Limitations of molecular-marker-aided selection in forest tree breeding
Authors: Strauss S. H. , Lande R. , Namkoong G. 
Published: March 2008

The advances to date with quantitative trait locus identification in agronomic crops, which have mostly been with studies of inter- and intra-specific hybrids, are of little relevance to assessing the potential for marker-aided selection in nonhybrid forest tree populations. Although molecular markers provide great opportunities for dissection of quantitative traits in experimental populations, we expect that their near-term usefulness in most operational tree breeding programs will be limited. In addition to cost, this limitation results from quantitative trait locus–marker associations being limited to specific genetic backgrounds as a result of linkage equilibrium, interactions of quantitative trait locus effects with genetic backgrounds, genotype by environment interaction, and changes of quantitative trait locus allele frequencies among generations. Marker-aided selection within individually mapped full-sib families can substantially aid phenotypic selection, but only where large restrictions of genetic base are tolerated, trait heritabilities are low, markers are able to explain much of the additive variance, selection intensities within families are high compared with that among families, and very large numbers of progeny are examined. Broad use of marker-aided selection in the longer term will require substantial technical advances in a number of areas, including means for precise quantitative trait locus identification; reduction of large-scale mapping and genotyping costs; and changes in breeding and propagation systems. Consideration of trait characteristics suggests that marker-aided selection will be most efficient in direct selection with high-value, low-heritability traits such as height and diameter growth. These traits, however, often show genotype by environment interaction and unfavorable genetic correlations with other desirable traits, and are likely to be controlled by a large number of minor genes rather than relatively few major ones. Traits with the most potential for marker-aided selection in nonhybrid tree populations will therefore be strongly inherited ones for which phenotypic assay is difficult; examples might include wood quality, resistance to biotrophic pathogens, and resistance to air pollutants. Because of the large disequilibrium generated during hybridization and the great phenotypic variance that segregates in F2 and backcross generations, interspecific hybrid programs lend themselves much more readily to marker-aideed selection. Segregation distortion and related meiotic aberrations, however, may substantially hamper precise estimation of quantitative trait locus locations and phenotypic effects. Nonadditive quantitative trait locus effects will likely be greater in hybrid populations than in intraspecific populations. Rapid decay of disequilibrium due to recombination, and allele frequency shifts due to selective breeding and natural selection during early generations after hybridization, are likely to cause instability for quantitative trait locus - marker associations and quantitative trait locus phenotypic effects. Finally, interspecific hybridization of highly heterozygous individuals from species in linkage equilibrium will impede marker-aided selection.