Genetic variation in red pine (Pinus resinosa) revealed by RAPB and RAPD-RFLP analysis

In this paper, we demonstrate that the RAPD technique, and variations thereof, can be used in conjunction with high-resolution agarose gel electrophoresis to detect genetic variation among individuals within and between seed sources in a genetically uniform species such as red pine (Pinus resinosa Ait). A total of 57 primers that gave consistent, strongly amplified fragments were selected for further screening with DNA from four mutant trees and a rangewide sample of 21 normal trees. Only three of these primers generated amplification fragment patterns that were polymorphic. Restriction endonuclease digestion of RAPD reaction products (RAPD-RFLP analysis), using enzymes with four base pair recognition sequences, was used to determine if fragments of identical electrophoretic mobility were the result of priming at either single or multiple genomic locations. Out of 64 primer/enzyme combinations tested, one primer/enzyme combination created reproducible polymorphic banding patterns in rangewide red pine DNA samples. Therefore, digestion of RAPD reaction products can be used as a method to increase the probability of detecting genetic variation between highly conserved genomes.