Building resiliency in conifer forests: Interior spruce crosses among weevil resistant and susceptible parents produce hybrids appropriate for multi-trait selection.

Tree planting programs now need to consider climate change increasingly, therefore, the resistance to pests plays an essential role in enabling tree adaptation to new ranges through tree population movement. The weevil Pissodes strobi (Peck) is a major pest of spruces and substantially reduces lumber quality. We revisited a large Interior spruce provenance/progeny trial (2,964 genotypes, 42 families) of varying susceptibility, established in British Columbia.

High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata.

Background: The growing availability of genomic resources in radiata pine paves the way for significant advances in fundamental and applied genomic research. We constructed robust high-density linkage maps based on exome-capture genotyping in two F populations, and used these populations to perform quantitative trait locus (QTL) scans, genomic prediction and quantitative analyses of genetic architecture for key traits targeted by tree improvement programmes.

Results: Our mapping approach used probabilistic error correction of the marker data, followed by an iterative approach based on stringent parameters.

Genomic selection for resistance to mammalian bark stripping and associated chemical compounds in radiata pine.

The integration of genomic data into genetic evaluations can facilitate the rapid selection of superior genotypes and accelerate the breeding cycle in trees. In this study, 390 trees from 74 control-pollinated families were genotyped using a 36K Axiom SNP array. A total of 15,624 high-quality SNPs were used to develop genomic prediction models for mammalian bark stripping, tree height, and selected primary and secondary chemical compounds in the bark.

Chasing genetic correlation breakers to stimulate population resilience to climate change.

Global climate change introduces new combinations of environmental conditions, which is expected to increase stress on plants. This could affect many traits in multiple ways that are as yet unknown but will likely require the modification of existing genetic relationships among functional traits potentially involved in local adaptation. Theoretical evolutionary studies have determined that it is an advantage to have an excess of recombination events under heterogeneous environmental conditions.

Genetic Variation in Drought-Tolerance Traits and Their Relationships to Growth in D. Don Under Water Stress.

The selection of drought-tolerant genotypes is globally recognized as an effective strategy to maintain the growth and survival of commercial tree species exposed to future drought periods. New genomic selection tools that reduce the time of progeny trials are required to substitute traditional tree breeding programs. We investigated the genetic variation of water stress tolerance in New Zealand-grown D.

Genetic Variation for Economically Important Traits in in New Zealand.

Increasing productivity and tolerance against cypress canker disease is an important goal in the Mexican white cypress breeding program in New Zealand, and screening has been in place since 1983. Cypress canker disease is caused by and , the current study presents the results of two progeny trials within the breeding program in the North Island of New Zealand. The trials were established as open-pollinated progeny tested and were assessed for diameter at breast height, branch size, canker severity score, malformation score, and stem straightness score and acceptability score.

Marker Selection in Multivariate Genomic Prediction Improves Accuracy of Low Heritability Traits.

Multivariate analysis using mixed models allows for the exploration of genetic correlations between traits. Additionally, the transition to a genomic based approach is simplified by substituting classic pedigrees with a marker-based relationship matrix. It also enables the investigation of correlated responses to selection, trait integration and modularity in different kinds of populations.

Quercus species divergence is driven by natural selection on evolutionarily less integrated traits.

Functional traits are organismal attributes that can respond to environmental cues, thereby providing important ecological functions. In addition, an organism's potential for adaptation is defined by the patterns of covariation among groups of functionally related traits. Whether an organism is evolutionarily constrained or has the potential for adaptation is based on the phenotypic integration or modularity of these traits.

Indication of Quantitative Multiple Disease Resistance to Foliar Pathogens in in New Zealand.

Increasing resistance against foliar diseases is an important goal in the D.Don breeding program in New Zealand, and screening for resistance has been in place for some time, since the late 1960s. The current study presents results of four progeny trials within the breeding program to investigate whether multiple disease resistance could be detected against three different needle diseases in : needle blight (DNB) caused by , needle cast (CNC) caused by , and red needle cast (RNC) caused by Four progeny trials in the North Island of New Zealand were available to estimate heritabilities and between-trait genetic correlations.

Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species.

Background: The presupposition of genomic selection (GS) is that predictive accuracies should be based on population-wide linkage disequilibrium (LD). However, in species with large, highly complex genomes the limitation of marker density may preclude the ability to resolve LD accurately enough for GS. Here we investigate such an effect in two conifer species with ~ 20 Gbp genomes, Douglas-fir (Pseudotsuga menziesii Mirb.

Effect of trait's expression level on single-step genomic evaluation of resistance to Dothistroma needle blight.

Background: Many conifer breeding programs are paying increasing attention to breeding for resistance to needle disease due to the increasing importance of climate change. Phenotyping of traits related to resistance has many biological and temporal constraints that can often confound the ability to achieve reliable phenotypes and consequently, reliable genetic progress. The development of next generation sequencing platforms has also enabled implementation of genomic approaches in species lacking robust reference genomes.

Genomic Diversity Evaluation of Germplasm for Rare Variant Genetic Association Studies.

Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale.

Genotype-by-environment interaction in coast redwood outside natural distribution - search for environmental cues.

