A Universal Core Genetic Map for Rice

In order to facilitate the creation of CSSL populations, we are developing a Universal Core Genetic Map (UCGM) for rice. The UCGM is constituted by anchors, which are groups of very tightly linked SSR in the genome and that may be considered as single points or loci at the resolution level we are working with. A set of 165 anchor conformed by 3 SSRs each was defined using automatic and manual selection. Thus, a total of 511 SSR markers were selected based on O. sativa acc. Nipponbare genomic sequence using the annotation data from The Institute for Genomic Research-2004 or TIGR (http://www.tigr.org/index.shtml) version 4, and with the CHARM tool of Cornell University (http://sliver.plbr.cornell.edu/ssr). Using PrimerBlaster tool from Orygenes database of CIRAD France (http://orygenesdb.cirad.fr), the class I markers were validated as single-locus sequences in the rice genome. Sixteen lines, AA genome parents of different populations developed in the framework of two Generation Challenge Program projects (including this one) were selected to evaluated the polymorphisms levels for each anchor. A mean of 83.2% polymorphism was observed for the different interspecific combinations. This level of polymorphism makes the concept of Universal Core Genetic Map both feasible and useful for genetic mapping and marker-aided backcross introgression purposes.

A simple database, Paddy Map, was created in order to facilitate the use of the UCGM and is available for free download.

See the publication Orjuela et al 2009 in Theoretical and Applied Genetics