Estimation of genetic parameters for height using spatial analysis in Tsuga heterophylla full-sibling family trials in British Columbia

Non-spatial and spatial analyses were carried out to study the effects on genetic parameters in ten-year height growth data across two series of 10 large second-generation full-sib progeny trials of western hemlock [Tsuga heterophylla (Raf.) Sarg.] in British Columbia. To account for different and complex patterns of environmental heterogeneity, spatial single trial analyses were conducted using an individual-tree mixed model with a two-dimensional smoothing surface with tensor product of B-spline bases. The spatial single trial analysis, in all cases, showed sizeable lower Deviance Information Criterion values relative to the non-spatial analysis. Also, fitting a surface displayed a consistent reduction in the posterior mean as well as a decrease in the standard deviations of error variance, no appreciable changes in the additive variance, an increase of individual narrow-sense heritability, and accuracy of breeding values. The tensor product of cubic basis functions of B-spline based on a mixed model framework does provide a useful new alternative to model different and complex patterns of spatial variability within sites in forest genetic trials. Individual narrow-sense heritabilities estimates from the spatial single trial analyses were low (average of 0.06), but typical of this species. Estimated dominance relative to additive variances were unstable across sites (from 0.00 to 1.59). The implications of these estimations will be discussed with respect to the western hemlock genetic improvement program in British Columbia.Fil: Cappa, Eduardo Pablo. British Columbia Ministry of Forests and Range; Canadá. University of British Columbia; Canadá. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Yanchuk, A. D.. British Columbia Ministry of Forests and Range; CanadáFil: Cartwright, C. V.. British Columbia Ministry of Forests and Range; Canad

Direct and Competition Additive Effects in Tree Breeding: Bayesian Estimation From an Individual Tree Mixed Model

An individual tree model with additive direct and competition effects is introduced to account for competitive effects in forest genetics evaluation. The mixed linear model includes fixed effects as well as direct and competition breeding values plus permanent environmental effects. Competition effects, either additive or environmental, are identified in the phenotype of a competitor tree by means of ‘intensity of competition’ elements (IC), which are non-zero elements of the incidence matrix of the additive competition effects. The ICs are inverse function of the distance and the number of competing individuals, either row-column wise or diagonally. The ICs allow standardization of the variance of competition effects in the phenotypic variance of any individual tree, so that the model accounts for unequal number of neighbors. Expressions are obtained for the bias in estimating additive variance using the covariance between half-sibs, when ignoring competition effects for row-plot designs and for single-tree plot designs. A data set of loblolly pines on growth at breast height is used to estimate the additive variances of direct and competition effects, the covariance between both effects, and the variance of permanent environmental effects using a Bayesian method via Gibbs sampling and Restricted Maximum Likelihood procedures (REML) via the Expectation-Maximization (EM) algorithm. No problem of convergence was detected with the model and ICs used when compared to what has been reported in the animal breeding literature for such models. Posterior means (standard error) of the estimated parameters were σˆ 2 Ad = 12.553 (1.447), σˆ 2 Ac = 1.259 (0.259), σˆ AdAc = –3.126 (0.492), σˆ 2 p = 1.186 (0.289), and σˆ 2 e = 5.819 (1.07). Leaving permanent environmental competition effects out of the model may bias the predictions of direct breeding values. Results suggest that selection for increasing direct growth while keeping a low level of competition is feasible.Fil: Cappa, Eduardo Pablo. Ministerio de Ciencia, Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica. Fondo para la Investigación Científica y Tecnológica; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Performance of alternative spatial models in empirical Douglas-fir and simulated datasets

Key message: Based on an empirical dataset originating from the French Douglas-fir breeding program, we showed that the bidimensional autoregressive and the two-dimensional P-spline regression spatial models clearly outperformed the classical block model, in terms of both goodness of fit and predicting ability. In contrast, the differences between both spatial models were relatively small. In general, results from simulated data were well in agreement with those from empirical data. Context: Environmental (and/or non-environmental) global and local spatial trends can lead to biases in the estimation of genetic parameters and the prediction of individual additive genetic effects. Aims: The goal of the present research is to compare the performances of the classical a priori block design (block) and two different a posteriori spatial models: a bidimensional first-order autoregressive process (AR) and a bidimensional P-spline regression (splines). Methods: Data from eight trials of the French Douglas-fir breeding program were analyzed using the block, AR, and splines models, and data from 8640 simulated datasets corresponding to 180 different scenarios were also analyzed using the two a posteriori spatial models. For each real and simulated dataset, we compared the fitted models using several performance metrics. Results: There is a substantial gain in accuracy and precision in switching from classical a priori blocks design to any of the two alternative a posteriori spatial methodologies. However, the differences between AR and splines were relatively small. Simulations, covering a larger though oversimplified hypothetical setting, seemed to support previous empirical findings. Both spatial approaches yielded unbiased estimations of the variance components when they match with the respective simulation data. Conclusion: In practice, both spatial models (i.e., AR and splines) suitably capture spatial variation. It is usually safe to use any of them. The final choice could be driven solely by operational reasons

