Timing Of Bud Set Research Articles

Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar

BackgroundDespite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome.ResultsWe present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe a biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring’s phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment.ConclusionsGenome-wide cytosine methylation patterns in symmetrical CG-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in CG-context can be used as biomarkers to infer a common ancestor and thus to investigate the recent environmental history of a specific Lombardy poplar. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.

Within- and between-population comparisons suggest independently acting selection maintaining parallel clines in Scots pine (Pinus sylvestris).

Parallel clines in traits related to adaptation in a species can be due to independent selection on a pair of traits, or due to selection in one trait resulting in a parallel cline in a correlated trait. To distinguish between the mechanisms giving rise to parallel adaptive population divergence of multiple traits along an environmental gradient we need to study variation, correlations, and selective forces within individual populations along the gradient. In many tree species, budset timing (BST) forms a latitudinal cline, and parallel clinal variation is also found in other seedling traits, such as first-year height (FYH) and fall frost injury (FFI). In this study, we set up a common garden experiment with open pollinated progeny from natural populations of Scots pine (Pinus sylvestris), with one large sample from single population (500 families) and smaller samples from across a latitudinal gradient. BST, FYH and induced FFI were first measured in a greenhouse. The seedlings were then planted in the field, where survival and height were measured at the age of 9 years as fitness proxies. We compared between- and within-population variation and genetic correlations of these three seedling traits, and estimated selection gradients at the family level in our main population, taking into account the potential effects of seed weight. Between-population genetic correlations between seedling traits were high (0.76-0.95). Within-population genetic correlations in the main population were lower (0.14-0.35), as in other populations (0.10-0.39). Within population, extensive adaptive variation persists in the seedling traits, in line with rather weak selection gradients, yet maintaining the clines. Although our sampling does not cover the whole cline equally, the results suggest that the individual clines in these traits are maintained by largely independently acting selection, which results in fewer constraints in adaptation under changing climate.

Aspen growth is not limited by starch reserves

All photosynthetic organisms balance CO2 assimilation with growth and carbon storage. Stored carbon is used for growth at night and when demand exceeds assimilation. Gaining a mechanistic understanding of carbon partitioning between storage and growth in trees is important for biological studies and for estimating the potential of terrestrial photosynthesis to sequester anthropogenic CO2 emissions.1,2 Starch represents the main carbon storage in plants.3,4 To examine the carbon storage mechanism and role of starch during tree growth, we generated and characterized low-starch hybrid aspen (Populus tremula×tremuloides) trees using CRISPR-Cas9-mediated gene editing of two PHOSPHOGLUCOMUTASE (PGM) genes coding for plastidial PGM isoforms essential for starch biosynthesis. We demonstrate that starch deficiency does not reduce tree growth even in short days, showing that starch is not a critical carbon reserve during diel growth of aspen. The low-starch trees assimilated up to ∼30% less CO2 compared to the wild type under a range of irradiance levels, but this did not reduce growth or wood density. This implies that aspen growth is not limited by carbon assimilation under benign growth conditions. Moreover, the timing of bud set and bud flush in the low-starch trees was not altered, implying that starch reserves are not critical for the seasonal growth-dormancy cycle. The findings are consistent with a passive starch storage mechanism that contrasts with the annual Arabidopsis and indicate that the capacity of the aspen to absorb CO2 is limited by the rate of sink tissue growth.

Interactive Effects of Light Quality during Day Extension and Temperature on Bud Set, Bud Burst and PaFTL2, PaCOL1-2 and PaSOC1 Expression in Norway Spruce (Picea abies (L.) Karst.)

