Henrik R. Hallingbäck

Genetic parameters for grain angle in 28-year-old Norway spruce progeny trials and their parent seed orchard

Abstract• Sawn wood which acquires twist during drying is a substantial problem for the sawmill industry and is to a large extent caused by spiralled grain in the tree.• In this study, the feasibility of using spiral grain angles as a selection trait in Norway spruce (Picea abies (L.) Karst) tree breeding and the extent of grain angle and its breeding values were investigated. Grain angles under bark and diameter were measured at breast height in three 28-year-old Norway spruce progeny trials and in their parent seed orchard.• The mean grain angle value was 1.76° in the progeny trials and 1.84° in the seed orchard. Estimated genetic standard deviations for grain angle were almost 1°. Progeny trial heritabilities (H2 > 0.3) were larger than the seed orchard heritability (H2 = 0.24). Genotype by environment interaction among the progeny trials was negligible for grain angle. Progeny trial grain angles exhibited genetic correlation with seed orchard grain angles in the range 0.66 to 0.84.• Thus, mature wood grain angles are also under considerable genetic control, raising the opportunity to reduce the occurence of left-grained trees, which are prone to producing twisted wood.Résumé• Les déformations au séchage du bois scié sont un problème majeur pour l’industrie du bois et sont pour une large part causées par l’angle du fil du bois.• Dans cette étude, nous avons étudié la possibilité d’utiliser l’angle du fil du bois comme critère de sélection pour l’amélioration génétique de cette propriété chez l’épicéa commun. Les angles du fil du bois sous écorce ainsi que le diamètre à 1,30 m ont été mesurés dans trois tests de descendances d’épicéa commun âgés de 28 ans et dans un verger à graines où sont localisés les parents.• L’angle moyen du fil du bois était de 1,76° dans les tests de descendances et de 1,84° dans le verger à graines. L’écart-type génétique estimé pour l’angle du fil était de presque 1°. Les héritabilités estimées en tests de descendances (H2 > 0,3) étaient plus fortes que celle obtenue en verger à graines (H2 = 0,24). L’interaction G×E était négligeable entre tests de descendances. Les angles du fil obtenus en tests de descendances montraient une corrélation génétique de 0,66–0,84 avec les angles obtenus en verger à graines.• En conclusion, nous montrons que les angles du fil du bois mature sont sous contrôle génétique fort, ce qui permet d’envisager la réduction de la fréquence d’arbres à fil gauche, très sujets à produire du bois vrillé.

Association mapping in Salix viminalis L. (Salicaceae) – identification of candidate genes associated with growth and phenology

Willow species (Salix) are important as short‐rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker‐assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnäs, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype‐by‐environment interactions (G × E) on trait–marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation ( Radj2 ) explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR < 0.2) with bud burst. The rare homozygous genotype exhibited 0.4–1.0 lower bud burst scores than the other genotype classes on a five‐grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small Radj2 estimates and to considerable G × E interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32–0.61).

Estimation of number and size of QTL effects in forest tree traits

Mapping the genetic architecture of forest tree traits is important in order to understand the evolutionary forces that have shaped these traits and to facilitate the development of genomic-based breeding strategies. We examined the number, size, and distribution of allelic effects influencing eight types of traits using 30 published mapping studies (linkage and association mapping) in forest trees. The sizes of allelic effects, measured as the phenotypic variance explained, generally showed a severely right-skewed distribution. We estimated the numbers of underlying causal effects (nqtl) for different trait categories by improving a method previously developed by Otto and Jones (Genetics 156:2093–2107, 2000). Estimates of nqtl based on association mapping studies were generally higher (median at 643) than those based on linkage mapping (median at 33). Comparisons with simulated linkage and association mapping data suggested that the lower nqtl estimates for the linkage mapping studies could partly be explained by fewer causal loci segregating within the full-sib family populations normally used, but also by the cosegregation of causal loci due to limited recombination. Disease resistance estimates based on linkage mapping studies had the lowest median of four underlying effects, while growth traits based on association mapping had about 580 effects. Theoretically, the capture of 50% of the genetic variation would thus require a population size of about 200 for disease resistance in linkage mapping, while growth traits in association mapping would require about 25,000. The adequacy and reliability of the improved method was successfully verified by applying it to the simulated data.

