Pedigrees, Predictions, and Pipelines: Genomic Resources for Radiata Pine in New Zealand

The New Zealand Radiata Pine Breeding Company is evaluating high density genomic selection SNP panels to increase the delivery of genetic gain. Analysis of various deployment scenarios suggest potential increases in genetic gain could be 80% or higher. There are also applications for low density SNP panels to reconstruct parentage in open-pollinated and control-pollinated mixed seedlots and for the verification of material in seed orchards and clonal propagation nurseries. After several years of developing genomic resources for the large conifer megagenome of radiata pine (Pinus radiata D. Don), the first application of tools for pedigree reconstruction, clone identification, and Genomic-estimated Breeding Value (GeBVs) prediction is underway. The program chose transcriptome-based variant calling to develop an exome capture genotype-by-sequencing (GBS) assay platform, in collaboration with Rapid Genomics LLC. This genome-wide assay, based in gene-space, is generating a rich resource of genetic variants albeit mostly rare, low-frequency alleles. Of the approximately 1.5 million SNPs called in our initial experimental and training populations, around 5% are present at minor allele frequencies greater than 0.03. However this is still proving to be a more than sufficient resource to predict GeBVs and reconstruct pedigrees. Here we describe the journey from in silico SNP discovery, through to design of targeted assays tested in a range of both experimental and operational radiata pine populations.