Low-copy microsatellite markers for Pinus taeda L.

Eighteen low-copy and genomic microsatellite markers were tested for Mendel ian inheritance and then assayed in 41 Pinus taeda L. samples drawn from fi ve regions in the southern United States. The PCR products had multiple all eles, high levels of polymorphism, and little non-specific priming. Fifteen of the 18 markers were informative for a P. taeda three-generation RFLP (r estriction fragment length polymorphism) pedigree, and a P. taeda populatio n survey revealed three to 28 alleles per locus. The highest allele numbers and polymorphic information content (PIC) values were associated with comp lex repeat sequences and (or) with sequences consisting of the longer strin gs of perfect repeats. The abundance of low- to rare-frequency alleles also accounted for high PIC values in both types of markers. Low-copy microsate llites are useful for the large, complex pine genome, especially in the abs ence of entire gene sequences in public databases and with the low levels o f polymorphism in markers developed from expressed sequence tags (ESTs).