Efficient genomics-based 'end-to-end' selective tree breeding framework.

Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingencies and concerns. Here, we introduce an "end-to-end" selective tree breeding framework that: (1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, (2) generates unprecedented resolution of genealogical relationships among tested individuals, and (3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals' breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits' correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method's superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.

Genomic evaluation for breeding and genetic management in Cordia africana, a multipurpose tropical tree species.

BACKGROUND: Planting tested forest reproductive material is crucial to ensure the increased resilience of intensively managed productive stands for timber and wood product markets under climate change scenarios. Single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) analysis is a cost-effective option for using genomic tools to enhance the accuracy of predicted breeding values and genetic parameter estimation in forest tree species. Here, we tested the efficiency of ssGBLUP in a tropical multipurpose tree species, Cordia africana, by partial population genotyping. A total of 8070 trees from three breeding seedling orchards (BSOs) were phenotyped for height. We genotyped 6.1% of the phenotyped individuals with 4373 single nucleotide polymorphisms. The results of ssGBLUP were compared with pedigree-based best linear unbiased prediction (ABLUP) and genomic best linear unbiased prediction (GBLUP), based on genetic parameters, theoretical accuracy of breeding values, selection candidate ranking, genetic gain, and predictive accuracy and prediction bias. RESULTS: Genotyping a subset of the study population provided insights into the level of relatedness in BSOs, allowing better genetic management. Due to the inbreeding detected within the genotyped provenances, we estimated genetic parameters both with and without accounting for inbreeding. The ssGBLUP model showed improved performance in terms of additive genetic variance and theoretical breeding value accuracy. Similarly, ssGBLUP showed improved predictive accuracy and lower bias than the pedigree-based relationship matrix (ABLUP). CONCLUSIONS: This study of C. africana, a species in decline due to deforestation and selective logging, revealed inbreeding depression. The provenance exhibiting the highest level of inbreeding had the poorest overall performance. The use of different relationship matrices and accounting for inbreeding did not substantially affect the ranking of candidate individuals. This is the first study of this approach in a tropical multipurpose tree species, and the analysed BSOs represent the primary effort to breed C. africana.

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.

Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine.

BACKGROUND: Genomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to identify alleles or genomic regions of complex traits in forest trees species. Here, 1490 interior lodgepole pine (Pinus contorta Dougl. ex. Loud. var. latifolia Engelm) trees from four open-pollinated progeny trials were genotyped with 25,099 SNPs, and phenotyped for 15 growth, wood quality, pest resistance, drought tolerance, and defense chemical (monoterpenes) traits. The main objectives of this study were to: (1) identify genetic markers associated with these traits and determine their genetic architecture, and to compare the marker detected by single- (ST) and multiple-trait (MT) GWA models; (2) evaluate and compare the accuracy and control of bias of the genomic predictions for these traits underlying different ST and MT parametric and non-parametric GP methods. GWA, ST and MT analyses were compared using a linear transformation of genomic breeding values from the respective genomic best linear unbiased prediction (GBLUP) model. GP, ST and MT parametric and non-parametric (Reproducing Kernel Hilbert Spaces, RKHS) models were compared in terms of prediction accuracy (PA) and control of bias. RESULTS: MT-GWA analyses identified more significant associations than ST. Some SNPs showed potential pleiotropic effects. Averaging across traits, PA from the studied ST-GP models did not differ significantly from each other, with generally a slight superiority of the RKHS method. MT-GP models showed significantly higher PA (and lower bias) than the ST models, being generally the PA (bias) of the RKHS approach significantly higher (lower) than the GBLUP. CONCLUSIONS: The power of GWA and the accuracy of GP were improved when MT models were used in this lodgepole pine population. Given the number of GP and GWA models fitted and the traits assessed across four progeny trials, this work has produced the most comprehensive empirical genomic study across any lodgepole pine population to date.

Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program.