Light and temperature are crucial factors for the annual growth rhythm of tree seedlings of the boreal and temperate zone. Dormant, vegetative winter buds are formed under short days (SD) and altered light quality. In the conifer Norway spruce, expression of FTL2 increases and PaCOL1-2 and PaSOC1 decrease under light regimes, inducing bud set. Although temperature is known to modulate the timing of bud set, information about combined effects of light climate and temperature on bud phenology and gene expression is limited. We studied the interactive effects of temperature (18, 22/24 °C) and day extension with blue (B), red (R) or far-red (FR) light or different R:FR ratios compared to SD on growth–dormancy cycling and expression of FTL2, PaCOL1-2 and PaSOC1 in Norway spruce seedlings. Day-extension with B light and all treatments involving FR light sustained shoot elongation, with increased growth at higher temperature. The R light treatment resulted in delayed/prevented bud set compared to SD, with more delay/prevented bud set at 24 °C than 18 °C. This was associated with lower PaFTL2-transcript levels at 24 °C and more rapid subsequent bud burst. For the growth-sustaining treatments (long days, FR and B light), the PaFTL2-transcript levels were generally lower and those of PaCO1-2 and PaSOC1 higher compared with SD and R light. In conclusion, our results demonstrate more reduced/prevented bud set and faster bud burst with increased temperature under day extension with R light, indicating less deep dormancy than at lower temperature. Also, sustained shoot elongation under the B light treatment (27 µmol m−2 s−1) in contrast to the lower B light-irradiances tested previously (≤13 µmol m−2 s−1), demonstrates an irradiance-dependent effect of day extension with B light.

A major locus controls local adaptation and adaptive life history variation in a perennial plant

BackgroundThe initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth and have important fitness effects in perennial plants. Such adaptive life-history traits often show strong local adaptation along environmental gradients but, despite their importance, the genetic architecture of these traits remains poorly understood.ResultsWe integrate whole genome re-sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). A single genomic region containing the PtFT2 gene mediates local adaptation in the timing of bud set and explains 65% of the observed genetic variation in bud set. This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation. Field and greenhouse experiments confirm that variation in PtFT2 gene expression affects the phenotypic variation in bud set that we observe in wild natural populations.ConclusionsOur results reveal a major effect locus that determines the timing of bud set and that has facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life-history trait is remarkable, given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large-effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.

Maternal temperature during seed maturation affects seed germination and timing of bud set in seedlings of European black poplar

Abstract The maternal temperature during seed development can significantly affect seed dormancy, germination and seedling performance. While the response of germination and seedling phenology to maternal temperatures has been well studied for annuals and conifers, very few studies focus on deciduous trees. To understand the responses of seedlings to variation in maternal temperature during seed maturation, we assessed the germination, bud phenology (bud burst, bud set) and height of full sib families in a common garden. We performed three controlled crosses between three different pairs of genotypes of European black poplar (Populus nigra) to achieve full sib families in three experiments in warm (+10 °C) and cold (control) maternal environments during crossing and seed maturation. Warmer (+10 °C) maternal temperatures decreased the seed germination success. The seedlings from the warmer maternal environment also displayed later bud burst and earlier bud set, but only in one out of the three crossings (Proven ♀ x Horrues ♂). Our results indicate that the maternal environment can considerably impact on seed germination and the phenological responses of even two-year old seedlings suggesting the existence of a memory of maternal temperature during seed maturation. The seedlings resulting from the colder maternal environment grew taller than those from the warmer environment during the first, but not second, growing season. Our results further our understanding of the responses of deciduous forest trees to rapid climate change, but more research is needed to better understand the mechanisms behind the observed effects of maternal warming.

Asymmetric effects of cooler and warmer winters on beech phenology last beyond spring.

In temperate trees, the timings of plant growth onset and cessation affect biogeochemical cycles, water, and energy balance. Currently, phenological studies largely focus on specific phenophases and on their responses to warming. How differently spring phenology responds to the warming and cooling, and affects the subsequent phases, has not been yet investigated in trees. Here, we exposed saplings of Fagus sylvatica L. to warmer and cooler climate during the winter 2013-2014 by conducting a reciprocal transplant experiment between two elevations (1,340 vs. 371m a.s.l., ca. 6°C difference) in the Swiss Jura mountains. To test the legacy effects of earlier or later budburst on the budset timing, saplings were moved back to their original elevation shortly after the occurrence of budburst in spring 2014. One degree decrease in air temperature in winter/spring resulted in a delay of 10.9days in budburst dates, whereas one degree of warming advanced the date by 8.8days. Interestingly, we also found an asymmetric effect of the warmer winter vs. cooler winter on the budset timing in late summer. Budset of saplings that experienced a cooler winter was delayed by 31days compared to the control, whereas it was delayed by only 10days in saplings that experienced a warmer winter. Budburst timing in 2015 was not significantly impacted by the artificial advance or delay of the budburst timing in 2014, indicating that the legacy effects of the different phenophases might be reset during each winter. Adapting phenological models to the whole annual phenological cycle, and considering the different response to cooling and warming, would improve predictions of tree phenology under future climate warming conditions.

Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis.

Local adaptation is a common feature of plant and animal populations. Adaptive phenotypic traits are genetically differentiated along environmental gradients, but the genetic basis of such adaptation is still poorly known. Genetic association studies of local adaptation combine data over populations. Correcting for population structure in these studies can be problematic since both selection and neutral demographic events can create similar allele frequency differences between populations. Correcting for demography with traditional methods may lead to eliminating some true associations. We developed a new Bayesian approach for identifying the loci underlying an adaptive trait in a multipopulation situation in the presence of possible double confounding due to population stratification and adaptation. With this method we studied the genetic basis of timing of bud set, a surrogate trait for timing of yearly growth cessation that confers local adaptation to the populations of Scots pine (Pinus sylvestris). Population means of timing of bud set were highly correlated with latitude. Most effects at individual loci were small. Interestingly, we found genetic heterogeneity (that is, different sets of loci associated with the trait) between the northern and central European parts of the cline. We also found indications of stronger stabilizing selection toward the northern part of the range. The harsh northern conditions may impose greater selective pressure on timing of growth cessation, and the relative importance of different environmental cues used for tracking the seasons might differ depending on latitude of origin.

From genotypes to phenotypes: expression levels of genes encompassing adaptive SNPs in black spruce.

Measuring transcript levels for adaptive genes revealed polymorphisms having cis -effect upon gene expression levels related to phenotype variation in a black spruce natural population. Trees growing in temperate and boreal regions must acclimate to changes in climatic factors such as low winter temperatures to survive to seasonal variations. Common garden studies have shown that genetic variation in quantitative traits helps species to survive and adapt to environmental changes and local conditions. Twenty-four genes carrying SNPs were previously associated with genetic adaptation in black spruce (Picea mariana [Mill.] BSP). The objectives of this study were to investigate the potential role of these genes in regulation of winter acclimation and adaptation by studying their patterns of expression as a function of the physiological stage during the annual growth cycle, tissue type, and their SNP genotypic class. Considerable variability in gene expression was observed between different vegetative tissues or organs, and between physiological stages. The genes were expressed predominantly in tissues that could be linked more directly to winter acclimation and adaptation. The expression levels of several of the genes were significantly related to variation in tree height growth or budset timing and expression level variation related to SNP genotypic classes was observed in four of the genes. An interaction between genotypic classes and physiological stages was also observed for some genes, indicating genotypes with different reaction norms in terms of gene expression.

Growth and development of Norway spruce and Scots pine seedlings under different light spectra

The goal of this study was to examine how different light spectra affect growth and development of Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) seedlings. The seedlings were grown in a darkened greenhouse under four light spectra consisting of different proportions of blue (B, 400–500nm), red (R, 600–700nm), and far-red (FR, 700–800nm) light, with high-pressure sodium lamps (HPS) serving as controls. The light treatments (250μmolm−2s−1 photosynthetically active radiation) were provided using light-emitting diodes (LEDs), and the treatments included the following: (1) 25% B+70% R+5% FR; (2) 25% B+75% R; (3) 55% B+45% R; and (4) HPS: 6% B+44% green (500–600nm)+41% R+9% FR. We measured germination, growth, morphology, gas exchange, N concentration in needles and stem, and terminal bud set of the seedlings after a 4-month growth period. Our results showed that the physiological and morphological responses of shade-intolerant Scots pine seedlings to light quality were more pronounced than those of the shade-tolerant Norway spruce seedlings. Growth under the FR-containing light treatments produced tall seedlings with larger needle dry mass. Removal of FR and addition of B in the growth light reduced the height growth, and it increased the sturdiness and altered the branching patterns in the seedlings. Growth under the treatment containing about 25% B and 75% R resulted in the highest root-to-shoot ratios in both species and highest root growth capacity and water-use efficiency in Scots pine. Timing of bud set was independent of growth light spectra. Our results show that it is possible to improve the seedling attributes that are contributing to good performance potential by using different wavelength combinations in growth light, particularly in Scots pine. However, the potential after-effects of growth under an incomplete light spectrum on seedling performance after planting to forest regeneration site are still unknown.