Functional Multi-Locus QTL Mapping of Temporal Trends in Scots Pine Wood Traits

Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.

Relationships between early assessments of stem and branch properties and sawn timber traits in a Pinus sylvestris progeny trial

Abstract A sample of 162 trees was harvested from a 36-year-old Scots pine (Pinus sylvestris L.) progeny trial to evaluate correlations between early measurements of branch diameter, and other stem and branch traits, with sawn timber traits, and hence their potential utility for predicting wood quality. The sample trees were assigned to three genetic groups of small, medium and large branch diameter, based on parental breeding values. Bottom logs were cut and sawn, and several important traits for the visual quality of the boards were assessed. Phenotypic correlations were then estimated between these traits and measurements of the height, diameter, branch diameter, branch angle, stem crookedness, number of branches and grain angle under bark of the corresponding trees when they were 16 and 36 years old. The diameter of the coarsest knot in the board was correlated with the branch diameter at the age of 16 years (0.50), and there were significant differences in this trait among the genetic branch diameter groups. In addition, the board twist was correlated with the grain angle under bark at the age of 36 years (0.54). Thus, the field assessments of branch diameter and grain angle under bark show relevance for the visual quality of centrally sawn small timber.

Allelic incompatibility can explain female biased sex ratios in dioecious plants

BackgroundBiased sex ratios are common among dioecious plant species despite the theoretical prediction of selective advantage of even sex ratios. Albeit the high prevalence of deviations from even sex ratios, the genetic causes to sex biases are rarely known outside of a few model species. Here we present a mechanism underlying the female biased sex ratio in the dioecious willow species Salix viminalis.ResultsWe compared the segregation pattern of genome-wide single nucleotide polymorphism markers in two contrasting bi-parental pedigree populations, the S3 with even sex ratio and the S5 with a female biased sex ratio. With the segregation analysis and comparison between the two populations, we were able to demonstrate that sex determination and sex ratio distortion are controlled by different genetic mechanisms. We furthermore located the sex ratio distorter locus to a Z/W-gametologous region on chromosome 15, which was in close linkage with the sex determination locus. Interestingly, all males in the population with biased sex ratio have in this sex ratio distorter locus the same genotype, meaning that males with the Z1/Z3-genotype were missing from the population, thereby creating the 2:1 female biased sex ratio.ConclusionsWe attribute the absence of Z1/Z3 males to an allelic incompatibility between maternally and paternally inherited alleles in this sex ratio distorter locus. Due to the tight linkage with the sex determination locus only male individuals are purged from the population at an early age, presumably before or during seed development. We showed that such allelic incompatibility could be stably maintained over evolutionary times through a system of overdominant or pseudooverdominant alleles. Thus, it is possible that the same mechanism generates the female biased sex ratio in natural willow populations.

Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years

Abstract Background and Aims Phenotypic plasticity can affect the geographical distribution of taxa and greatly impact the productivity of crops across contrasting and variable environments. The main objectives of this study were to identify genotype–phenotype associations in key biomass and phenology traits and the strength of phenotypic plasticity of these traits in a short-rotation coppice willow population across multiple years and contrasting environments to facilitate marker-assisted selection for these traits. Methods A hybrid Salix viminalis × (S. viminalis × Salix schwerinii) population with 463 individuals was clonally propagated and planted in three common garden experiments comprising one climatic contrast between Sweden and Italy and one water availability contrast in Italy. Several key phenotypic traits were measured and phenotypic plasticity was estimated as the trait value difference between experiments. Quantitative trait locus (QTL) mapping analyses were conducted using a dense linkage map and phenotypic effects of S. schwerinii haplotypes derived from detected QTL were assessed. Key Results Across the climatic contrast, clone predictor correlations for biomass traits were low and few common biomass QTL were detected. This indicates that the genetic regulation of biomass traits was sensitive to environmental variation. Biomass QTL were, however, frequently shared across years and across the water availability contrast. Phenology QTL were generally shared between all experiments. Substantial phenotypic plasticity was found among the hybrid offspring, that to a large extent had a genetic origin. Individuals carrying influential S. schwerinii haplotypes generally performed well in Sweden but less well in Italy in terms of biomass production. Conclusions The results indicate that specific genetic elements of S. schwerinii are more suited to Swedish conditions than to those of Italy. Therefore, selection should preferably be conducted separately for such environments in order to maximize biomass production in admixed S. viminalis × S. schwerinii populations.

