Scar markers in a longleaf pine x slash pine F₁ family

Abstract

Sequence characterized amplified region (SCAR) markers were derived from random amplified polymorphic DNAs (RAPDs) that segregate in a longleaf pine x slash pine F₁ family. Nine RAPD fragments, five from longleaf pine 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 FGP004, FGP005, FGE006, FGE007, FGP008, FGE009, FGPO10, FGE011, and FGP012) were designed by extending the RAPD primers; three (for FGE001, FGP002, and FGE003) were based on the internal 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 FGP004, FGE006, and FGE007 amplified polymorphic bands between the parents. The primer pair for FGP013 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 FGP005 by digesting the polymerase chain reaction (PCR) products with the restriction enzyme SmaI. FGP005 and FGPO12 were found to be polymorphic when the PCR products were separated on a 3 percent acrylamide sequencing gel. The segregation of four of the six polymorphic SCARs was confirmed in 64 longleaf x slash F₁ individuals.

Citation

Weng, C.; Kubisiak, Thomas L.; Stine, M. 1998. Scar markers in a longleaf pine x slash pine F₁ family. Forest Genetics. 5(4): 239-247.