FTL2 expression preceding bud set corresponds with timing of bud set in Norway spruce under different light quality treatments

Shoot elongation and bud set in temperate zone trees is under photoperiodic control, but light quality also plays a role with far-red (FR) light sustaining growth, and blue (B) affecting timing of bud set. This may suggest a role of B light receptors in addition to the photoperiod- and red (R)-FR-sensing phytochrome (phy) system. However, there is limited information on effect of light quality on genes thought to be involved in growth-dormancy cycling. In this study we have examined effect of light quality on expression of genes known to be affected by photoperiod as well as CRY and PHY genes, which were also characterised in this study. In contrast to growth-sustaining FR and reference LD treatment, bud-inducing R and B light and reference SD exposure resulted in accumulation of transcripts of PaFTL2, and reduction in PaCOL1, PaCOL2 and PaSOC1 before visible morphological changes associated with bud set. The light receptor transcripts (CRY1, CRY2, PHYN, PHYO, PHYP) also accumulated, but with the largest changes after growth cessation. Reduced or slightly delayed bud set under R compared to B light and SD, was in most cases reflected in changes in transcript levels. Of the studied genes, FTL2 expression preceding bud set correlated the most closely with timing of bud set in in the studied provenances under the different light quality treatments. These results demonstrate action of light quality and photoperiod through a common pathway in control of bud set in Norway spruce, with FTL2 as a key factor.

Effect of alternating day and night temperature on short day-induced bud set and subsequent bud burst in long days in Norway spruce.

Young seedlings of the conifer Norway spruce exhibit short day (SD)-induced cessation of apical growth and bud set. Although different, constant temperatures under SD are known to modulate timing of bud set and depth of dormancy with development of deeper dormancy under higher compared to lower temperature, systematic studies of effects of alternating day (DT) and night temperatures (NT) are limited. To shed light on this, seedlings of different provenances of Norway spruce were exposed to a wide range of DT-NT combinations during bud development, followed by transfer to forcing conditions of long days (LD) and 18°C, directly or after different periods of chilling. Although no specific effect of alternating DT/NT was found, the results demonstrate that the effects of DT under SD on bud set and subsequent bud break are significantly modified by NT in a complex way. The effects on bud break persisted after chilling. Since time to bud set correlated with the daily mean temperature under SD at DTs of 18 and 21°C, but not a DT of 15°C, time to bud set apparently also depend on the specific DT, implying that the effect of NT depends on the actual DT. Although higher temperature under SD generally results in later bud break after transfer to forcing conditions, the fastest bud flush was observed at intermediate NTs. This might be due to a bud break-hastening chilling effect of intermediate compared to higher temperatures, and delayed bud development to a stage where bud burst can occur, under lower temperatures. Also, time to bud burst in un-chilled seedlings decreased with increasing SD-duration, suggesting that bud development must reach a certain stage before the processes leading to bud burst are initiated. The present results also indicate that low temperature during bud development had a larger effect on the most southern compared to the most northern provenance studied. Decreasing time to bud burst was observed with increasing northern latitude of origin in un-chilled as well as chilled plants. In conclusion, being a highly temperature-dependent process, bud development is strongly delayed by low temperature, and the effects of DT is significantly modified by NT in a complex manner.

Association of FLOWERING LOCUS T/TERMINAL FLOWER 1-like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris).

Understanding the genetic basis of the timing of bud set, an important trait in conifers, is relevant for adaptation and forestry practice. In common garden experiments, both Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) show a latitudinal cline in the trait. We compared the regulation of their bud set biology by examining the expression of PsFTL2, a Pinus sylvestris homolog to PaFTL2, a FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like gene, the expression levels of which have been found previously to be associated with the timing of bud set in Norway spruce. In a common garden study, we analyzed the relationship of bud phenology under natural and artificial photoperiods and the expression of PsFTL2 in a set of Scots pine populations from different latitudes. The expression of PsFTL2 increased in the needles preceding bud set and decreased during bud burst. In the northernmost population, even short night periods were efficient to trigger this expression, which also increased earlier under all photoperiodic regimes compared with the southern populations. Despite the different biology, with few limitations, the two conifers that diverged 140million yr ago probably share an association of FTL2 with bud set, pointing to a common mechanism for the timing of growth cessation in conifers.

