Genetic maps have been constructed for many different forest tree species. A variety of genetic marker types have been used (RFLPs, RAPDs, SSRs, AFLPs) and more recently with the SNPs. Quantitative trait loci (QTLs) have also been mapped for many different traits. Sadly, it is nearly impossible to compare genetic maps between and even with species and develop a synthesis of genome information in forestry. This unfortunate fact is due to two shortcomings within the forest tree genome mapping community; (1) orthologous genetic markers are lacking and not shared among labs, and (2) reference mapping populations have not been developed and made publicly available. We have formed an international collaboration called the Conifer Comparative Genomics Project (CCGP) to begin to rectify this situation. The immediate goals of the CCGP are to:
- Develop, map, and freely distribute a framework set of orthologous genetic markers based on loblolly pine ESTs. and complete the comparative maps for several pines and other conifers.
- Freely distribute mapping population DNA and marker segregation data for two immortalized loblolly pine reference genetic mapping populations belonging to the Weyerhaeuser Company.
- Genetically map a small set of single- or low-copy pine BACs to the loblolly pine reference mapping populations so that in the future these BACs can be mapped physically to pine chromosomes using FISH, allowing the integration of of pine genetic linkage groups with each of the 12 pine chromosomes.
The development of genetic resources for comparative genomic analysis in conifers would have significant impact in many areas of genome research. Comparative mapping would facilitate: (1) verification of QTLs, (2) identification of candidate genes, and (3) the understanding of evolutionary relationships. It should be possible to treat pines and even all conifers as a single genetic system as is being done in other plant groups. The forestry genome research community is small, poorly funded, and not organized around a single model species. Comparative genomics will partially alleviate these limitations and deepen the understanding of conifer genomes.
The objective of this work would be to create a comparative catalog of all genetic maps for the chosen conifers, in order that we facilitate the study of these species as a single genetic system. Thus, helping us understand the genome organization and evolution of these forest trees. All this would also end up increasing our knowledge on experimental approaches towards studying conifers and also provide breeders with more efficient methods of MAS (Marker aided selection).