RAPD mapping in a doubled haploid population of rice (Oryza sativa L.)

To examine the distribution and genome coverage of RAPDs, a total of 242 Random Amplified Polymorphic DNA (RAPD) markers generated by 73 random decamer primers were mapped onto 12 rice chromosomes by linkage analysis using a doubled haploid population, developed from an indica x japonica cross. The RAPD markers were derived from both parents equally and were well distributed over the rice genome. Furthermore, multiple RAPD markers generated from the same primer were dispersed over different chromosomes rather than clustered. The RAPD technique provided improved marker coverage on a previously developed RFLP map. A set of primers producing reproducible markers originating from either parent and equally spaced over all the 12 chromosomes were selected for application in marker-assisted backcross breeding. The RAPD analysis as a realistic and practical alternative to RFLP and their usefulness in anchoring the identified BAC contigs directly to chromosomes is discussed.