Abstract
Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial breeding. Leveraging off a previously developed exome capture panel, we tested the performance of 438,744 single nucleotide polymorphisms (SNPs) on a screening array (NZPRAD01) and then selected 36,285 SNPs for a final genotyping array (NZPRAD02). These SNPs aligned to 15,372 scaffolds from the Pinus taeda L. v. 1.01e assembly, and 20,039 contigs from the radiata pine transcriptome assembly. The genotyping array was tested on more than 8000 samples, including material from archival progenitors, current breeding trials, nursery material, clonal lines, and material from Australia. Our analyses indicate that the array is performing well, with sample call rates greater than 98% and a sample reproducibility of 99.9%. Genotyping in two linkage mapping families indicated that the SNPs are well distributed across the 12 linkage groups. Using genotypic data from this array, we were also able to differentiate representatives of the five recognized provenances of radiata pine, Año Nuevo, Monterey, Cambria, Cedros and Guadalupe. Furthermore, principal component analysis of genotyped trees revealed clear patterns of population structure, with the primary axis of variation driven by provenance ancestry and the secondary axis reflecting breeding activities. This represents the first commercial use of genomics in a radiata pine breeding program.
Highlights
Genomics has the potential to change forest tree breeding from traditional backward selection approaches based on progeny test results to faster and earlier forward selections based on genomic predictions [1]
We report on early applications of this tool, including distinguishing radiata pine provenances and describing the population structure of the New Zealand breeding program
There were a large proportion of markers in the “not recommended” category; this is common with species with complex genomes, such as radiata pine
Summary
Genomics has the potential to change forest tree breeding from traditional backward selection approaches based on progeny test results to faster and earlier forward selections based on genomic predictions [1]. It has the potential to increase the rate of genetic gain through shortening radiata pine’s long generation intervals through predicting unobserved phenotypes and early selection of superior genotypes [2,3,4]. Radiata pine (Pinus radiata D.Don) is the primary forestry species in New Zealand, comprising nearly 90% of the 1.7 million hectares of planted forest [13]. It is regarded as the world’s most widely planted exotic conifer [14]. Current genetic research in radiata pine has been focused on the development of genomic resources to enable new genomics-based breeding approaches for this species [15,16,17,18]. Exome capture genotyping-by-sequencing (GBS) [23] has allowed for the simultaneous discovery and genotyping of more than 80K single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) greater than
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