Bayesian inference for multi-environment spatial individual-tree models with additive and full-sib family genetic effects for large forest genetic trials

Context: The gain in accuracy of breeding values with the use of single trial spatial analysis is well known in forestry. However, spatial analyses methodology for single forest genetic trials must be adapted for use with combined analyses of forest genetic trials across sites. Aims: This paper extends a methodology for spatial analysis of single forest genetic trial to a multi-environment trial (MET) setting. Methods: A two-stage spatial MET approach using an individual-tree model with additive and full-sib family genetic effects was developed. Dispersion parameters were estimated using Bayesian techniques via Gibbs sampling. The procedure is illustrated using height growth data at age 10 from eight large Tsuga heterophylla (Raf.) Sarg. second-generation full-sib progeny trials from two series established across seven sites in British Columbia (Canada) and on one in Washington (USA). Results: The proposed multi-environment spatial mixed model displayed a consistent reduction of the posterior mean and an increase in the precision of error variances than the model with Sets in Replicates or incomplete block alpha designs. Also, the multi-environment spatial model provided an average increase in the posterior means of the narrow- and broad-sense individual-tree heritabilities (h2N and h2B, respectively). No consistent changes were observed in the posterior means of additive genetic correlations (rAjj'). Conclusion: Although computationally demanding, all dispersion parameters were successfully estimated from the proposed multi-environment spatial individual-tree model using Bayesian techniques via Gibbs sampling. The proposed two-stage spatial MET approach produced better results than the commonly used non-spatial MET analysis.Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Yanchuk, Alvin D.. British Columbia Forest Service; CanadáFil: Cartwright, Charlie V.. British Columbia Forest Service; Canad

Intraclonal Variation in Wood Density of Trembling Aspen in Alberta

Four trees from each of three putative clones of trembling aspen (Populus tremuloides Michx.) at one site in north-central Alberta were sampled to determine the patterns of wood density variation within stems and within clones. Sample disks were removed at five heights from each tree to examine variation among cardinal directions and across the southern radius at each height. Although only three clones were sampled, there were significant differences (0.05 level) among clones. Wood density tends to be high at the bottom of the tree, decreases to a minimum at midheight, then increases again near the top of the tree. In the radial direction, wood density is high near the pith (at all heights), decreases, then increases again in the mature wood zone (after rings 15-20+). Average wood density values within the twelve stems varied from 0.348 g/cc to 0.402 g/cc

Climatic drivers of genotype-environment interactions in lodgepole pine based on multi-environment trial data and a factor analytic model of additive covariance

The optimum deployment of select material from tree breeding programs is affected by the presence of genotype-environment (GxE) interactions and further complicated by future climate change. Here, we analyzed tree height data from 28 progeny test sites in a multi-environment trial (MET) dataset for two testing cycles of the lodgepole pine (Pinus contorta Douglas ex Loudon) breeding program in British Columbia to characterize one approach to investigating the climatic variables influencing GxE, and the potential impacts of climate change. Linear mixed model analysis was conducted using an approximate reduced animal model with a factor analytic (FA) variance model to estimate the complex additive (co)variance structure. Test sites were grouped according to patterns of GxE and climate modelling was employed to project historical and future deployment zones for each group. Based on these findings, it appears that breeding groups with historically wide deployment zones from northern environments will become less important as the climate warms, and therefore investment should be directed toward southern breeding groups which will be useful across a very wide geographic range in the near to mid-term future.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Supplementary Material Douglas-fir data [Conjunto de datos]

Supplementary information of the three Douglas-fir trials, family numbers, and pedigree data including identity information of trees, fathers, and mothers of the paper entitled: Identification and joint modeling of competition effects and environmental heterogeneity in three Douglas-fir (Pseudotsuga menziesii var. menziesii) trials. Tree genetics & genomes 12 (6) : 102. (December 2016)Instituto de Recursos BiológicosFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Cappa, Eduardo Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Stoehr, Michael U. British Columbia Ministry of Forests. Lands and Natural Resource Operations. Tree Improvement Branch; CanadáFil: Chang-Yi, Xie. British Columbia Ministry of Forests. Lands and Natural Resource Operations. Tree Improvement Branch; CanadáFil: Yanchuk, Alvin D. British Columbia Ministry of Forests. Lands and Natural Resource Operations. Tree Improvement Branch; Canad

Red alder defense mechanisms against western tent caterpillar defoliation

Red alder (Alnus rubra Bong.) is a tree of high economic and ecological importance but subject to severe defoliation during episodic outbreaks of tent caterpillars (Malacosoma spp.). We evaluated variation in western tent caterpillar (M. californicum Packard, 1864) (WTC) resistance among and within red alder populations and clones, and investigated potential defense mechanisms. Bioassay feeding trials were conducted with WTC on 20 red alder clones from 10 provenances (two clones per provenance). Phenology and quality of red alder leaves were analyzed to determine if budburst, leaf chemical content, water content or physical traits are determinants of WTC preference. Alder clones differed in percent leaf area eaten by WTC and in leaf defense traits. The concentrations of total phenolics, condensed tannin and the diarylheptanoid oregonin negatively correlated with the percent leaf area eaten by the caterpillars, and a potential threshold was observed, above which the concentration of each of the chemicals appeared to reduce WTC feeding. Particularly, foliar concentrations of oregonin greater than 20 % of leaf dry weight were consistently associated with reduced feeding. The effects of oregonin concentration in red alder leaves on tent caterpillar feeding is a novel finding.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

The western redcedar genome reveals low genetic diversity in a self-compatible conifer.

We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one of the most complete genome assemblies for a conifer. Population genomic analysis revealed WRC to be one of the most genetically depauperate wild plant species, with an effective population size of approximately 300 and no significant genetic differentiation across its geographic range. Nucleotide diversity, π, is low for a continuous tree species, with many loci showing zero diversity, and the ratio of π at zero- to fourfold degenerate sites is relatively high (approximately 0.33), suggestive of weak purifying selection. Using an array of genetic lines derived from up to five generations of selfing, we explored the relationship between genetic diversity and mating system. Although overall heterozygosity was found to decline faster than expected during selfing, heterozygosity persisted at many loci, and nearly 100 loci were found to deviate from expectations of genetic drift, suggestive of associative overdominance. Nonreference alleles at such loci often harbor deleterious mutations and are rare in natural populations, implying that balanced polymorphisms are maintained by linkage to dominant beneficial alleles. This may account for how WRC remains responsive to natural and artificial selection, despite low genetic diversity