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Background Growing demand for food and fiber, and a rapidly changing climate will require that plant breeders accelerate the improvement of germplasm adapted to new sources of biotic and abiotic stress. In trees, the threat from climate change is more evident and the solutions more challenging than in any other plant species, due to the complexity and cost of breeding programs, and the long breeding cycles. Therefore, the discovery of genetic polymorphism that can be exploited for early selection of better adapted and productive individuals is essential. Quantitative trait loci (QTL) analysis provided an initial glimpse at the architecture of complex traits, but limited transferability across populations and resolution hampered the adoption of markers in tree breeding programs. Recently, association studies have become the method of choice for detection of markers implicated in trait variation, because of higher resolution, population transferability and allelic diversity captured relative to the QTL approach. However, in tree species, association studies have been largely constrained to sampling the genetic diversity in a limited fraction of the genome, and in small populations. Evidence from genome-wide association studies (GWAS) in humans and advanced crops clearly show that larger populations, and the sampling of regulatory variants and rare alleles is critical to dissect the genetic control of complex traits for markerassisted breeding (MAB). As the limitations of QTL and GWAS approaches become evident, “hybrid” intermediate strategies that combine the advantages of both methods have emerged. Notably, genomic selection has become an alternative to MAB. Genomic selection (GS), which relies on developing genome-wide marker-based models that predict the genetic value of progeny, will be particularly valuable for early selection in tree breeding programs. However, the implications of GS may also be highly valuable to identify mating designs that generate progeny with optimal allelic combinations for superior growth and wood properties, and adaptive capabilities.

Capturing and genotyping the genome-wide genetic diversity of trees for association mapping and genomic selection