Key Points
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Rice, one of the most important food crops for humans, is the first crop plant to have its genome sequenced.
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This article describes the availability and application of functional genomic tools for rice, including a discussion of rice whole-genome microarrays, genome tiling arrays, genome-wide gene-indexed mutant collections, gene-silencing tools, transient assay systems, integration of gene-expression profiling, insertional mutant analyses and phylogenomics.
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With the availability of these resources, discovery of the function of the estimated 41,000 rice genes is now within reach.
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Such discoveries have broad practical implications for understanding the biological processes of rice and other economically important grasses such as cereals and bioenergy crops.
Abstract
Rice, one of the most important food crops for humans, is the first crop plant to have its genome sequenced. Rice whole-genome microarrays, genome tiling arrays and genome-wide gene-indexed mutant collections have recently been generated. With the availability of these resources, discovering the function of the estimated 41,000 rice genes is now within reach. Such discoveries have broad practical implications for understanding the biological processes of rice and other economically important grasses such as cereals and bioenergy crops.
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Acknowledgements
We thank B. C. Meyers, L. Bartley, C. Dardick, L. Comai, D. Neale, J. Schroeder, J. Leach, G. L. Wang, K. Shimamoto, V. Sundaresan and R. C. Buell for comments and discussions. We also thank S. Ouyang, Y. S. Lee and P. Cao for helping to generate tables and figures. This work was supported by National Institutes of Health grants 5R01GM055962-0 United States Department of Agriculture grant 2004-63560416640 and National Science Foundation grants DBI-0313887 to P. R., the 21st Century Frontier Program CG1111 and Biogreen 21 Program to G. A, Korea Research Foundation grant 2005-C00155 to K. H. J.
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DATABASES
Entrez Genome Project
GRAMENE
NCBI gene expression omnibus
FURTHER INFORMATION
Agilent Rice Oligo Microarray Kit
Current TIGR rice genome pseudomolecules release
European Molecular Biology Laboratory
International Rice Functional Genomics Consortium
International Rice Genome Sequencing Project
Knowledge-based Oryza Molecular Biological Encyclopedia
Magnaporthe grisea–Oryza sativa Interaction Database
NIAS Tos17 insertion mutant database
NSF Rice Oligonucleotide Array Project
POSTECH rice T-DNA insertion sequence database
Rice Annotation Project database
Rice Functional Genomic Express Database
RiceGE: database sources, details and summary
Rice Multi-Platform Microarray Search tool
Rice Mutant Database, Huazhong Agricultural University, China
Shanghai T-DNA Insertion Population
Taiwan Rice Insertional Mutants Database
TIGR multiexperiment viewer 4.0
University of California, Davis Rice Functional Genomics Databases
Glossary
- Pseudomolecules
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Virtual contiguous sets of clones constructed by resolving discrepancies between overlapping F-factor-based bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) clones, trimming the overlapping regions at junction points in which the phase 3 BAC–PAC sequences are preferably used, and linking the unique sequences to form a contiguous sequence.
- Map-based cloning
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A process of identifying the gene responsible for a mutant phenotype by defining a small physical interval through linkage analysis and then systematically testing all candidate genes residing in the interval.
- Allelic series
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An allele is one or more alternative forms of a DNA sequence. To create an allelic series, molecular geneticists create mutations in a gene of interest and analyse the resulting phenotypes. Such allelic series are useful for determining gene function.
- Cosegregation
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The tendency for closely linked genes and genetic markers to segregate together.
- Protoplast
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A plant cell with the cell wall removed. Transient assays using protoplasts are effective for processing large quantities of genetic data coming out of high-throughput assays.
- Somaclonal variation
-
Describes the genetic variation sometimes observed in plants that have passed through plant tissue culture. Chromosomal rearrangements are an important source of this variation.
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Jung, KH., An, G. & Ronald, P. Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet 9, 91–101 (2008). https://doi.org/10.1038/nrg2286
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DOI: https://doi.org/10.1038/nrg2286
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