Omics Knowledge Portal for Rice

What is Omics?

• Omics is a discipline of science and engineering for analyzing the functions and interactions of biological information entities in various –ome layers(clusters) of life. It is involved with a series of state of the art technology for large-scale studies of genes (genomics and epigenomics), transcripts (transcriptomics), proteins (proteomics), metabolites (metabolomics), lipids (lipidomics), interactions (interactomics) and phenotype (Phenomics). Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. The main focus is on: 1) mapping information objects such as genes, proteins, and ligands; 2) finding interaction relationships among the objects; 3) engineering the networks and objects to understand and manipulate the regulatory mechanisms; and 4) integrating various omes and omics subfields."
  
  

• The rapid advances in 'omics' technologies for both model and non-model organism transformed biological research from a relatively data-poor discipline into the one that is data rich (The Big Data Area in Biology), marking a significant phase transition in the history of biological research. Integration of genome and functional omics data with genetic and phenotypic information is leading to the identification of genes and pathways responsible for important agronomic phenotypes. In addition, high-throughput genotyping technologies enable the screening of large germplasm collections to identify novel alleles from diverse sources, thus offering a major expansion in the variation available for breeding.
  
  

• Take the Model of "Multi-Dimensional Approaches to Systems Understanding of Leaf Senescence" from Jeongsik Kim (pulished in June 2016 ) (Figure 1) for example, Given the multifaceted nature of the leaf senes- cence process, multi-dimensional approaches are required for the systems understanding of the mechanistic principles governing leaf senescence. The Age/environment dimension includes internal (age) and external (environmental) factors that regulate leaf senescence. The Organization dimension refers to various analytic layers, including organelle, cell, organ, and organism. The Analysis dimension defines diverse high-throughput ‘‘omics’’ technologies. Efforts to integrate multi-omics data, including genomic, epigenomic, transcriptomic, proteomic, metabolomic, and phenomic data, on leaf senescence are essential for an in-depth understanding of the molecular nature of leaf senescence.
  
  

The Omics Knowledge Portal for Rice

• In order to make a comprehensive integration of published omics knowledge for rice, here we establish Omics Knowledge Portal for Rice (OKP4R) in RiceWiki. We invite concerned biologits all around the world to join this the portal to share the precious related knowledge.
  
  

Figure 1. Multi-Dimensional Approaches to Systems Understanding of Leaf Senescence

Genomic Studies in Rice

• The basis of all biological life is the genetic code. Thus, access to the primary DNA sequence, i.e. the genome, and how genes are encoded within the genome, has become a fundamental resource in biology. Genome sequencing (also known as full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.(More...)
  
  

Transcriptomic Studies in Rice

• The 'transcriptome' is defined as 'the complete of RNA molecules generated by a cell or population of cells'. The term was first proposed by Charles Auffray in 1996. and first used in a scientific paper in 1997. It encompass many species of RNA, for example, mRNA, miRNA, lnRNA et al. Over the past decades, transcriptomic study has advanced from traditional Northern blotting to Highthroughput RNA sequencing (RNA-seq). Besides them, the quantitative polymerase chain reaction (PCR) and microarray are also very impressive technology.

mRNA-Seq Related Studies in Rice

• RNA-seq (RNA sequencing), also called whole transcriptome sequencing, uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample representing a specific tissue and at a specific given moment in time. RNA-seq can be used to analyze the continually changing transcriptome in cells. It can facilitate the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and changes in gene expression. It can also be used to determine exon/intron boundaries and verify or amend previously annotated 5' and 3' gene boundaries.(More...)

miRNA-Seq Related Studies in Rice

microRNA (abbreviated miRNA) is a kind of small non-coding RNA molecules (containing about 22 nucleotides) that functions in RNA silencing and post-transcriptional regulation of gene expression. In short， MicroRNAs (miRNAs) are a class of small, endogenous, nonoding RNAs with a big impact on virtually all biological processes. Investigations suggest that miRNAs control the gene expression of at least 30% of the protein-coding genes in human beings. Although the diverse fundamental functions of miRNAs have now been well demonstrated in both plants and animals over the past several years,(More...)