TY - JOUR
T1 - A universal core genetic map for rice
AU - Orjuela, Julie
AU - Garavito, Andrea
AU - Bouniol, Matthieu
AU - Arbelaez, Juan David
AU - Moreno, Laura
AU - Kimball, Jennifer
AU - Wilson, Gregory
AU - Rami, Jean François
AU - Tohme, Joe
AU - McCouch, Susan R.
AU - Lorieux, Mathias
N1 - Funding Information:
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”.
PY - 2010/1
Y1 - 2010/1
N2 - 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 × c 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.
AB - 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 × c 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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U2 - 10.1007/s00122-009-1176-1
DO - 10.1007/s00122-009-1176-1
M3 - Article
C2 - 19847389
AN - SCOPUS:75949128344
SN - 0040-5752
VL - 120
SP - 563
EP - 572
JO - Theoretical and Applied Genetics
JF - Theoretical and Applied Genetics
IS - 3
ER -