Anders Fries

Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modeling

A novel hierarchical quantitative trait locus (QTL) mapping method using a polynomial growth function and a multiple-QTL model (with no dependence in time) in a multitrait framework is presented. The method considers a population-based sample where individuals have been phenotyped (over time) with respect to some dynamic trait and genotyped at a given set of loci. A specific feature of the proposed approach is that, instead of an average functional curve, each individual has its own functional curve. Moreover, each QTL can modify the dynamic characteristics of the trait value of an individual through its influence on one or more growth curve parameters. Apparent advantages of the approach include: (1) assumption of time-independent QTL and environmental effects, (2) alleviating the necessity for an autoregressive covariance structure for residuals and (3) the flexibility to use variable selection methods. As a by-product of the method, heritabilities and genetic correlations can also be estimated for individual growth curve parameters, which are considered as latent traits. For selecting trait-associated loci in the model, we use a modified version of the well-known Bayesian adaptive shrinkage technique. We illustrate our approach by analysing a sub sample of 500 individuals from the simulated QTLMAS 2009 data set, as well as simulation replicates and a real Scots pine (Pinus sylvestris) data set, using temporal measurements of height as dynamic trait of interest.

Marker-based parentage analysis facilitates low input ‘breeding without breeding’ strategies for forest trees

Controlled crosses and progeny testing are important components of tree breeding programs. Recently, a new approach, ‘breeding without breeding’ (BWB), has been proposed to obtain structured pedigrees for the breeding and testing from wind-pollinated progenies; the technique uses high-resolution markers instead of conventional approaches. The BWB approach is attractive for outcrossing conifers where the breeding cycle is long and reproductive maturity is often delayed. For the application of the BWB approach, the accurate assignment of parents is essential. The first step in the application of the BWB approach is to conduct tests into the reliability of paternity and parent-pair exclusion procedures in complex situations. In this study we conducted multi-locus-based empirical and simulation analyses for a Scots pine seed orchard crop, in order to develop the appropriate parentage assignment techniques for BWB and to investigate whether pedigrees from a seed orchard crop can be determined with sufficient accuracy. The results were promising, as 93–97% of the seeds generated by mating among the seed orchard clones were correctly assigned to a parent-pair. When mating occurred with foreign pollen, the success rate of identifying mother clones was 60–78%. Based on these results, we propose three novel low input breeding strategies for forest trees. The principles of the different options and their potential benefits and costs are described and discussed using Scots pine as a case study.

Evaluation of Pollen Contamination in an Advanced Scots Pine Seed Orchard

Abstract The pollination pattern in a Scots pine (Pinus sylvestris L.) seed orchard consisting of 28 clones was studied using nine microsatellite (SSR) loci. The nine SSR loci produced unique multilocus genotypes for each of the orchard’s 28 clones and allowed paternal assignment of the studied 305 seed using paternity exclusion probability of 99.9%. Fifty two percent of the studied seeds were sired by outside the orchard pollen sources (i.e., pollen contamination) and as expected, low selfing (2.3%) was detected. These results are valuable for the evaluation of the seed orchard function and the impact of contamination on the expected genetic gain.

High negative genetic correlations between growth traits and wood properties suggest incorporating multiple traits selection including economic weights for the future Scots pine breeding programs

ContextThe development of multiple trait selection indices for solid (structure) wood production in the Scots pine (Pinus sylvestris L.) breeding program requires genetic variances and covariances estimated among wood quality traits including stiffness.AimsGenetic control and relationships among Scots pine growth, fiber, and wood quality traits were assessed by estimating heritability, phenotypic and genetic correlation using a Scots pine full-sib family trial.MethodWood quality traits including clearwood and dynamic acoustic stiffness were measured using SilviScan and Hitman in a 40-year-old progeny trial and by sampling increment cores of 778 trees of 120 families. Genetic parameters were estimated using the mixed model by the ASReml software.ResultsHeritability ranged from 0.147 to 0.306 for growth, earlywood, transition wood and latewood proportion traits and from 0.260 to 0.524 for fiber dimension, wood density, MFA and stiffness traits. The highly unfavorable genetic correlation between diameter and whole core density (−0.479) and clearwood stiffness (−0.506) and dynamic acoustic stiffness (−0.382) was observed in this study.ConclusionThe unfavorable genetic correlations between growth traits and stiffness indicate that multiple traits selection using optimal economic weights and optimal breeding strategies are recommended for the advanced Scots pine breeding program.

