A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata

Development of genome-wide resources for application in genomic selection or genome-wide association studies, in the absence of full reference genomes, present a challenge to the forestry industry, where longer breeding cycles could benefit from the accelerated selection possible through marker-based breeding value predictions. In particular, large conifer megagenomes require a strategy to reduce complexity, whilst ensuring genome-wide coverage is achieved. Using a transcriptome-based reference template, we have successfully developed a high density exome capture genotype-by-sequencing panel for radiata pine (Pinus radiata D.Don), capable of capturing in excess of 80,000 single nucleotide polymorphism (SNP) markers with a minor allele frequency above 0.03 in the population tested. This represents approximately 29,000 gene models from a core set of 48,914 probes. A set of 704 SNP markers capable of pedigree reconstruction and differentiating individual genotypes were tested within two full-sib mapping populations. While as few as 70 markers could reconstruct parentage in almost all cases, the impact of missing genotypes was noticeable in several offspring. Therefore, 60 sets of 110 randomly selected SNP markers were compared for both parentage reconstruction and clone differentiation. The performance in parentage reconstruction showed little variation over 60 iterations. However, there was notable variation in discriminatory power between closely related individuals, indicating a higher density SNP marker panel may be required to elucidate hidden relationships in complex pedigrees.