Conifers represent over 670 species , some ranking as the largest, tallest, and longest living terrestrial organisms on Earth. They dominate many terrestrial landscapes, represent the largest terrestrial carbon sink, and provide significant ecological services to human societies. They are also of great economic importance, as they are primarily used for biomass, timber and pulp production worldwide. Domestication of conifers started about 60 years ago through traditional genetic improvement programs , which have resulted in substantial improvements of overall growth, wood quality, pest resistance and adaptation to present and future climatic conditions. However, the long generation intervals and the difficulty of accurately evaluating traits in early stages have hampered progress through breeding . Furthermore, their extraordinary large genome size (seven times higher than the human genome, ) prohibits classical map-based cloning approaches of major-effect quantitative trait loci (QTL).
During the past 20 years, many sophisticated genomic tools have been developed to accelerate the domestication process by exploring in depth their genetic diversity. Linkage maps represent a major tool in genomic-based breeding because of their central role in dissecting the genetic architecture of quantitative trait variation . Moreover, the relatively well conserved genome organization in conifers makes it possible to transfer genetic information from one species to another by comparative mapping (e.g. ). Genetic mapping activities, therefore, will continue to dominate research in conifer genetics  at least until a conifer genome sequence has been completely decoded.
The progress of genetic mapping in conifers is reflected by the development of different generations of molecular markers. The first (RFLP: Restriction Fragment Length Polymorphism) and second generation (RAPD: Random Amplified Polymorphic DNA and AFLP: Amplified Fragment Length Polymorphisms) markers made it possible to construct genetic linkage maps for twelve pine (Pinus taeda, P. pinaster, P. sylvestris, P. strobus, P. radiata, P. palustris, P. elliottii, P. edulis, P. densiflora, P. contorta, P. caribaea, and P. brutia) and four spruce species (Picea abies, P. glauca, P. mariana and P. rubens) (reviewed by ). Furthermore, over the last decade, the increasing availability of expressed sequence tags (ESTs) has provided a valuable source of new PCR-based molecular markers, such as EST-derived microsatellites (EST-SSRs), EST-based polymorphisms (EST-Ps) and single nucleotide polymorphisms (SNPs). Because of their abundance, higher availability and stability compared with simple sequence repeats (SSRs), and the ease with which data can be standardized due to their bi-allelic nature, SNP markers provide enhanced possibilities for genetic and breeding applications, such as construction of linkage maps and detection of genotype/phenotype associations . Several SNP genotyping approaches have been developed in the last few years. These approaches vary in terms of sensitivity, reproducibility, accuracy, capability of multiplexing and throughput [9, 10]. Among the SNP genotyping technologies available to date, the GoldenGate assay developed by Illumina has demonstrated high success rates within plant genomes of differing complexities, such as pea , soybean , barley , maize , spruces  and pines [[16–18]].
In the present study, a custom GoldenGate assay containing 1,536 SNPs derived from gene sequences was designed to genotype two maritime pine (Pinus pinaster Ait., 2n = 2x = 24) mapping populations, while earlier studies have heavily relied on anonymous markers such as RAPDs  and AFLPs [[20–22]]. The information contained within each individual map was then synthesized into a single consensus map, from which a set of orthologous markers allowed the alignment with the reference Pinus taeda linkage map. The present study is therefore an important step for advancing comparative genomics in conifers.