Marker informed breeding could be a favorable opportunity to accelerate cultivar selection in poplar. Linking genotype to phenotypic variation of important economical and adaptive traits is the prerequisite. The two strategies chosen are QTL detection in mapping pedigrees and association studies in natural populations. An intra-specific mapping pedigree Populus nigra x P. nigra of 300 individuals segregating for leaf rust resistance is available. Another large progeny of 1400 individuals derived from a cross P. deltoides x P. trichocarpa for which two major factors and QTL of rust resistance segregated is already available. QTL for phenology and water use efficiency were also mapped. Large scale phenotyping of wood properties is underway. An association mapping population of 1100 P. nigra individuals coming from France, Germany, Netherlands and Spain was evaluated for rust resistance in both controlled and field conditions. Even if most of the genetic variation for rust resistance could be observed at the genotype level, significant differentiation between natural populations was detected. Taking advantages of genomics development in poplar including structural and functional genomics, positional, functional and expressional candidate genes were identified for rust resistance, phenology and wood properties. It became clear that SNP in those genes could be ideal combined to HTP genotyping technologies to identify causative polymorphism for phenotypic variation. We developed collections of SNP useful for both genetic and association mapping. With the help of the genome sequence, unique primer pairs were automatically designed and tested for their uniqueness before PCR amplification and HTP Sanger re-sequencing. Based on the analysis of 850 gene fragments, an average of 1SNP/90bp were found in the three Populus species studied. SNP appeared fixed in each species after comparison of SNP position between the three species. Analysis of linkage disequilibrium in P. nigra showed a rapid decline of LD with physical distance