Molecular breeding is the use of molecular markers to assist and accelerate conventional tree breeding and selection programs. Notably, genetic diversity studies in Arborea aim to enable the development of such molecular marker applications for tree breeding. Our program is enviably positioned to be among the first to successfully develop molecular breeding applications in commercially important conifers, through an integrated research approach.  Our comprehensive plan is built upon the unique natural and pedigreed populations that  we have assembled for analyses in conjunction with high throughput genotyping and large-scale expression profiling technologies.

Phase 1 – Establishing the diversity analytical pipeline   (2002-2006)

An analytical pipeline has been developed for the analysis of functional diversity of transcription factors at the sequence level, which resulted in the finding of significant associations with key phenotypic characters related to meristematic growth in white spruce. We have extracted and characterized 12,000 SNPs from our white spruce EST database. These SNPs represent the raw material for building molecular breeding systems. They are available to the research community through a SNP-table in ForestTreeDB. Proof-of-concept experiments with high-throughput (HT) genotyping have been conducted, with the construction of a 768-SNP array for mapping over 400 transcription factors and identification of co-localizing quantitative trait loci (QTL) related to growth and phenology. For this purpose, a mapping population has been assembled, cloned and phenotyped for juvenile growth and phenology.  Composite genetic maps containing over 100 anchor markers of coding genes and microsatellites have also been constructed for white spruce and also for black spruce and Norway spruce, in collaboration with our partners at INRA in France. These maps represent an invaluable resource for facilitating gene marker transfer among pedigrees and species.</>

Phase 2 – mapping 3000 genes and building molecular breeding systems for characters related to growth and wood quality (2006-2010)

The proposed gene mapping research aims to identify gene loci, molecular functions and sequence polymorphisms to enable the development of molecular breeding systems in conifers. We will make extensive use of materials derived from natural and pedigreed populations developed by the Canadian Forest Service and the Ministère des Ressources naturelles et de la faune du Québec for deploying association and QTL mapping strategies in white spruce. Integrated large-scale gene mapping and expression profiling studies will be conducted in conjunction with high resolution phenotyping for growth related characters, adaptation and wood property traits. Overall, we plan to map 3000 white spruce genes. Large-scale mapping will rely on the discovery of thousands of single nucleotide polymorphisms (SNPs) as a virtually unlimited source of robust genetic markers,  and the use of HT genotyping SNP-arrays to implement methods for genotyping of thousands of expressed genes.