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A universal core genetic map for rice

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Abstract

To facilitate the creation of easily comparable, low-resolution genetic maps with evenly distributed markers in rice (Oryza sativa L.), we conceived of and developed a Universal Core Genetic Map (UCGM). With this aim, we derived a set of 165 anchors, representing clusters of three microsatellite or simple sequence repeat (SSR) markers arranged into non-recombining groups. Each anchor consists of at least three, closely linked SSRs, located within a distance below the genetic resolution provided by common, segregating populations (<500 individuals). We chose anchors that were evenly distributed across the rice chromosomes, with spacing between 2 and 3.5 Mbp (except in the telomeric regions, where spacing was 1.5 Mbp). Anchor selection was performed using in silico tools and data: the O. sativa cv. Nipponbare rice genome sequence, the CHARM tool, information from the Gramene database and the OrygenesDB database. Sixteen AA-genome accessions of the Oryza genus were used to evaluate polymorphisms for the selected markers, including accessions from O. sativa, O. glaberrima, O. barthii, O. rufipogon, O. glumaepatula and O. meridionalis. High levels of polymorphism were found for the tested O. sativa × O. glaberrima or O. sativa × wild rice combinations. We developed Paddy Map, a simple database that is helpful in selecting optimal sets of polymorphic SSRs for any cross that involves the previously mentioned species. Validation of the UCGM was done by using it to develop three interspecific genetic maps and by comparing genetic SSR locations with their physical positions on the rice pseudomolecules. In this study, we demonstrate that the UCGM is a useful tool for the rice genetics and breeding community, especially in strategies based on interspecific hybridisation.

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Acknowledgments

We are grateful to the Generation Challenge Programme for their financial support through the project No G3005.10 “Exploring natural genetic variation: Developing genomic resources and introgression lines for four AA-genome rice relatives”.

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Author notes

  1. Julie Orjuela

    Present address: Plant Genome and Development Laboratory (UMR 5096, CNRS, IRD, UPVD), Institut de Recherche pour le Développement (IRD), 911 Av. Agropolis, 34394, Montpellier Cedex 5, France

Authors and Affiliations

  1. Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia

    Julie Orjuela, Andrea Garavito, Matthieu Bouniol, Juan David Arbelaez, Laura Moreno, Joe Tohme & Mathias Lorieux

  2. Plant Genome and Development Laboratory (UMR 5096, CNRS, IRD, UPVD), Institut de Recherche pour le Développement (IRD), 911 Av. Agropolis, 34394, Montpellier Cedex 5, France

    Andrea Garavito, Matthieu Bouniol & Mathias Lorieux

  3. Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853-1901, USA

    Jennifer Kimball, Gregory Wilson & Susan R. McCouch

  4. Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR DAP, TA A-96/03, Avenue Agropolis, Montpellier, France

    Jean-François Rami

Authors
  1. Julie Orjuela
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  2. Andrea Garavito
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  3. Matthieu Bouniol
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  4. Juan David Arbelaez
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  6. Jennifer Kimball
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  7. Gregory Wilson
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  8. Jean-François Rami
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  9. Joe Tohme
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  10. Susan R. McCouch
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  11. Mathias Lorieux
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Corresponding author

Correspondence to Mathias Lorieux.

Additional information

Communicated by E. Guiderdoni.

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Orjuela, J., Garavito, A., Bouniol, M. et al. A universal core genetic map for rice. Theor Appl Genet 120, 563–572 (2010). https://doi.org/10.1007/s00122-009-1176-1

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  • DOI: https://doi.org/10.1007/s00122-009-1176-1

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