Timing for success: expression phenotype and local adaptation related to latitude in the boreal forest tree, Populus balsamifera

Timing of seasonal dormancy is among the most important traits allowing forest tree populations to span latitudinal gradients of temperature and growing season length. We used RNA-sequencing (RNA-seq) data to identify gene expression differences between latitude-adapted populations and search for elevated genetic differentiation, a signature of adaptation, between northern and southern populations of Populus balsamifera. RNA was extracted from leaf tissues collected from trees originating from two northern (65° N) and two southern (50° N) populations and growing in a common garden. Leaves for RNA-seq were collected on the same day in late July, when southern trees were actively growing and northern trees had set bud. Transcripts of 2,594 genes were more abundant in actively growing leaves, whereas 1,424 were more abundant in leaves of trees that had set bud. The actively growing southern trees exhibited overexpression of genes in the biological process gene ontology (GO) domain, whereas dormant northern trees exhibited overexpression of genes in the cellular component domain. We identified relatively few genes (641) bearing signatures consistent with local adaptation to latitude for three or more SNPs. Exons from differentially expressed (DE) genes were not more likely than non-DE genes to exhibit patterns of latitudinal differentiation consistent with local adaptation. These results indicate that genes associated with differences in the timing of bud set, which is correlated with initiation of dormancy, were not more likely than other categories to exhibit latitudinal differentiation in exonic regions.

FLOWERING LOCUS T/TERMINAL FLOWER1-Like Genes Affect Growth Rhythm and Bud Set in Norway Spruce

The timing of bud set, as one determinant of the annual growth rhythm, is critical for local adaptation of the conifer Norway spruce (Picea abies). Previous gene expression and population genetic studies have suggested a role for P. abies FLOWERING LOCUS T/TERMINAL FLOWER1-Like2 (PaFTL2) in the control of growth cessation and bud set in Norway spruce as well as in local adaptation resulting in clinal variation for timing of bud set. Using transgenic plants with PaFTL2 driven by an inducible promoter, we found that PaFTL2 indeed induces bud set and most probably also growth cessation. PaFTL2 shows high expression around the procambium and vascular tissue and in the crown region in buds of both seedlings and older trees. Furthermore, PaFTL2 expression is induced in vegetative shoots and all bud types in late summer, when growth cessation occurs. This supports the notion that PaFTL2 is involved in growth cessation. A close paralog to PaFTL2, PaFTL1, is strongly expressed in meristems during the summer, possibly to repress meristem activity and the formation of needle primordia during this period. The temporal and spatial expression of PaFTL1 and PaFTL2 largely complement each other, which suggests that they act in concert to control perennial growth in Norway spruce.

The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce

BackgroundThe genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the genomic architecture of adaptive traits in black spruce, which is a widely distributed conifer of the North American boreal forest. As an alternative to the usual candidate gene approach, a candidate SNP approach was developed for association testing.ResultsA genetic map containing 231 gene loci was used to identify QTL that were related to budset timing and to tree height assessed over multiple years and sites. Twenty-two unique genomic regions were identified, including 20 that were related to budset timing and 6 that were related to tree height. From results of outlier detection and bulk segregant analysis for adaptive traits using DNA pool sequencing of 434 genes, 52 candidate SNPs were identified and subsequently tested in genetic association studies for budset timing and tree height assessed over multiple years and sites. A total of 34 (65%) SNPs were significantly associated with budset timing, or tree height, or both. Although the percentages of explained variance (PVE) by individual SNPs were small, several significant SNPs were shared between sites and among years.ConclusionsThe sharing of genomic regions and significant SNPs between budset timing and tree height indicates pleiotropic effects. Significant QTLs and SNPs differed quite greatly among years, suggesting that different sets of genes for the same characters are involved at different stages in the tree’s life history. The functional diversity of genes carrying significant SNPs and low observed PVE further indicated that a large number of polymorphisms are involved in adaptive genetic variation. Accordingly, for undomesticated species such as black spruce with natural populations of large effective size and low linkage disequilibrium, efficient marker systems that are predictive of adaptation should require the survey of large numbers of SNPs. Candidate SNP approaches like the one developed in the present study could contribute to reducing these numbers.

