Rice is an important crop that feeds almost half the world population. As climate change models predict floods, drought and extreme temperatures in rice production areas, the need to better understand the genetic basis of adaptation and tolerance to abiotic and biotic stresses is vital to sustain our food supply. To elucidate stress-tolerance casual genes, we designed a time-series transcriptome experiment on two contrasting varieties of Oryza sativa subspecies indica and japonica in the drought (abiotic) and sheath blight (biotic), respectively. These varieties were chosen based on their contrasting tolerant and sensitive characteristics. Using a systems biology approach, our goal was to identify genes expressed and genetic variants inherited in response to stress tolerance. Discoveries from these projects will help accelerate the genetic gains in breeding stress resilient rice varieties.
In both studies, plants from the susceptible and tolerant varieties were subjected to either inoculated sheath blight (SB) or drought-induction. Plant materials was collected on untreated and treated (early, late and in the biotic stress very late) timepoints post-treatment. The total mRNA was isolated from treated and untreated samples for Next Generation Sequencing (NGS) at CGRB facility at OSU. This was followed by statistical and transcriptome data analysis.
The sequence data generated was analyzed against the reference rice genome and between the two experimental varieties. Analysis includes, calling genetic variation, de-novo assembling transcript (mRNA) isoforms, differential gene expression levels, and identifying stress-induced pathways specific to each variety and tolerance level. The statistically significant results of these analyses were further annotated using various standardized ontologies and by aligning against previously studied quantitative trait loci (QTLs) for stress tolerance traits. The selected set of genes were further queried against functional annotations including predicted consequential disruption of gene function or structure due to genetic variation. This resulted in 1-4 genes with favorable gene-expression response under stress that also carried significantly important genetic variation disrupting the gain/loss of gene function. Thus, identifying functional markers and candidate genes for introducing in developing new stress-tolerant rice varieties.