Effects of temperature on the site productivity of Pinus sylvestris and lodgepole pine in Finland and Sweden

The influence of temperature regime on forest production in the northern boreal forest was studied by analysing the variation in site index for 20 provenance tests of lodgepole pine (Pinus contorta Dougl. var. latifolia Engelm.) in Finland and Sweden with respect to temperature. The site indices were regressed with several different temperature variables, which were obtained from interpolated monthly averages over 30 years from permanent meteorological stations nearby. There were strong correlations between all tested temperature variables and site index (r = 0.80–0.94). Site fertility influenced site index to some extent but the slope of the test sites did not. An increase in temperature sum from 600 to 1200 degree days (corresponding to an increase of the mean temperature in July from 13 to 15°C) was associated with an increase in site index of Scots pine (Pinus sylvestris L.) from 12.2 to 21.6 m (77%). Such an increase in site index can be assumed to correspond to an increase of 6.5 m3 ha−1 wood (183%)...

Genetic parameters for earlywood and latewood densities and development with increasing age in Scots pine

Abstract• Each annual ring in pines consists of earlywood and latewood with considerable difference in density and width. To get a better determination of the genetic regulation of total wood density in Scots pine (Pinus sylvestris L.), density and width of those ring sections were measured in annual ring numbers 12 to 21 of Scots pines in a full-sib progeny test. Tree height and stem diameter were also measured.• Heritabilities for the annual ring sections increased with age for earlywood density from 0.08 to approximately 0.25; latewood density showed similar reductions. Heritability over all 10 annual rings was 0.25 for earlywood density, 0.22 for latewood density, 0.29 for height and 0.10 for stem diameter. Genetic correlations between earlywood and latewood density and growth traits were negative, while they were strongly positive between densities of adjacent annual rings (0.70–1.0).• Despite the higher heritability of earlywood density, the strong positive genetic correlation between those traits indicates little benefit from focusing solely on earlywood density when selecting for wood density. Analysing earlywood and latewood separately does not benefit from including the width of the corresponding ring section as a covariate. Juvenile wood may possibly turn into mature wood 15–20 y from the pith.Résumé• Chaque cerne annuel chez les pins est composé de bois initial et de bois final avec une différence de densité et de largeur. Pour obtenir une meilleure détermination de la régulation génétique de la densité totale de bois chez le pin sylvestre (Pinus sylvestris L.), la densité et la largeur de ces sections de cernes annuels ont été mesurées chez 12 à 21 pins sylvestres dans un essai de descendance de plein frères. La hauteur des arbres et le diamètre des troncs ont également été mesurés.• Les héritabilités pour les sections de cernes annuels augmentent avec l’âge pour la densité du bois initial de 0,08 à environ 0,25 ; la densité du bois final a montré des réductions similaires. L’héritabilité sur l’ensemble de 10 cernes a été de 0,25 pour la densité du bois initial, de 0,22 pour la densité du bois final, de 0,29 pour la hauteur et de 0,10 pour diamètre du tronc. Les corrélations génétiques entre densité du bois initial et du bois final et caractéristiques de la croissance ont été négatives, alors qu’elles ont été fortement positives entre la densité des cernes adjacents (0,70–1,0).• Malgré la plus forte héritabilité de la densité du bois initial, la forte corrélation génétique entre ces caractéristiques montre qu’il y a peu d’intérêt à se concentrer uniquement sur la densité du bois initial lors de la sélection pour la densité du bois. Analyser bois initial et bois final séparément ne bénéficie pas de l’inclusion comme covariable de la largeur de la section du cerne correspondant. Le bois juvénile peut devenir à son tour du bois adulte, 15–20 ans à partir de la moelle.

