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 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

Genetic improvement of sawn-board shape stability in Scots pine (Pinus sylvestris L.)

Adequate shape stability is a prerequisite for utilization of sawn boards in the building industry. This study investigated the possibility of indirect genetic improvement of Scots pine (Pinus sylvestris L.) sawn-board shape stability (specifically the bow, crook and twist) via selective breeding based on traits that can be non-destructively measured on standing trees. Relationships between shape stability and wood quality traits measured on logs and sawn boards were also determined. A total of 1896 standing trees from a 39-year-old Scots pine full-sib progeny test were non-destructively measured. A subset of 496 trees was harvested and sawn into 50 x 100 mm boards, the quality of which was assessed both non-destructively and destructively. Among the traits assessed on standing trees, grain angle (GRA) appeared to be the best predictor of sawn-board twisting and crooking (r(A) = 0.84 and 0.62, respectively). The individual-tree narrow-sense heritability (h(i)(2)) was moderate for twist and GRA (0.37 and 0.40, respectively), low for bow (0.21) and very low for crook (0.05). Selective breeding targeting lower GRA would result in lower twist and crook but could also increase sawn-board density, stiffness and strength

Genetic variation of biomass recalcitrance in a natural Salix viminalis (L.) population

Background: Salix spp. are high-productivity crops potentially used for lignocellulosic biofuels such as bioethanol. In general, pretreatment is needed to facilitate the enzymatic depolymerization process. Biomass resistance to degradation, i.e., biomass recalcitrance, is a trait which can be assessed by measuring the sugar released after combined pretreatment and enzymatic hydrolysis. We have examined genetic parameters of enzymatic sugar release and other traits related to biorefnery use in a population of 286 natural Salix viminalis clones. Furthermore, we have evaluated phenotypic and genetic correlations between these traits and performed a genomewide association mapping analysis using a set of 19,411 markers. Results: Sugar release (glucose and xylose) after pretreatment and enzymatic saccharifcation proved highly variable with large genetic and phenotypic variations, and chip heritability estimates (h2 ) of 0.23–0.29. Lignin syringyl/guaiacyl (S/G) ratio and wood density were the most heritable traits (h2=0.42 and 0.59, respectively). Sugar release traits were positively correlated, phenotypically and genetically, with biomass yield and lignin S/G ratio. Association mapping revealed seven marker–trait associations below a suggestive signifcance threshold, including one marker associated with glucose release. Conclusions: We identifed lignin S/G ratio and shoot diameter as heritable traits that could be relatively easily evaluated by breeders, making them suitable proxy traits for developing low-recalcitrance varieties. One marker below the suggestive threshold for marker associations was identifed for sugar release, meriting further investigation while also highlighting the difculties in employing genomewide association mapping for complex trait

Development of Secondary Woodland in Oak Wood Pastures Reduces the Richness of Rare Epiphytic Lichens

Wooded pastures with ancient trees were formerly abundant throughout Europe, but during the last century, grazing has largely been abandoned often resulting in dense forests. Ancient trees constitute habitat for many declining and threatened species, but the effects of secondary woodland on the biodiversity associated with these trees are largely unknown. We tested for difference in species richness, occurrence, and abundance of a set of nationally and regionally red-listed epiphytic lichens between ancient oaks located in secondary woodland and ancient oaks located in open conditions. We refined the test of the effect of secondary woodland by also including other explanatory variables. Species occurrence and abundance were modelled jointly using overdispersed zero-inflated Poisson models. The richness of the red-listed lichens on ancient oaks in secondary woodland was half of that compared with oaks growing in open conditions. The species-level analyses revealed that this was mainly the result of lower occupancy of two of the study species. The tree-level abundance of one species was also lower in secondary woodland. Potential explanations for this pattern are that the study lichens are adapted to desiccating conditions enhancing their population persistence by low competition or that open, windy conditions enhance their colonisation rate. This means that the development of secondary woodland is a threat to red-listed epiphytic lichens. We therefore suggest that woody vegetation is cleared and grazing resumed in abandoned oak pastures. Importantly, this will also benefit the vitality of the oaks