Genetic information from progeny trials: a comparison between progenies generated by open pollination and by controlled crosses

When conifer progenies generated by open pollination are assessed in field tests, it is usually assumed that all progenies of the same mother are true half-sibs. This assumption may be invalid, leading to overestimation of additive genetic variation and heritability and to biased breeding values. From one Scots pine (Pinus sylvestris) and one Norway spruce (Picea abies) seed orchard, containing 28 and 36 parent clones, respectively, progenies generated by open pollination (OP) and by controlled crosses (CC) were planted in adjacent trials at two to three sites in southern Sweden. The tree height and diameter at breast height were measured, and genetic parameters based on these traits were estimated for OP and CC progenies separately, in order to enable comparisons. Narrow-sense heritability estimates for Scots pine and Norway spruce OP progenies (in the ranges 0.04–0.13 and 0.15–0.38, respectively) did not differ significantly from CC estimates (0.07–0.12 and 0.23–0.30), suggesting that OP-based heritability values were not overestimated to any great extent. Similarly, genetic correlations between OP and CC progenies were in the ranges of 0.87–0.88 and 0.74–0.77 for Scots pine and Norway spruce, respectively, being significantly lower than unity only in the case of Norway spruce. OP-based breeding values for both species should therefore correspond well with those predicted from CC progenies, albeit not perfectly for Norway spruce. In conclusion, the assumption of true half-sibs for OP progenies was not violated to the extent that genetic parameter estimates or breeding value predictions were seriously biased.

Performance of Seven Tree Breeding Strategies Under Conditions of Inbreeding Depression

In the domestication and breeding of tree species that suffer from inbreeding depression (ID), the long-term performance of different breeding strategies is poorly known. Therefore, seven tree breeding strategies including single population, subline, selfing, and nucleus breeding were simulated using a multi-locus model with additive, partial, and complete dominance allele effects, and with intermediate, U-shaped, and major allele distributions. The strategies were compared for genetic gain, inbreeding accumulation, capacity to show ID, the frequencies and fixations of unfavorable alleles, and genetic variances in breeding and production populations. Measured by genetic gain of production population, the nucleus breeding and the single breeding population with mass selection strategies were equal or superior to subline and single breeding population with within-family selection strategies in all simulated scenarios, in spite of their higher inbreeding coefficients. Inbreeding and cross-breeding effectively decreased ID and could in some scenarios produce genetic gains during the first few generations. However, in all scenarios, considerable fixation of unfavorable alleles rendered the purging performance of selfing and cross-breeding strategies ineffective, and resulted in substantial inferiority in comparison to the other strategies in the long-term.

Functional Quantitative Trait Loci (QTL) analysis for adaptive traits in a three-generation Scots pine pedigree

In forest tree breeding, QTL identification aims to accelerate the breeding cycle and increase the genetic gain of traits with economical and ecological value. In our study, both phenotypic data and predicted breeding values were used in the identification QTL linked to the adaptive value in a three-generation pedigree population, for the first time in a conifer species (Pinus sylvestris L.). A total of 11 470 open pollinated F2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and estimated breeding values (EBVs). Different levels of genotype-by-environment (G×E) effects among sites and ages were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBVs accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%, mostly for traits based on phenotypic data. Two SNP-QTL showed pleiotropic effects for traits related with survival, seed and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity and QTL-by-environment effects.