Background: Effective matching of genotypes and environments is required for the species to reach optimal productivity and act effectively for carbon sequestration. A common garden experiment across five different environments was undertaken to assess genotype x environment interaction (GxE) of coast redwood in order to understand the performance of genotypes across environments.

Results: The quantitative genetic analysis discovered no GxE between investigated environments for diameter at breast height (DBH).

Genomic selection for non-key traits in radiata pine when the documented pedigree is corrected using DNA marker information.

Background: Non-key traits (NKTs) in radiata pine (Pinus radiata D. Don) refer to traits other than growth, wood density and stiffness, but still of interest to breeders. Branch-cluster frequency, stem straightness, external resin bleeding and internal checking are examples of such traits and are targeted for improvement in radiata pine research programmes.

Modelling of population structure through contemporary groups in genetic evaluation.

Background: Forest trees can occupy extensive geography and environmentally highly variable areas which result in high genetic variability in the direction of pressure from natural selection. At the same time, the majority of conifer species are wind-pollinated from both short and long distances, resulting in wide-spread gene flow, which can lead to maladaptation to local conditions. Quantitative analyses of provenance/progeny tests correct for genetic differences between populations to ensure unbiased genetic parameters are obtained.

A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata.

Development of genome-wide resources for application in genomic selection or genome-wide association studies, in the absence of full reference genomes, present a challenge to the forestry industry, where longer breeding cycles could benefit from the accelerated selection possible through marker-based breeding value predictions. In particular, large conifer megagenomes require a strategy to reduce complexity, whilst ensuring genome-wide coverage is achieved. Using a transcriptome-based reference template, we have successfully developed a high density exome capture genotype-by-sequencing panel for radiata pine (Pinus radiata D.

Evolutionary potential of a widespread clonal grass under changing climate.

Adaptive responses are probably the most effective long-term responses of populations to climate change, but they require sufficient evolutionary potential upon which selection can act. This requires high genetic variance for the traits under selection and low antagonizing genetic covariances between the different traits. Evolutionary potential estimates are still scarce for long-lived, clonal plants, although these species are predicted to dominate the landscape with climate change.

A role for SPEECHLESS in the integration of leaf stomatal patterning with the growth vs disease trade-off in poplar.

Occurrence of stomata on both leaf surfaces (amphistomaty) promotes higher stomatal conductance and photosynthesis while simultaneously increasing exposure to potential disease agents in black cottonwood (Populus trichocarpa). A genome-wide association study (GWAS) with 2.2M single nucleotide polymorphisms generated through whole-genome sequencing found 280 loci associated with variation in adaxial stomatal traits, implicating genes regulating stomatal development and behavior.

Genomic selection of juvenile height across a single-generational gap in Douglas-fir.

Here, we perform cross-generational GS analysis on coastal Douglas-fir (Pseudotsuga menziesii), reflecting trans-generational selective breeding application. A total of 1321 trees, representing 37 full-sib F families from 3 environments in British Columbia, Canada, were used as the training population for (1) EBVs (estimated breeding values) of juvenile height (HTJ) in the F generation predicting genomic EBVs of HTJ of 136 individuals in the F generation, (2) deregressed EBVs of F HTJ predicting deregressed genomic EBVs of F HTJ, (3) F mature height (HT35) predicting HTJ EBVs in F, and (4) deregressed F HT35 predicting genomic deregressed HTJ EBVs in F. Ridge regression best linear unbiased predictor (RR-BLUP), generalized ridge regression (GRR), and Bayes-B GS methods were used and compared to pedigree-based (ABLUP) predictions.

Author Correction: Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Correction to: Efficiency of genomic prediction across two Eucalyptus nitens seed orchards with different selection histories.

Published online: 6 July 2018This article was originally published under standard licence, but has now been made available under a [CC BY 4.0] license. The PDF and HTML versions of the paper have been modified accordingly.

Effect of Hidden Relatedness on Single-Step Genetic Evaluation in an Advanced Open-Pollinated Breeding Program.

Open-pollinated (OP) mating is frequently used in forest tree breeding due to the relative temporal and financial efficiency of the approach. The trade-off is the lower precision of the estimated genetic parameters. Pedigree/sib-ship reconstruction has been proven as a tool to correct and complete pedigree information and to improve the precision of genetic parameter estimates.

Efficiency of genomic prediction across two Eucalyptus nitens seed orchards with different selection histories.

Genomic selection is expected to enhance the genetic improvement of forest tree species by providing more accurate estimates of breeding values through marker-based relationship matrices compared with pedigree-based methodologies. When adequately robust genomic prediction models are available, an additional increase in genetic gains can be made possible with the shortening of the breeding cycle through elimination of the progeny testing phase and early selection of parental candidates. The potential of genomic selection was investigated in an advanced Eucalyptus nitens breeding population focused on improvement for solid wood production.

Ecological genomics of variation in bud-break phenology and mechanisms of response to climate warming in Populus trichocarpa.

Spring bud-break phenology is a critical adaptive feature common to temperate perennial woody plants. Understanding the molecular underpinnings of variation in bud-break is important for elucidating adaptive evolution and predicting outcomes relating to climate change. Field and controlled growth chamber tests were used to assess population-wide patterns in bud-break from wild-sourced black cottonwood (Populus trichocarpa) genotypes.

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.