Rice Grain Development Database

Being the staple food crop across the world, rice (<em>Oryza</em>) 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.水稻作为全球主流粮食作物，兼具重要商业价值，其谷粒/种子为可食用部分。受全球人口持续快速增长及其带来的资源限制影响，水稻产量亟待提升，而谷粒尺寸是最优的改良靶点。水稻同时富含多种营养物质，包括碳水化合物、蛋白质、钙、铁、叶酸及少量B族维生素，因此成为缓解营养不良的理想作物。只有在分子层面详细阐明谷粒发育的调控机制，才能实现水稻的营养强化与谷粒尺寸改良。根据种子发育过程中发生的生理与形态变化，水稻谷粒发育可划分为五个阶段：S1（0-2 DAP，授粉后天数（Days After Pollination））、S2（3-4 DAP）、S3（5-10 DAP）、S4（11-20 DAP）及S5（21-29 DAP）。为解析调控水稻谷粒尺寸的基因与通路，研究团队针对上述五个发育阶段及剑叶（作为营养生长对照，用于消除基因型效应），对两个谷粒尺寸性状极端分化的水稻基因型开展了RNA测序（RNAseq）。其中，SN（Sonasal）为小粒水稻，LGR（Large grain rice，大粒水稻）如其名称所示，谷粒尺寸显著偏大。该数据集的转录组数据可通过RGAP位点ID进行检索，以获取各发育阶段的表达图谱（以FPKM值为指标）或差异表达数据（以折叠变化值为指标）。对于差异表达基因，仅展示具有统计学显著性的结果。可通过转录因子（TF）、植物激素、转座因子（TE）及推定功能关键词检索，批量下载位点ID。此外还可针对种子特异性基因进行检索。微小RNA（miRNAs）已成为各类生物过程中关键的调控因子。为明确其调控功能，本数据集还支持检索上述所有组织（五个谷粒发育阶段及剑叶）中SN与LGR的miRNA组学（miRNOme）数据。通过miRNA ID，可下载其表达数据（以TPM值为指标）或差异表达数据（以折叠变化值为指标）。对于差异表达的miRNAs，仅展示具有统计学显著性的结果。