Ad hoc breeding of a genetically depauperate landrace of noble fir (Abies procera Rehder) using SNP genotyping via high-throughput targeted sequencing

Pedigree reconstruction via DNA markers and subsequent quantitative genetic analyses in production stands of trees is an alternative to traditional forest tree breeding. The method requires variable DNA markers; preferably cost-efficient to genotype. We tested the approach in breeding for Christmas tree traits in a Danish landrace of Abies procera. Initial analysis with simple sequence repeats (SSRs) revealed a substantial reduction in genetic diversity of Danish A. procera compared with direct imports from the USA, indicating a genetic bottleneck. Due to the reduced genetic variation, the SSRs were not variable enough for pedigree reconstruction, and 145 single nucleotide polymorphisms (SNPs) were therefore identified and genotyped via high-throughput targeted sequencing. In the field, we phenotypically selected 674 superior trees, based on criteria for good Christmas trees, among 21,000 trees in three Christmas tree plantations originating from an A. procera clonal seed orchard. By SNP-genotyping and parentage analysis, pedigree was reconstructed for the selected individuals, and genetic predictions for the Christmas tree traits were estimated. A final selection of 45 trees out of the 674 genotyped, based on an index of predicted values for different traits, foresees a gain in the Christmas tree score and branch angle score of 16% and 10%, respectively. The study clearly demonstrated the benefits of pedigree reconstruction, even though mass selection seemed to give similar gain. Primarily, the possibilities to control the level of inbreeding, and to check whether the production stands, from where we select trees, actually originate from the declared and desired parent pool.