Douglas-fir is the most commercially important timber species in the US Pacific Northwest due to its ecological prevalence and its superior wood attributes, especially strength and stiffness properties that make it highly prized for structural applications. Its economic significance has led to extensive establishment and management of plantations over the last few decades. Cultural treatments and genetic improvement designed to increase production of utilizable wood volume also impact tree morphology and wood properties. Many of these impacts are mediated by crown development, particularly the amount and distribution of foliage and size and geometry of branches. Natural selection for branch architecture that optimizes reproductive fitness may not necessarily be optimal for stem volume growth rate or for wood properties controlling the quality of manufactured solid wood products. Furthermore, Douglas-fir does not self-prune within the rotation lengths currently practiced. This paper synthesizes extensive Douglas-fir research in the Pacific Northwest addressing: (1) the effects of silviculture and genetics on branch structure and associated consequences for wood quality and the product value chain; and (2) methods to measure, monitor, modify, and model branch attributes to assist managers in selecting appropriate silvicultural techniques to achieve wood quality objectives and improve the value of their Douglas-fir resource.

Background: In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding. Recently, new, efficient technologies for genotyping thousands to millions of single nucleotide polymorphisms (SNPs) have finally made large-scale use of genetic markers widely available. These methods will be exceedingly valuable for improving tree breeding and understanding the ecological genetics of Douglas-fir, one of the most economically and ecologically important trees in the world. Results: We designed SNP assays for 55,766 potential SNPs that were discovered from previous transcriptome sequencing projects. We tested the array on ~ 2300 related and unrelated coastal Douglas-fir trees (Pseudotsuga menziesii var. menziesii) from Oregon and Washington, and 13 trees of interior Douglas-fir (P. menziesii var. glauca). As many as ~ 28 K SNPs were reliably genotyped and polymorphic, depending on the selected SNP call rate. To increase the number of SNPs and improve genome coverage, we developed protocols to ‘rescue’ SNPs that did not pass the default Affymetrix quality control criteria (e.g., 97% SNP call rate). Lowering the SNP call rate threshold from 97 to 60% increased the number of successful SNPs from 20,669 to 28,094. We used a subset of 395 unrelated trees to calculate SNP population genetic statistics for coastal Douglas-fir. Over a range of call rate thresholds (97 to 60%), the median call rate for SNPs in Hardy-Weinberg equilibrium ranged from 99.2 to 99.7%, and the median minor allele frequency ranged from 0.198 to 0.233. The successful SNPs also worked well on interior Douglas-fir. Conclusions: Based on the original transcriptome assemblies and comparisons to version 1.0 of the Douglas-fir reference genome, we conclude that these SNPs can be used to genotype about 10 K to 15 K loci. The Axiom genotyping array will serve as an excellent foundation for studying the population genomics of Douglas-fir and for implementing genomic selection. We are currently using the array to construct a linkage map and test genomic selection in a three-generation breeding program for coastal Douglas-fir.

Measurements on growth traits up to 41 years of age from 68 progeny sites in eight first-generation breeding zones of coastal Douglas-fir (Pseudotsuga menziesii [MIRB.] FRANCO var. menziesii) in the US Pacific Northwest were used to investigate age trends of genetic parameters and to determine optimum age of selection. Heritabilities and age-age genetic correlations were estimated using univariate or bivariate mixed model analyses. Heritability estimates tended to increase with age for both total growth and growth increment traits. The estimates showed different age trends among breeding zones, but the differences were generally small. Age-age genetic correlations for total growth traits fitted Lambeth’s model surprisingly well, despite the data being collected from multiple breeding zones. Using rotation-age (i.e., 50yr) volume as the selection criterion, the greatest correlated gains per year were achieved by making family selection at juvenile ages (i.e., 9 for height, 13 for diameter, and 11 for volume). Similar results were obtained for within-family selection except that the optimum ages of selection were 2~4 years later than that from family selection, i.e., 11 for height, 15 for diameter and volume. Early selection on total height was always more efficient and had earlier optimum ages than on other growth traits. The optimum ages of early family selection on total growth were 4~11 years earlier than on the corresponding growth increment traits. It was also evident that the optimum ages of selection occurred later for slow-growth trials than for fast-growing trials.

The past three decades have seen considerable research into the molecular genetics and genomics of forest trees, and a variety of new tools and methods have emerged that could have practical applications in applied breeding programs. Applied breeders may lack specialized knowledge required to evaluate claims made about the advantages of new methods over existing practices and are faced with the challenge of deciding whether to invest in new approaches or continue with current practices. Researchers, on the other hand, often lack experience with constraints faced by applied breeding programs and may not be well-equipped to evaluate the suitability of the method they have developed to a particular program. Our goal here is to outline social, biological, and economic constraints relevant to applied breeding programs to inform researchers, and to summarize some new methods and how they may address those constraints to inform breeders. The constraints faced by programs breeding tropical species grown over large areas in relatively uniform climates with rotations shorter than 10 years differ greatly from those facing programs breeding boreal species deployed in many different environments, each with relatively small areas, with rotations of many decades, so different genomic tools are likely to be appropriate.

Genetic parameters are reported for coastal Douglas-fir, from measurements on 24,000 first-generation open-pollinated families (786 test sites) and 2,400 second-cycle crosses (120 test sites) over a period of 45 years. The following were estimated: across-site narrow-sense individual heritability (h²_A), narrow-sense family mean heritability (h²_F), and type B genetic correlation (r_B), and_. narrow-sense single-site heritability (h²_w). The main traits were height, diameter at breast height (dbh), volume index (both cycles), and incidence of stem forking and ramicorn branching, upper stem sinuosity, and second flushing in the leader (second cycle). Smaller datasets were available for progression of budburst, straightness, needle retention, wood specific gravity and acoustic velocity. Measurements were between three and 30 years from planting. The dataset contained at least one trait measured for 2.602 million trees . Heritability (h²_A) estimates for height, dbh, volume and sinuosity ranged from 0.15 to 0.30, with a wider range for h²_w estimates. Heritabilities were higher in the second cycle. Forking and ramicorn branching had good h²_F heritabilities. Second flushing had high h²_A and r_B values; the same is often true for AV. Budburst was the most strongly inherited trait. h²_w for height, dbh, volume, forking and ramicorns was correlated with means for those traits.

The current planting of economically important timber species, such as Douglas-fir, mainly relies on genetically improved seeds from seed orchards. However, published research on the effects of climate change has largely focused on natural populations. To bridge this gap, data from 80 cooperative second-cycle coastal Douglas-fir progeny tests across eight breeding zones in western Washington and Oregon were analyzed. Climate transfer functions for age-12 growth were derived, showing significant results for the US Pacific Northwest. Region-specific transfer functions (Coast, Inland, and Cascade) displayed stronger correlations. Mean annual temperature and mean coldest month temperature were the most important climatic variables explaining growth. The study found that populations from slightly warmer areas tended to grow better but moving populations from colder to warmer areas by 2 °C (analogous to projected global warming) would result in an 8% genetic loss in age-12 height and a 25% genetic loss in age-12 volume. However, substantial diversity in climatic response was found among full-sib families within large breeding zones, suggesting that breeding and selecting suitable families for future climatic conditions within breeding zones is feasible. The study discusses potential strategies to adapt current breeding programs to address the impacts of future climate change while maintaining high population growth rates in Douglas-fir breeding programs.