SNPs including indels, and pairwise comparison between time points and varieties for differential gene expression (DGE). In the process we also carried out a benchmarking analysis using different sequence aligners, STAR, Kalisto and BOWTIE2, and DGE caller software, Cuffdiff and DESEQ2, to investigate optimal computational times and results that are statistically relevant to the experimental design. Our time-course analysis, by cross-referencing DGE with significant variants, of two phenotypically different varieties is a useful approach to validate previously annotated genetic variations and discover new ones that may play a role throughout the resistant rice’s physiological response to SB.