A Method to Estimate Fibre Length Distribution in Conifers Based on Wood Samples from Increment Cores

Summary We propose a method to estimate fibre length distribution in conifers based on wood samples from increment cores processed by automatic optical fibre-analysers. Automatic fibre-analysers are unable to distinguish: a) fibres from other tissues, “fines”, and b) cut from uncut fibres. However, our proposed method can handle these problems if the type of distributions that fibre lengths and fines follow is known. In our study the length distributions of fines and fibres were assumed to follow truncated normal distributions, characterised by means and standard deviations of the two distributions. Parameter estimates were obtained by the maximum likelihood method. Wood samples from two 22-year-old Scots pine trees at breast height were used to evaluate the performance of the method. From stem discs at 1.5 m, adjacent samples of 5 mm increment cores and wood pieces were taken. The cores were trimmed 1 mm at each side and samples were, after maceration, analysed in a Kajaani FiberLab 3.0. The results showed that the method works well and gives a possibility to distinguish fine and fibre length distribution.

Genetic variation among and within populations of Cordia africana in seed size and germination responses to constant temperatures

Cordia africana Lam. is a commercial timber species that grows naturally throughout sub-Saharan Africa and tropical Arabia. At present very little is known about genetic variation in this species and baseline information is needed to initiate improvement programs in Ethiopia. Thus, the objectives of the study were to quantify the inter- and intra-population variations in seed size traits and germination responses to different constant temperature regimes. Seeds were collected from 30 open-pollinated families within each of the five populations representing the natural distribution of the species in Ethiopia. To examine seed size variations, seed length, seed width, and 1,000-seed weight were quantified. Inter- and intra-population variations in seed germination were investigated under different constant temperature regimes from 20 to 35°C in climate chambers. Significant variations in seed length, width and weight were detected both at inter- and intra-population levels, and family heritabilities of 0.63–0.76 showed that much of the phenotypic variation in seed size traits were additive genetic variation. Significant variation in germination was also found among and within populations as well as between the different constant temperature regimes. Generally the variation in germination was considerably higher within population than between populations. The optimal temperature for germination of C. africana seeds was 25–30°C with family heritabilities for germination ranging between 0.20 and 0.33, depending on the germination temperature.

Variation in spring and autumn frost tolerance among provenances of Russian larches (Larix Mill.)

Abstract Spring and autumn frost tolerance was measured using material from a range-wide (50–67° N, 38–158° E) provenance trial of four Russian larch species (Larix sukaczewii Dyl., L. sibirica Ledeb., L. gmelinii Rupr. and L. cajanderi Mayr.) growing in northern Sweden. Shoots were collected in early May and late September and frozen at −8, −12, −16 and −20°C. Cambial damage was assessed visually after development under ideal conditions for 2 weeks. Differences in frost damage among provenances were highly significant in both spring and autumn. Autumn frost damage was significantly correlated with provenance latitude and longitude and spring frost damage was significantly correlated with provenance longitude but not latitude. Frost damage was not correlated with provenance elevation. North-western provenances showed the least damage and far-eastern provenances the greatest damage in both spring and autumn. A possible explanation for less spring frost damage to north-western provenances is adaptation to maritime conditions in proximity to the Barents Sea, which is often ice free in late winter. This would counteract early loss of frost tolerance and bud flushing if warm spells occurred in late winter. North-eastern Siberian provenances did not show similar adaptation and may exhibit increased spring frost damage if global warming eventually results in the Arctic Ocean north of Siberia becoming ice free in late winter.

Measuring Relative Fibre Length in Scots Pine by Non-Destructive Wood Sampling

Summary Wood fibre length of Scots pine (Pinus sylvestris L.) was measured in wood sticks and 5-mm increment cores. The aim was to evaluate whether fibre length estimates from such small-diameter cores could be used to calculate genetic parameters, in spite of the increased amount of cut fibres produced at boring. The correlation between mean fibre lengths obtained from cores and sticks, with substantially fewer cut fibres, was high (r = 0.87, n = 53) and of the same magnitude as the correlation between samples from varied positions in the same tree (r = 0.87, n = 46). As regards evaluation of genetic tests and ranking for selection purposes, values from non-destructively sampled 5-mm cores from 0.5 m tree height appear to serve well. Fibre length development along annual ring classes started to differentiate between trees at annual rings 13–15, and after ring 16 there was a slight tendency towards stabilisation which may be interpreted as a reasonably advanced transition from juvenile wood to mature wood.