Molecular genetics tools for research and breeding of forest tree species

The amount of genetic diversity within forest tree breeding programs is much higher than in crop species. While the development of molecular tools for forest tree species has been lagging behind crop species, there are currently a large amount of resources developed for major species. The large amount of genetic diversity and other population characteristics has been cited as an advantage for the application of recently developed techniques such as association mapping. The application of molecular tools to forest tree breeding is complicated by the long generation times and the implications of clonal forestry. The use of neutral DNA markers can assist tree breeding programs in identification and characterisation of breeding material, but cannot be used to replace phenotypic selection. Gene expression studies have long been used to elucidate the molecular genetics response of organisms to biotic and abiotic stresses. However, while the genetic variation at the DNA level has been widely studied in forest tree species, the variation in gene expression levels has not. Results from our laboratory indicate that large variations exist within Pinus sylvestris breeding material for gene expression, gene copy numbers as well as for other genetic elements such as retrotransposons, all of which may contribute to the adaptive variation being selected for within these breeding programs. Our results have indicated a correlation between induced expression levels and copy number variation of the TLP gene in Scots pine. We have also examined more indirect indicators of genetic diversity and adaptation such as retrotransposon fragment number variation within Scots pine populations. Given the large amount of genetic variation, the heterogeneous genetic background, and the large number of individuals in forest tree breeding programs, the use of DNA assays is preferable to gene expression analyses. Investigation of the variation in gene expression as well as other genetic factors will allow for a better assessment of the amount of adaptive variation found within forest tree breeding programs as well as developing tools for the more efficient utilisation of this variation.