Improving genetic analysis of corymbia citriodora subsp. variegata with single- And multiple-trait spatial-competition models

Environmental heterogeneity and/or genetic and environmental competition were quantified on two growth traits, diameter at breast height and total height, and wood density in a progeny trial of Corymbia citriodora subsp. variegata. Three single-trait mixed models with random spatial and/or competition effects were compared to a standard analysis by analyzing fit, dispersion parameters, accuracy of breeding values, genetic gains, and ranking of trees. In addition, a multiple-trait spatial-competition model was fitted to estimate correlations among direct and indirect additive genetic effects, and to explore relations between traits. Single-trait analyses with spatial and/or competition effects outperformed the standard model. However, the performance of these models depended on the sensitivity of each trait to detect each effect. Direct-indirect genetic correlations from the multiple-trait spatial-competition model showed inverse and strong relations among growth traits and wood density, suggesting that growth traits can be affected by competition and environmental heterogeneity, but also wood density might be influenced by these effects. The approach proposed was useful to improve the genetic analysis of the species as well as to gain an understanding of the genetic relations between traits under the influence of environmental heterogeneity and competition.Fil: Hernández, Mariano Agustín. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; ArgentinaFil: López, Juan Adolfo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; ArgentinaFil: Cappa, Eduardo Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; Argentin

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

Genetic parameter estimation for Ilex paraguariensis St. Hill. in Argentina using spatial analysis

Spatial and non-spatial analyses were conducted to estimate genetic parameters for the traits leaf mass weight (LMW), crown height (CH), crown diameter (CD), and crown volume (CV) for ages between 21 and 27 in 10 half-sib progeny trials of Ilex paraguariensis St. Hill. The spatial model gave a better fit than the base model in 87.2% of the analysed dataset, with reductions in residual and plot variances. The narrow-sense heritability estimates ranged from low to moderate for LMW trait (0.01 to 0.43) and from low to high for crown traits (0.08 to 0.74). The additive genetic coefficient of variation for the LMW trait was over 12.4%, while for CH and CD it was below 10%. Generally, the additive genetic correlations (râ) between the LMW evaluations and between LMW and crown traits were greater than 0.70.Fil: Schoffen, Vanesa Carolina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Misiones. Estación Experimental Agropecuaria Cerro Azul; ArgentinaFil: Cappa, Eduardo Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales; ArgentinaFil: Gauchat, María Elena. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Misiones. Estación Experimental Agropecuaria Montecarlo; ArgentinaFil: Belaber, Ector Cesar. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Misiones. Estación Experimental Agropecuaria Montecarlo; Argentin

Evaluación del crecimiento y estado nutricional de híbridos interespecíficos de Eucalyptus sometidos a estrés por anegamiento y salinidad

57-68Se realizó un experimento en condiciones controladas durante 90 días para estudiar la respuesta de dos combinaciones híbridas de Eucalyptus (Eucalyptus grandis x Eucalyptus camaldulensis y Eucalyptus grandis x Eucalyptus tereticornis), sometidos al efecto de 3 niveles de agua (A): 1) riego normal; 2) ciclos de 30 días de anegamiento seguido de 15 días de riego normal y 3) napa de agua permanente. A su vez, los ratamientos A2 y A3 se combinaron con 3 niveles de salinidad (CE): < 4 (control), 6 y 12 dS m-1. Quincenalmente se midió la altura y el diámetro del cuello de las plantas y se registró la mortalidad. A los 83 días se determinó materia seca en hojas, ramas y tallos, la concentración de macronutrientes foliares y se caracterizó la fertilidad del suelo de las macetas. El crecimiento de las plantas y la materia seca disminuyó significativamente con el aumento de la salinidad asociada a la inundación y la napa salina alta. La concentración foliar de Na aumentó y descendió la de K en los tratamientos con salinidad (moderada y alta). El efecto sobre el crecimiento y la biomasa fue menos adverso cuando la solución no fue salina. La solución salina agregada al suelo desplazó las bases intercambiables (Ca+Mg) y aumentó el Na y el PSI, pero la CE del suelo no superó los 4 dS m-1. El híbrido E. grandis x E. camaldulensis mostró mayores crecimientos, concentraciones foliares y biomasa en comparación con E. grandis x E. tereticornis. La menor tolerancia de este híbrido también se evidenció por la mortalidad más temprana