Tree improvement programs often focus on improving productivity-related traits; however, under present climate change scenarios, climate change-related (adaptive) traits should also be incorporated into such programs. Therefore, quantifying the genetic variation and correlations among productivity and adaptability traits, and the importance of genotype by environment interactions, including defense compounds involved in biotic and abiotic resistance, is essential for selecting parents for the production of resilient and sustainable forests. Here, we estimated quantitative genetic parameters for 15 growth, wood quality, drought resilience, and monoterpene traits for Picea glauca (Moench) Voss (white spruce). We sampled 1,540 trees from three open-pollinated progeny trials, genotyped with 467,224 SNP markers using genotyping-by-sequencing (GBS). We used the pedigree and SNP information to calculate, respectively, the average numerator and genomic relationship matrices, and univariate and multivariate individual-tree models to obtain estimates of (co)variance components. With few site-specific exceptions, all traits examined were under genetic control. Overall, higher heritability estimates were derived from the genomic- than their counterpart pedigree-based relationship matrix. Selection for height, generally, improved diameter and water use efficiency, but decreased wood density, microfibril angle, and drought resistance. Genome-based correlations between traits reaffirmed the pedigree-based correlations for most trait pairs. High and positive genetic correlations between sites were observed (average 0.68), except for those pairs involving the highest elevation, warmer, and moister site, specifically for growth and microfibril angle. These results illustrate the advantage of using genomic information jointly with productivity and adaptability traits, and defense compounds to enhance tree breeding selection for changing climate.

Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP.

Modeling environmental spatial heterogeneity can improve the efficiency of forest tree genomic evaluation. Furthermore, genotyping costs can be lowered by reducing the number of markers needed. We investigated the impact on variance components, breeding value accuracy, and bias of two phenotypic data adjustments (experimental design and autoregressive spatial models), and a relationship matrix calculated from a subset of markers selected for their ability to infer ancestry. Using a multiple-trait multiple-site single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) approach, four scenarios (2 phenotype adjustments × 2 marker sets) were applied to diameter at breast height (DBH), height (HT), and resistance to western gall rust (WGR) in four open-pollinated progeny trials of lodgepole pine, with 1490 (out of 11,188) trees genotyped with 25,099 SNPs. As a control, we fitted the conventional ABLUP model using pedigree information. The highest heritability estimates were achieved for the ABLUP followed closely by the ssGBLUP with the full marker set and using the spatial phenotype adjustments. The highest predictive ability was obtained by using a reduced marker subset (8000 SNPs) when either the spatial (DBH: 0.429, and WGR: 0.513) or design (HT: 0.467) phenotype corrections were used. No significant difference was detected in prediction bias among the six fitted models, and all values were close to 1 (0.918-1.014). Results demonstrated that selecting informative markers, such as those capturing ancestry, can improve the predictive ability. The use of spatial correlation structure increased traits' heritability and reduced prediction bias, while increases in predictive ability were trait-dependent.

Single-step genomic prediction of Eucalyptus dunnii using different identity-by-descent and identity-by-state relationship matrices.

Genomic selection based on the single-step genomic best linear unbiased prediction (ssGBLUP) approach is becoming an important tool in forest tree breeding. The quality of the variance components and the predictive ability of the estimated breeding values (GEBV) depends on how well marker-based genomic relationships describe the actual genetic relationships at unobserved causal loci. We investigated the performance of GEBV obtained when fitting models with genomic covariance matrices based on two identity-by-descent (IBD) and two identity-by-state (IBS) relationship measures. Multiple-trait multiple-site ssGBLUP models were fitted to diameter and stem straightness in five open-pollinated progeny trials of Eucalyptus dunnii, genotyped using the EUChip60K. We also fitted the conventional ABLUP model with a pedigree-based covariance matrix. Estimated relationships from the IBD estimators displayed consistently lower standard deviations than those from the IBS approaches. Although ssGBLUP based in IBS estimators resulted in higher trait-site heritabilities, the gain in accuracy of the relationships using IBD estimators has resulted in higher predictive ability and lower bias of GEBV, especially for low-heritability trait-site. ssGBLUP based on IBS and IBD approaches performed considerably better than the traditional ABLUP. In summary, our results advocate the use of the ssGBLUP approach jointly with the IBD relationship matrix in open-pollinated forest tree evaluation.

