A Synergistic Union Of Conifer Genome Projects Across Canada: SMarTForests

The SMarTForests project develops genomic resources and breeding applications in white spruce, a keystone conifer of forests in North America and of prime importance to the forest industry. The project encompasses genome sequencing, marker development for breeding, and comparative genomics.

For genome sequencing, our strategy uses shotgun sequencing of a diploid individual with150 bp paired end (PE) HiSeq reads, long virtual reads from overlapping 300 bp PE reads on 500 bp fragments with MiSeq, and mate-pair libraries of 3 to 15 Kb. For assembly we use the ABySS software, developed by the Genome Sciences Center, which has the unique ability to use parallel processing to enable large scale assemblies.  Our strategy includes sequencing many libraries to minimize representation biases. The most recent assembly has 65x coverage with a scaffold N50 of 7.2 kb, reconstructing a total of 21.5 Gb sequence in 5 million scaffolds.  Annotation uses previously developed Fl-cDNA resources, and RNA-seq data of multiple tissues.  A high-density genetic map is under construction for high-level genome assembly and comparative structural genomic purposes. A consensus map of 1941 cM with 8287 genes has been obtained by genotyping 2000 progeny.

For breeding applications of the spruce genomics resources, we employ (1) RNA-seq to identify SNPs for genomic selection, (2) expression QTL mapping and network inference of putative master regulatory genes, and (3) identification of biomarkers.