Rice Grain Development Database

Being the staple food crop across the world, rice (Oryza) is commercially important. The grain/seed is the edible part. Owing to a steeply increasing population, and the limitations imposed by it, rice yield needs to be increased, and grain size is the best target. Rice also provides an array of nutrients, including carbohydrates, proteins, calcium, iron, folic acid and few B vitamins. This makes it an ideal crop to help alleviate malnutrition. Rice can be nutritionally enhanced and its size increased only when the process of its grain development has been elucidated in detail at the molecular level. Depending on the physiological and morphological changes occurring in the seed, over the period of its development, it has been divided into five stages. S1 (0-2 DAP, Days After Pollination), S2 (3-4 DAP), S3 (5-10 DAP), S4 (11-20 DAP) and S5 (21-29 DAP).

In order to understand the genes/pathways regulating rice grain size, RNAseq has been performed on the above five stages and flag leaf (as a vegetative control, to remove genotypic effects), in two rice genotypes with contrasting grain size. SN (Sonasal) is small grained while LGR (Large grain rice) is as the name suggests, with a very large grain. The transcriptome data can be searched with the RGAP locus ID to obtain the expression graph (in terms of FPKM values) or differential expression data (in terms of fold change values) for all stages. For differentially expressed genes, only significant values will be displayed. Bulk locus IDs can be downloaded with transcription factor (TF), phytohormone, transposable element (TE), and putative function search. Seed-specific genes can also be searched for.

miRNAs have emerged as important regulatory players in any process. In order to understand their role, miRNOme data of both SN and LGR from all the tissues mentioned above, can also be searched for. By using the miRNA ID, the expression data (in terms of TPM) or differential expression data (in terms of fold changes) can be downloaded. For differentially expressed miRNAs, only significant values will be displayed.