The future of rice genomics: Sequencing the collective Oryza genome

Jose Luis Goicoechea, Jetty Siva S Ammiraju, Pradeep Reddy Marri, Mingsheng Chen, Scott Jackson, Yeisoo Yu, Steve Rounsley, Rod A Wing

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

The main objectives of the "Oryza Map Alignment Project" (OMAP) are to characterize the rice genome from a comparative standpoint by establishing a genuswide and genome-scale comparative framework from representative species. Here, we report our progress in the analyses of these datasets and emerging "comparative phylogenomics" insights into Oryza evolution at two different resolutions-chromosomal and sequence levels. We demonstrate the abundance and impact of structural variations (SV) on genome diversity using African Oryza as a model. The molecular basis of SV was inferred using three genus-wide vertical sequence datasets. Combined, these data demonstrate that a single reference genome sequence for the genus Oryza is insufficient to comprehensively capture the genomic and allelic diversity present within the genus. Towards this end, we present a strategy to generate high-quality and cost-effective de novo reference sequences of collective Oryza. The application and broader scientific impact of the OMAP resources under an international cooperative effort (I-OMAP) are discussed.

Original languageEnglish (US)
Pages (from-to)89-97
Number of pages9
JournalRice
Volume3
Issue number2-3
DOIs
Publication statusPublished - Sep 2010

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Keywords

  • Comparative genomics
  • OMAP
  • Oryza
  • Rice

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science
  • Soil Science

Cite this

Goicoechea, J. L., Ammiraju, J. S. S., Marri, P. R., Chen, M., Jackson, S., Yu, Y., ... Wing, R. A. (2010). The future of rice genomics: Sequencing the collective Oryza genome. Rice, 3(2-3), 89-97. https://doi.org/10.1007/s12284-010-9052-9