Genomic Selection in Radiata Pine in New Zealand

New Zealand has approximately 1.8 million hectares of commercial plantation forests, of which 89% is radiata pine (Pinus radiata D. Don). Radiata pine contributes approximately 2.5% to New Zealand GDP and has been subjected to intensive breeding and propagation for over 60 years. Recently our research focus in molecular breeding has moved to Genomic Selection (GS). Reasons include (a) a significant proportion of trait variation can be explained by genome-wide SNP arrays; (b) genotyping of large SNP arrays are becoming increasingly affordable for tree breeders; and (c) prospects for accelerating speed of genetic gain delivery to forest growers due to relatively low effective population sizes (N_e< 60) in advanced ‘elite’ breeding populations.

 A collaborative project has commenced between the Radiata Pine Breeding Company and Scion, consisting of four workstreams:

(1)   Development of a genome-wide SNP panel based on SNP-discovery via extensive RNAseq and gDNA resequencing of multiple genotypes;

(2)   Development of a 20X coverage genomic sequence of radiata pine via a collaboration with UCDavis using short read libraries aligned to a Pinus taedareference genome;

(3)   Development of cheap and quick DNA extraction procedures that ensures affordability to tree breeders; and

(4)   Development of implementation strategies that identify and prioritise ‘injection points’ for application of SNP arrays when they become available.

 Timelines for this work are still being evaluated, but initial analyses indicate GS could be implemented in radiata pine improvement programmes within 4-6 years, with GS-selected germplasm becoming available 2-3 years later.