Towards Genomic Selection in Pine Breeding

Genomic selection requires repeatable, cost-efficient and high throughput genotyping platforms to succeed. Publicly funded research projects in the USA have produced vast genomic resources for Pinus taeda L. and Pinus lambertiana Douglas. With funding from USDA-NIFA program we aim to discover informative single nucleotide polymorphic markers (SNPs) for genomic selection based on re-sequencing efforts carried out in multiple USA laboratories. Scaffolds of the de novo assembled P. taeda and P. lambertiana genomes are available by the PineRefSeq project to allow mapping of the flanking sequences of the identified SNPs. Genomic information for tropical and sub-tropical pines related to P. taeda has also been generated from several international laboratories using target sequencing and RNAseq techniques. Our group is coordinating SNP discovery efforts to bring the resources together for multiple pine species and use consistent bioinformatics tools for selection of SNPs. The genomic resources will be organized in the TreeGenes database for public access and our Pine SNP chip consortium will be established to bring the forest genetics community together. The consortium will negotiate with different providers to genotype large numbers of samples to lower genotyping costs. Genomic selection has the potential to be a paradigm shift in pine breeding. Our efforts intend to bring genomics to forest tree breeding to sustainably increase timber, fiber, and biofuel production and stimulate a new wave of novel research ideas aimed at understanding the genetic basis of growth, disease and pest resistance, and adaptation to climate change.