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).