Rice Genomics in Brazil

Antonio Costa de Oliveira
Professor of Genetics and Plant Breeding
Plant Genomics and Breeding Center
Universidade Federal de Pelotas

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.

Publications

Pegoraro C, Farias DR, Mertz LM, Santos RS, Maia LC, Rombaldi CV, Oliveira AC (2013) Ethylene response factors gene regulation and expression profiles under different stresses in rice. Theor. Exptl. Plant Physiol. 25:261-274.

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.

Victoria FC, Bervald CMP, Maia LC, Sousa RO, Panaud O, Oliveira AC (2012) Phylogenetic relationships and selective pressure on gene families related to iron homeostasis in land plants. Genome 55: 883-900.

Victoria FC, Maia LC, Oliveira AC (2011) In silico comparative analysis of SSR markers in plants. BMC Plant Biol. 11: 5-21.

Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokssar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, Tice H, Grimwood J, Mckenzie N, Huo N, Gu YQ, Lazo GR, Anderson OD, You FM, Luo MC, Dvorak J, Wright J, Febrer M, Idziak D, Hasterok R, Lindquist E, Wang M, Fox SE, Priest HD, Filichkin SA, Givan SA, Bryant DW, Chang JH, Wu H, Wu W, Oliveira AC, Maia LC et al. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.

Lima MF, Eloy NB, Pegoraro C, Sagit R, Rojas C, Bretz T, Vargas L, Elofsson A, Oliveira AC, Hemerly AS, Ferreira PCG (2010) Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants. BMC Plant Biol. 10: 254-265.

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.