Quantitative genetic parameters for growth and wood properties in Eucalyptus "urograndis" hybrid using near-infrared phenotyping and genome-wide SNP-based relationships.

A thorough understanding of the heritability, genetic correlations and additive and non-additive variance components of tree growth and wood properties is a requisite for effective tree breeding. This knowledge is essential to maximize genetic gain, that is, the amount of increase in trait performance achieved annually through directional selection. Understanding the genetic attributes of traits targeted by breeding is also important to sustain decade-long genetic progress, that is, the progress made by increasing the average genetic value of the offspring as compared to that of the parental generation. In this study, we report quantitative genetic parameters for fifteen growth, wood chemical and physical traits for the world-famous Eucalyptus urograndis hybrid (E. grandis × E. urophylla). These traits directly impact the optimal use of wood for cellulose pulp, paper, and energy production. A population of 1,000 trees sampled in a progeny trial was phenotyped directly or following the development and use of near-infrared spectroscopy calibration models. Trees were genotyped with 33,398 SNPs and 24,001 DArT-seq genome-wide markers and genomic realized relationship matrices (GRM) were used for parameter estimation with an individual-tree additive-dominant mixed model. Wood chemical properties and wood density showed stronger genetic control than growth, cellulose and fiber traits. Additive effects are the main drivers of genetic variation for all traits, but dominance plays an equally or more important role for growth, singularly in this hybrid. GRM´s with >10,000 markers provided stable relationships estimates and more accurate parameters than pedigrees by capturing the full genetic relationships among individuals and disentangling the non-additive from the additive genetic component. Low correlations between growth and wood properties indicate that simultaneous selection for wood traits can be applied with minor effects on genetic gain for growth. Conversely, moderate to strong correlations between wood density and chemical traits exist, likely due to their interdependency on cell wall structure such that responses to selection will be connected for these traits. Our results illustrate the advantage of using genome-wide marker data to inform tree breeding in general and have important consequences for operational breeding of eucalypt urograndis hybrids.

Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP.

Genomic Best Linear Unbiased Prediction (GBLUP) in tree breeding typically only uses information from genotyped trees. However, information from phenotyped but non-genotyped trees can also be highly valuable. The single-step GBLUP approach (ssGBLUP) allows genomic prediction to take into account both genotyped and non-genotyped trees simultaneously in a single evaluation. In this study, we investigated the advantage, in terms of breeding value accuracy and bias, of including phenotypic observation from non-genotyped trees in a standard tree GBLUP evaluation. We compared the efficiency of the conventional pedigree-based (ABLUP), GBLUP and ssGBLUP approaches to evaluate eight growth and wood quality traits in a Eucalyptus hybrid population, genotyped with 33,398 single nucleotide polymorphisms (SNPs) using the EucHIP60k. Theoretical accuracies, predictive ability and bias were calculated by ten-fold cross validation on all traits. The use of additional phenotypic information from non-genotyped trees by means of ssGBLUP provided higher predictive ability (from 37% to 75%) and lower prediction bias (from 21% to 73%) for the genetic component of non-phenotyped but genotyped trees when compared to GBLUP. The increase (decrease) in the prediction accuracy (bias) became stronger as trait heritability decreased. We concluded that ssGBLUP is a promising breeding tool to improve accuracies and bias over classical GBLUP for genomic evaluation in Eucalyptus breeding practice.

Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding.

