A universal core genetic map for rice

Orjuela Julie, Garavito Andrea, Bouniol Matthieu, Arbelaez Juan David, Moreno Laura, Kimball Jennifer, Wilson Gregory, Rami Jean-François, Mc Couch Susan R., Lorieux Mathias. 2010. A universal core genetic map for rice. Theoretical and Applied Genetics, 120 (3) : 536-572.

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

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Quartile : Q1, Sujet : AGRONOMY / Quartile : Q1, Sujet : HORTICULTURE / Quartile : Q1, Sujet : PLANT SCIENCES / Quartile : Q2, Sujet : GENETICS & HEREDITY

Résumé : 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 .

Mots-clés Agrovoc : Oryza, carte génétique, microsatellite, marqueur génétique, polymorphisme génétique, variation génétique, PCR, Oryza glaberrima, Oryza sativa, Oryza rufipogon

Mots-clés géographiques Agrovoc : Brésil, France

Mots-clés complémentaires : SSR, Oryza barthii, Oryza meridionalis, Oryza glumaepatula

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

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