Early rooting and flooding tolerance in cuttings from a Populus deltoides full-sib family under greenhouse conditions

Eastern cottonwood (Populus deltoides Bartr. ex Marsh.) is an important forest tree, with elite genotypes propagated mainly as unrooted dormant cuttings. Several areas where P. deltoides is planted periodically experience flooding episodes. The aims of this work were to analyze the early rooting capability and flooding tolerance of a P. deltoides full-sib family, and to identify growth, wood, and leaf traits that correlate with flooding tolerance. We analyzed the early rooting capability of the parental genotypes and 30 clones from the F1 generation under greenhouse conditions. The rooting percentage of the cuttings ranged from 50% to 100%. There was a positive genetic correlation between shoot weight and root traits (number, biomass, and total length). In a separate experiment, 2-month-old plants growing in pots from the same genotypes were subjected to two treatments: watering (control) and flooding for 35 days. Most genotypes showed an intermediate flooding tolerance with respect to the parental clones. Height, diameter, growth rate, biomass, plant leaf area, leaf number, and leaf increase rate had a positive phenotypic correlation with flooding tolerance, while wood density did not. Height and diameter are traits recommended for selection because they correlate with flooding tolerance, are easy to measure, and have moderate to high narrow sense heritability.Fil: Rodríguez, María Emilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; ArgentinaFil: Mozo, Irina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; ArgentinaFil: Cortizo, Silvia. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria Delta del Paraná; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; ArgentinaFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; ArgentinaFil: Luquez, Virginia Martha Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentin

Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca

Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce (Picea glauca) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm.Inst. de Recursos BiológicosFil: Rateliffe, Blaise. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: El-Dien, Omnia Gamal. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá. Alexandria University. Faculty of Pharmacy. Pharmacognosy Department; EgiptoFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Porth, Ilga. Université Laval Québec. Faculté de Foresterie, de Géographie et Géomatique. Départment des Sciences du Bois et de la Forêt; CanadáFil: Klapste, Jaroslav. Czech University of Life Sciences Prague. Faculty of Forestry and Wood Sciences. Department of Genetics and Physiology of Forest Trees; República Checa. Scion (New Zealand Forest Research Institute Ltd.); Nueva ZelandaFil: El-Kassaby, Yousry A. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados Unido

Unweaving the population structure and genetic diversity of Canadian shrub willow

Perennial shrub willow are increasingly being promoted in short-rotation coppice systems as biomass feedstocks, for phytoremediation applications, and for the diverse ecosystem services that can accrue. This renewed interest has led to widespread willow cultivation, particularly of non-native varieties. However, Canadian willow species have not been widely adopted and their inherent diversity has not yet been thoroughly investigated. In this study, 324 genotypes of Salix famelica and Salix eriocephala collected from 33 sites of origin were analyzed using 26,016 single nucleotide polymorphisms to reveal patterns of population structure and genetic diversity. Analyses by Bayesian methods and principal component analysis detected five main clusters that appeared to be largely shaped by geoclimatic variables including mean annual precipitation and the number of frost-free days. The overall observed (HO) and expected (HE) heterozygosity were 0.126 and 0.179, respectively. An analysis of molecular variance revealed that the highest genetic variation occurred within genotypes (69%), while 8% of the variation existed among clusters and 23% between genotypes within clusters. These findings provide new insights into the extent of genetic variation that exists within native shrub willow species which could be leveraged in pan-Canadian willow breeding programs.Fil: Murphy, Emily K. University of British Columbia. Faculty of Forestry. Department of Wood Science; CanadáFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Soolanayakanahally, Raju Y. Agriculture and Agri-Food Canada. Indian Head Research Farm; Canadá. Agriculture and Agri-Food Canada. Saskatoon Research and Development Centre; Canadá.Fil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Parkin, Isobel A.P. Agriculture and Agri-Food Canada. Saskatoon Research and Development Centre; Canadá.Fil: Schroeder, William R. Agriculture and Agri-Food Canada. Indian Head Research Farm; CanadáFil: Mansfield, Shawn D. University of British Columbia. Faculty of Forestry. Department of Wood Science; Canad