Predicting Adaptive Phenotypes From Multilocus Genotypes in Sitka Spruce (Picea sitchensis) Using Random Forest

Climate is the primary driver of the distribution of tree species worldwide, and the potential for adaptive evolution will be an important factor determining the response of forests to anthropogenic climate change. Although association mapping has the potential to improve our understanding of the genomic underpinnings of climatically relevant traits, the utility of adaptive polymorphisms uncovered by such studies would be greatly enhanced by the development of integrated models that account for the phenotypic effects of multiple single-nucleotide polymorphisms (SNPs) and their interactions simultaneously. We previously reported the results of association mapping in the widespread conifer Sitka spruce (Picea sitchensis). In the current study we used the recursive partitioning algorithm ‘Random Forest’ to identify optimized combinations of SNPs to predict adaptive phenotypes. After adjusting for population structure, we were able to explain 37% and 30% of the phenotypic variation, respectively, in two locally adaptive traits—autumn budset timing and cold hardiness. For each trait, the leading five SNPs captured much of the phenotypic variation. To determine the role of epistasis in shaping these phenotypes, we also used a novel approach to quantify the strength and direction of pairwise interactions between SNPs and found such interactions to be common. Our results demonstrate the power of Random Forest to identify subsets of markers that are most important to climatic adaptation, and suggest that interactions among these loci may be widespread.

Sequence variation patterns along a latitudinal cline in Scots pine (Pinus sylvestris): signs of clinal adaptation?

Adaptive clinal variation is abundant in nature, and its genetic basis is of great interest. The polygenic nature of this variation poses a challenge for identifying the causative loci underlying these adaptations. Here, we have examined the patterns of sequence variation in ten candidate genes for timing of bud set and cold tolerance, traits that form strong latitudinal clines in Scots pine (Pinus sylvestris). A set of reference genes was used for comparison and to infer a simplified demographic background model with approximate Bayesian computation methods. Against the resulting bottleneck model, the neutrality tests show little signs for local adaptation, but species-wide selection is suggested in some of the studied genes. In line with the theoretical expectations, we see little evidence for adaptive differentiation with F ST methods. Instead, allele frequency clines were found in three genes (dhn1, ftl2, and prr1). Our results add to the discussion on which molecular signals best characterize a gene subject to clinally varying selection. This will be especially relevant when these kinds of observations can be examined in parallel with association study results.

Association mapping of local adaptation traits of Scots pine in a European wide population sample

Traits related to local adaptation by definition show high phenotypic differentiation. The underlying genetic patterns could be clines at individual loci or small effects and extensive linkage disequilibrium at the underlying loci. In any case, including many populations in an analysis provides more information, but may simultaneously induce problems due to genetic structure. Even if the neutral loci have little genetic structure, loci related to other clinally selected traits could show more structure. Here we have developed an approach to efficiently use the information along a latitudinal environmental gradient. Scots pine populations from central Europe to the species' northern range were sampled and patterns of phenotypic variation of both timing of budset and frost tolerance were measured in common garden experiments, (10 populations, a total of 270 halfsib families, 25 trees per family). By hierarchical modelling of the phenotype's clinal variation and accounting for varying allele frequencies across the 10 populations, the statistical approach simultaneously exploits the genetic variation between and within populations to detect association signals. We apply shrinkage-based Bayesian variable selection to detect genetic associations between timing of bud set and ~450 SNPs in Scots pine.

A roadmap of apical bud formation in white spruce identifies potential regulators of time to bud set

Background Bud development is an adaptation that temperate forest trees have acquired to survive inclement winter conditions and resume growth the following spring. Bud development is a complex physiological and developmental process comprising bud formation, cold and desiccation tolerance development, and dormancy acquisition [1]. Because bud formation is accompanied by growth cessation, the timing of bud formation represents a trade-off between acquisition of winter hardiness and duration of active growth [2]. This is particularly true for determinate species such as white spruce (Picea glauca [Moench] Voss), where preformed stem units contained within the apical bud constitute most of next season’s growth. Timing of bud set in white spruce shows genetic variation [3]. Our goal is to identify genes that exert genetic control over time to bud set in white spruce. As first steps towards that goal, we have conducted microarray gene expression profiling of shoot tips during the transition from active growth to dormancy in white spruce, and identified candidate regulators of bud formation by comparing these differentially expressed (DE) genes to results obtained from QTL analyses of time to bud set conducted using the same genes as molecular markers.