High Resolution Transcriptome Analysis of Rice Salt Response Enabled by Gramene Resources

Improving yield and maintaining high quality in rice is essential to meet growing demands and address challenges posed by abiotic and biotic stress. To explore the rice diversity for candidate genes and genetic loci that may contribute to stress tolerance, we conducted a salt stress responsive RNA-seq based transcriptome study of two Oryza sativavarieties, the salt-tolerant Pokkali and salt-sensitive breeding line IR29. To find early and late response genes, a series of RNA samples were collected at 1, 2, 5, 10 and 24 hours after salt treatment.

The Oryza genome browser hosted by Gramene database enabled us to upload our de novotranscriptomes assembled from the RNA-seq data for Pokkali and IR29. Although our assemblies mapped to ~90% of the current reference gene models, we observed some structural differences between salt stress related genes in our assemblies and the reference gene models. These differences suggest a possibility at improving current annotations.

Our investigation of differentially expressed genes revealed 7,209 and 6,595 salt-induced transcripts from Pokkali and IR29, respectively, over all time points. Expression data was also utilized on Gramene’s Plant Reactome to address metabolic and regulatory pathways unique to Pokkali and IR29. Sequence reads from each transcriptome were aligned to the reference genome for genetic marker discovery. High consequence variants were identified with Gramene’s Variant Effect Predictor tool.

Our study provides insight into transcriptional programming during salt stress, references for improving Oryza genome annotations, and genetic variation sites with an association to differential gene expression and potential gene function. The talk would also highlight Gramene's genomics resources and tools that users may be able to adopt for similar studies.