FOREST GENETICS 5(4):239-247,199s SCAR MARKERS IN A LONGLEAF PINE x SLASH PINE F, FAMILY

Sequence characterized amplifled region (SCAR) markers were derived from random amplified polymorphic DNAs (RAPDs) that segregate in a longleaf pine x slash pine Fi family. Nine RAPD fragments, five from longleafpine and four from slash pine, were cloned and end sequenced. A total of 13 SCAR primer pairs, with lengths between 17 and 24 nucleotides, were developed. Nine (for SCAR loci FGPO04, FGPOOS, FGEO06, FGEO07, FGPOO8, FGEOO9, FGPOlO, FGEOI 1, and FGP012) were designed by extending the RAPD primers; three (for FGEOOl , FGP002, and FGE003) were based on the interna1 sequences of corresponding cloned RAPD fragments; and one (for FGP013) was based on the sequence of the original cloned RAPD fragment as well as the sequence of the cloned SCAR fragment amplified from the other parent. All SCAR primer pairs amplified bands of expected sizes. The primer pairs for FGPO04, FGEOOó, and FGE007 amplified polymorphic bands between the parents. The primer pair for FGPO13 revealed a polymorphism between the parents, but lost the within-tree polymorphism. The other nine primer pairs amplified monomorphic bands when separated on agarose gels. A polymorphism between the parents was identified for FGPOOS by digesting the polymerase chain reaction (PCR) products with the restriction enzyme SmuI. FGPOOS and FGP012 were found to be polymorphic when the PCR products were separated on a 3% acrylamide sequencing gel. The segregation of four of the six polymorphic SCARs was confirmed in 64 longleaf x slash F, individuals.