Theoretical and Applied Genetics

, Volume 120, Issue 3, pp 563–572 | Cite as

A universal core genetic map for rice

  • Julie Orjuela
  • Andrea Garavito
  • Matthieu Bouniol
  • Juan David Arbelaez
  • Laura Moreno
  • Jennifer Kimball
  • Gregory Wilson
  • Jean-François Rami
  • Joe Tohme
  • Susan R. McCouch
  • Mathias Lorieux
Original Paper

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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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Julie Orjuela
    • 1
    • 2
  • Andrea Garavito
    • 1
    • 2
  • Matthieu Bouniol
    • 1
    • 2
  • Juan David Arbelaez
    • 1
  • Laura Moreno
    • 1
  • Jennifer Kimball
    • 3
  • Gregory Wilson
    • 3
  • Jean-François Rami
    • 4
  • Joe Tohme
    • 1
  • Susan R. McCouch
    • 3
  • Mathias Lorieux
    • 1
    • 2
  1. 1.Agrobiodiversity and Biotechnology ProjectInternational Center for Tropical Agriculture (CIAT)CaliColombia
  2. 2.Plant Genome and Development Laboratory (UMR 5096, CNRS, IRD, UPVD)Institut de Recherche pour le Développement (IRD)Montpellier Cedex 5France
  3. 3.Department of Plant Breeding and GeneticsCornell UniversityIthacaUSA
  4. 4.Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)UMR DAPMontpellierFrance

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