Genetic improvement of shape stability in Norway spruce and Scots pine sawn timber

Poor shape stability of sawn softwood timber, causes substantial economic losses for sawmills and the building industry. Sawn timber twist is regarded to be the most severe deformation and has been shown to be controlled by intrinsic wood properties like wood shrinkage and spiral grain angle. The aim of the studies this thesis is based upon was to investigate the possibility to improve sawn timber shape stability, by genetic selection of genotypes of Norway spruce (Picea abies L. Karst.) and Scots pine (Pinus sylvestris L.) with a favourable spiral grain angle. Genetic parameters were estimated for the spiral grain angle in the mature wood of trees in four progeny trials (age 27–36 years) and two clonal trials (age 19 years) of Norway spruce. In addition, in a 36-year-old Scots pine progeny trial, the grain angle was measured and shape stability traits of the boards sawn from sampled trees were assessed. The estimates of genetic standard deviation (0.7°–0.9°) and heritability (0.29–0.42) in the mature wood of both species suggested that grain angle could be altered by genetic selection. The grain angle measured in single annual rings of Scots pine showed substantial phenotypic correlations (0.54–0.70) with the twist of small sawn timber dried to a 12% moisture content. As an example, twist could potentially be reduced by 0.3°–0.7° by selecting 20% of the parents displaying the lowest grain angle, thereby appreciably decreasing the percentage of excessively twisted boards. Grain angle under bark exhibited non-significant genetic correlations, close to zero, with growth traits, stem form, and branch traits in both species, and with pilodyn penetration in Norway spruce, suggesting that genetic selection for this trait would not generate any appreciable response in the other traits. The results of the studies imply that the grain angle measured under bark is utilisable in terms of genetic parameter estimation and for predicting the twist propensity of small sawn timber. This suggests that there is potential to improve sawn timber shape stability by genetic selection for a lower grain angle under bark and thus reducing the twist of sawn timber

Genetic Improvement of Sawn-Board Stiffness and Strength in Scots Pine (Pinus sylvestris L.)

Given an overall aim of improving Scots pine structural wood quality by selective tree breeding, we investigated the potential of non-destructive acoustic sensing tools to accurately predict wood stiffness (modulus of elasticity, MOE) and strength (modulus of rupture, MOR) of sawn boards. Non-destructive measurements of wood density (DEN), acoustic velocity (VEL) and MOE were carried out at different stages of wood processing chain (standing trees, felled logs and sawn boards), whilst destructively measured stiffness and strength served as benchmark traits. All acoustic based MOE and VEL estimates proved to be good proxies (r(A) > 0.65) for sawn-board stiffness while MOETREE, VELHIT and resistograph wood density (DENRES) measured on standing trees and MOELOG and VELFAK measured on felled logs well reflected board strength. Individual-tree narrow-sense heritability (hi2) for VEL, MOE and MOR were weak (0.05-0.26) but were substantially stronger for wood density (0.34-0.40). Moreover, additive genetic coefficients of variation for MOE and MOR were in the range from 5.4% to 9.1%, offering potential targets for exploitation by selective breeding. Consequently, selective breeding based on MOETREE, DENRES or stem straightness (STR) could improve several structural wood traits simultaneously

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

$\bullet$ 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. $\bullet$ 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. $\bullet$ 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 ($H^{2}>0.$3) were larger than the seed orchard heritability ($H^{2}$ = 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. $\bullet$ 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.Paramètres génétiques de l'angle du fil du bois étudiés dans des descendances d'épicéa commun âgés de 28 ans et chez leurs parents en verger à graines. $\bullet$ 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. $\bullet$ 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. $\bullet$ 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 ($H^{2}>0$,$3$) étaient plus fortes que celle obtenue en verger à graines ($H^{2}$ = 0,24). L'interaction G$\times$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. $\bullet$ 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

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 (n(qtl)) for different trait categories by improving a method previously developed by Otto and Jones (Genetics 156: 2093-2107, 2000). Estimates of n(qtl) 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 n(qtl) 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.Bio4Energ

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

Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis

Background Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus. Results A total of 19,592 markers were used in association analyses using both Fisher's exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region. Conclusions Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome