The rice genome has been used in many breeding programs in the country, for the comparison of genotypes and mining of new favorable alleles. Traits such as quality, cold, iron and drought have been extensively studied and new markers and genes are in the pipeline for MAS and GMO rice development.
The sequence has been extensively used in the last ten years in my laboratory, a golden resource for every genome comparison performed and gene searches. Also, tools developed in the lab for SSR (SSR Locator) and cis element searches (PLANTCIS) all use the rice genome to infer statistical comparisons. It is difficult to describe such a great change that occurred before and after the release of the IRGSP genome sequence.
Several functional studies have been carried in the lab for the last decade and many more are planned. The sequence has been used by the bioinformatics team to assemble wild genomes, assemble transcripts and perform comparative and structural genome analyses.
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Santos RS, Kruger MM, Pegoraro C, Madabula FP, Maia LC, Rombaldi CV, Oliveira AC (2013) Transcriptional regulation of seven ERFs in rice under oxygen depletion and iron overload stress. Tropical Plant Biol. 6: 16-25.
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Lu F, Ammiraju JSS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X, Cheng Z, Oliveira AC, Bennetzen J, Jackson SA, Wing RA, Chen M (2009) Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc. Natl. Acad. Sci. USA 106: 2071-2076.
Maia LC, de Souza VQ, Kopp MM, Carvalfo FIF, Oliveira AC (2009) Tandem repeat distribution of gene transcripts in three plant families. Genet. Mol. Biol. 32: 822-833.
The Rice Genome Annotation Project (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17: 184-191.
The International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.