Single-trial and across-trial spatial analyses using autoregressive error structures were conducted for growth traits based on 1,146 data sets from 275 Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] progeny trials in 45 first-generation breeding zones in the US Pacific Northwest. The breeding zones encompassed a wide range of latitude, longitude, and elevation. Efficiency of using spatial analysis in reducing variation due to site heterogeneity, estimating genetic parameters, and increasing prediction accuracy was compared among different experimental designs, traits, assessment ages, and tree spacings. More than 97% of the data sets showed significant model improvement with spatial analysis, and height showed more improvement than diameter or volume. Spatial analysis on average removed 14~34% of residual variance due to spatial heterogeneity, which resulted in an up to 20% increase in accuracy of breeding value prediction. The coefficient of variation decreased substantially due to spatial adjustment. Rank correlation between predicted gains before and after spatial analysis was about 0.96, and spatial analysis had little effect on the average predicted gain of the top 20% of parents. We did not observe substantial geographic trends in improvements due to spatial adjustment. Across-site spatial analysis had almost no effect on genotype-by-environment interaction but tended to increase among-trial heterogeneity of residual variance. Two different methods for across-trial spatial analysis were compared and discussed.

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Application . Grafting is widely used to propagate conifers . Selected rootstocks can be used to improve graft success, reduce incompatibility, alter scion vigor and increase seed production . It may also be possible to alter crown characters and scion physiology.Abstract . The literature on rootstock effects (on scions) in conifers was reviewed, specifically: graft success, compatibility, size, reproduction, phenology, crown and needle characters, mineral content, organic compounds, water relations, disease resistance and wood properties . Scions usually had higher graft success and less incompatibility on more closely related rootstocks although there were exceptions . Even intergeneric grafts have succeeded on occasion . Although there were marked rootstock effects on growth and reproduction, the effects did not follow a pattern with increasing relationship . It is also likely that some crown characters and the nutrient content of scions can be manipulated by the use of rootstocks. For many characters, a specific rootstock may give a desired result only for a limited number of scion types (species, cultivars or clones) . With some exceptions, the review shows that the subject has not been comprehensively studied . Many of the studies were either short-term, inadequately replicated, or poorly designed to allow firm conclusions about rootstock effects . The physiological and biochemical mechanisms, which cause the changes seen in morphology, are not well understood . Further research and more comprehensive study of rootstock effects on scion biology are recommended .

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.

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