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

9 Citations (Scopus)

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
StatePublished - Sep 2010

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Oryza
genomics
rice
genome
cooperatives
resource
cost
alignment
project

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

The future of rice genomics : Sequencing the collective Oryza genome. / Goicoechea, Jose Luis; Ammiraju, Jetty Siva S; Marri, Pradeep Reddy; Chen, Mingsheng; Jackson, Scott; Yu, Yeisoo; Rounsley, Steve; Wing, Rod A.

In: Rice, Vol. 3, No. 2-3, 09.2010, p. 89-97.

Research output: Contribution to journalArticle

Goicoechea, JL, Ammiraju, JSS, Marri, PR, Chen, M, Jackson, S, Yu, Y, Rounsley, S & Wing, RA 2010, 'The future of rice genomics: Sequencing the collective Oryza genome', Rice, vol. 3, no. 2-3, pp. 89-97. https://doi.org/10.1007/s12284-010-9052-9
Goicoechea JL, Ammiraju JSS, Marri PR, Chen M, Jackson S, Yu Y et al. The future of rice genomics: Sequencing the collective Oryza genome. Rice. 2010 Sep;3(2-3):89-97. https://doi.org/10.1007/s12284-010-9052-9
Goicoechea, Jose Luis ; Ammiraju, Jetty Siva S ; Marri, Pradeep Reddy ; Chen, Mingsheng ; Jackson, Scott ; Yu, Yeisoo ; Rounsley, Steve ; Wing, Rod A. / The future of rice genomics : Sequencing the collective Oryza genome. In: Rice. 2010 ; Vol. 3, No. 2-3. pp. 89-97.
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