RAPD mapping and its application in slash pine breeding

Random amplified polymorphic DNA (RAPD) was evaluated as a genetic marker system in slash pine breeding, and was used as tool for tagging genes for fusiform rust resistance.;Low concordance between individual trees is one of the serious problems of RAPD markers in breeding programs for forest trees. In the first experiment, this problem was analyzed comprehensively using materials from 11 unrelated trees. For 29 marker fragments identified in a single tree, the chance of occurrence of the makers in the other trees varied dramatically among the markers, but was not affected by the sequences of the primers, the sizes of the markers or the copy number of the marker sequences. Using SCAR analysis, we found that most RAPD sequences existed in the trees where the original RAPD bands were absent. In most cases, the observed RAPD polymorphism either within or among trees in slash pine were caused by point mutations in primer annealing sites, not by insertion/deletion between them. SCAR analysis has the potential to integrate RAPD linkage maps developed from different trees.;In the second experiment, the inheritance of RAPD markers was analyzed in a two generation pedigree. Ninety percent of the polymorphic fragments detected in the haploid tissues of the female parent tree were inherited as expected in the F1 progenies. Non-parental amplified fragments were not observed in the progeny.;In the third experiment, resistance traits to fusiform rust were dissected by genomic mapping in the progeny of a cross of a resistant tree and a susceptible polymix. A step by step sampling method was developed to detect the cosegregation of RAPD markers and the resistance traits. A dominant gene controlling a major resistance trait (galled or not galled) was mapped.