Forest tree breeding has been successful at delivering genetically improved material for multiple traits based on recurrent cycles of selection, mating, and testing. However, long breeding cycles, late flowering, variable juvenile-mature correlations, emerging pests and diseases, climate, and market changes, all pose formidable challenges. Genetic dissection approaches such as quantitative trait mapping and association genetics have been fruitless to effectively drive operational marker-assisted selection (MAS) in forest trees, largely because of the complex multifactorial inheritance of most, if not all traits of interest. The convergence of high-throughput genomics and quantitative genetics has established two new paradigms that are changing contemporary tree breeding dogmas. Genomic selection (GS) uses large number of genome-wide markers to predict complex phenotypes. It has the potential to accelerate breeding cycles, increase selection intensity and improve the accuracy of breeding values. Realized genomic relationships matrices, on the other hand, provide innovations in genetic parameters' estimation and breeding approaches by tracking the variation arising from random Mendelian segregation in pedigrees. In light of a recent flow of promising experimental results, here we briefly review the main concepts, analytical tools and remaining challenges that currently underlie the application of genomics data to tree breeding. With easy and cost-effective genotyping, we are now at the brink of extensive adoption of GS in tree breeding. Areas for future GS research include optimizing strategies for updating prediction models, adding validated functional genomics data to improve prediction accuracy, and integrating genomic and multi-environment data for forecasting the performance of genetic material in untested sites or under changing climate scenarios. The buildup of phenotypic and genome-wide data across large-scale breeding populations and advances in computational prediction of discrete genomic features should also provide opportunities to enhance the application of genomics to tree breeding.

Genomic-based multiple-trait evaluation in Eucalyptus grandis using dominant DArT markers.

We investigated the impact of combining the pedigree- and genomic-based relationship matrices in a multiple-trait individual-tree mixed model (a.k.a., multiple-trait combined approach) on the estimates of heritability and on the genomic correlations between growth and stem straightness in an open-pollinated Eucalyptus grandis population. Additionally, the added advantage of incorporating genomic information on the theoretical accuracies of parents and offspring breeding values was evaluated. Our results suggested that the use of the combined approach for estimating heritabilities and additive genetic correlations in multiple-trait evaluations is advantageous and including genomic information increases the expected accuracy of breeding values. Furthermore, the multiple-trait combined approach was proven to be superior to the single-trait combined approach in predicting breeding values, in particular for low-heritability traits. Finally, our results advocate the use of the combined approach in forest tree progeny testing trials, specifically when a multiple-trait individual-tree mixed model is considered.

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.

Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus.

The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model ( UMM ) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S:G ratio), a key wood property trait. The two DArT markers associated with S:G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly heterozygous forest trees, and provides additional insights into the nature of complex quantitative traits in Eucalyptus.

Breeding without breeding: is a complete pedigree necessary for efficient breeding?

Complete pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for selection and deployment decisions. DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring. Here, we report on the efficacy of a breeding concept called "Breeding without Breeding" (BwB) that circumvents artificial matings, focusing instead on a subset of randomly sampled, maternally known but paternally unknown offspring to delineate their paternal parentage. We then generate the information needed to rank those offspring and their paternal parents, using a combination of complete (full-sib: FS) and incomplete (half-sib: HS) analyses of the constructed pedigrees. Using a random sample of wind-pollinated offspring from 15 females (seed donors), growing in a 41-parent western larch population, BwB is evaluated and compared to two commonly used testing methods that rely on either incomplete (maternal half-sib, open-pollinated: OP) or complete (FS) pedigree designs. BwB produced results superior to those from the incomplete design and virtually identical to those from the complete pedigree methods. The combined use of complete and incomplete pedigree information permitted evaluating all parents, both maternal and paternal, as well as all offspring, a result that could not have been accomplished with either the OP or FS methods alone. We also discuss the optimum experimental setting, in terms of the proportion of fingerprinted offspring, the size of the assembled maternal and paternal half-sib families, the role of external gene flow, and selfing, as well as the number of parents that could be realistically tested with BwB.