Forest tree species are increasingly subject to severe mortalities from exotic pests, diseases, and invasive organisms, accelerated by climate change. Forest health issues are threatening multiple species and ecosystem sustainability globally.

Applications of molecular markers for genetic analysis of host–pathogen systems are presented within the framework of the gene-for-gene model. The literature on complementary genetic interactions in host–pathogen systems is briefly reviewed. Flor's gene-for-gene hypothesis is summarized, and the design, execution, and genetic interpretation of experiments to test this hypothesis are described in detail. Various molecular techniques that have been used to complement the traditional gene-for-gene approach are also briefly reviewed. Three alternative approaches to developing molecular markers using the gene-for-gene framework are presented to illustrate the potential for applying molecular markers in forest tree–pathogen systems. Two of these alternative approaches allow partial confirmation of a hypothesized gene-for-gene genetic model without the usual requirement for advanced pedigrees. Such alternative approaches could greatly accelerate the development of marker-aided selection for disease resistance in forest tree–pathogen systems.

The grass stage is an inherent and distinctive developmental trait of longleaf pine (Pinus palustris), in which height growth in the first few years after germination is suppressed. In operational forestry practice the grass stage extends for two to several years and often plays a role in planting failures and decisions to plant alternative species. Interspecies hybrids involving loblolly (P. taeda) and slash (P. elliottii var. elliottii) pines have been investigated as a means to produce planting stock with improved early height growth and to develop backcross populations for advanced generation breeding. We have reevaluated data from several interspecies populations, with the objective of estimating the number of genes contributing to the difference in first-year height growth between longleaf and loblolly pines. Estimates based on means and variances of parental and interspecies hybrid and backcross families suggest a minimum of 4 to 10 genes with standard errors less than half the estimates. These results suggest that the grass stage has evolved through the accumulation of alleles at several loci, each with small effects on various components of first-year height growth. Given the complexity of the grass-stage trait, tree breeders may need to combine genetic marker analysis with recurrent backcross breeding to efficiently develop longleaf pine planting stock for improved reforestation.

Chloroplast DNA BamHI restriction fragments were studied in Pinuselliottii Engelm. var. elliottii (11 trees), P. elliottii var. densa (2 trees), the three taxonomic varieties of Pinuscaribaea Morelet (39 trees), and Pinusoocarpa Schiede (9 trees). Polymorphism was detected within both P. elliottii varieties, but not within P. oocarpa. Each of the P. caribaea varieties was monomorphic, but the Cuban variety, P. caribaea var. caribaea, differed clearly from the Bahamian (P. caribaea var.bahamensis) and Honduran (P. caribaea var. hondurensis) varieties. Variety caribaea shared the most frequent chloroplast genotype of P. elliottii var. elliottii, while varieties bahamensis and hondurensis shared the second most frequent genotype of P. elliottii var. elliottii. The P. oocarpa chloroplast genotype was not found in other taxa of the present study, but was found previously in Pinusechinata Mill, and Pinuspalustris Mill. The results of this study, taken together with other chloroplast data from subsection Australes, suggest a close relationship between P. caribaea and P. elliottii. This confirms previous morphological and biochemical evidence, but several discrepancies were apparent and are discussed.