Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.)

Nucleotide variation at several cold candidate genes including seven members of the dehydrin gene family was surveyed in haplotypes of Scots pine (Pinus sylvestris) sampled in populations showing divergence for cold tolerance in Europe. Patterns of nucleotide diversity, linkage disequilibrium, and frequency spectrum of alleles were compared between north and south populations to search for signs of directional selection potentially underlying adaptation to cold. Significant differentiation between populations in allelic frequency or haplotype structure was detected at dhn1, dhn3, and abaH loci. Allelic dimorphism with no evidence of haplotype clustering by geographical distribution was found at dhn9. An excess of fixed non-synonymous mutations as compared to the outgroup P. pinaster pine species was found at dhn1. Differences in nucleotide polymorphisms were found between the members of the Kn class of dehydrin upregulated during cold acclimation (average π_sil = 0.004) as compared to the SKn class (average π_sil = 0.024). The multilocus nucleotide diversity at silent sites (θ _W = 0.009) was moderate compared to other conifer species, but higher than previous estimates for Scots pine. There was an excess of rare and high frequency derived variants as revealed by significantly negative multilocus value of Tajima’s D (D = −0.72, P < 0.01) and negative mean value of Fay and Wu H statistics (H = −0.50). The level of linkage disequilibrium decayed rapidly with an average expected r ² of 0.2 at about 200 bp. Overall, there was a positive correlation between polymorphism and divergence at ten loci when outgroup sequence was available. The discovered polymorphism will be used for further evaluation of the adaptive role of genes through association mapping studies. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

High genetic similarity between Polish and North European Scots pine (Pinus sylvestris L.) populations at nuclear gene loci

Nucleotide polymorphisms in a set of 32 nuclear genes were studied in 19 mountain, peatbog and lowland populations of Scots pine representing known phenotypic races and populations of presumably relict character for the species in Poland. At 29 genes, the pattern of genetic variation was compared to 11 reference populations from Northern, Western and Southern Europe. Similar levels of nucleotide polymorphism and excess of low-frequency mutations were observed in Polish populations (π _tot?=?0.0055, D?=??0.308) and as compared to the reference samples (π _tot?=?0.0054, D?=??0.170). Bayesian assignment and conventional frequency-based statistics indicate that Polish populations share the same genetic background at the analysed nuclear gene markers. However, the populations showed a much closer genetic relationship with North European samples than other regional groups of populations. Across the very uniform genetic background of the populations, we identified several genes with outlier patterns of haplotype, polymorphism frequency variation and departures from compound neutrality tests. Our data indicate that the Central and North European parts of the Scots pine distribution seem particularly suitable for association genetic studies to link phenotypic and genetic variation at a large geographical scale.     

Among population differentiation at nuclear genes in native Scots pine (Pinus sylvestris L.) in Scotland

In the Scottish Highlands, Scots pine is at the north-western extreme of its wide natural distribution. Here, the remaining native populations are patchily distributed in highly variable environments, from the more continental, drier eastern Highlands to the milder, wetter Atlantic Ocean coast. As these pinewoods are the remnants of a naturally established forest, they form a valuable system for analysis of genetic and adaptive variation in heterogeneous environments. Using samples from across the Scottish population, we analysed data from nuclear and mitochondrial genes to assess patterns of within and between population genetic variation. Within population diversity levels were high, and significant genetic differentiation among pairs of Scottish populations at relatively small spatial scales was present at several nuclear loci. At these loci, no differentiation had been found among continental populations, even those separated by large geographic distances. Overall, no clear clustering of Scottish samples was found in population structure analysis suggesting that geographically distant populations with high intra-population nucleotide diversity are not strongly isolated or diverged from each other. Scottish populations lacked a mitotype that is widespread in eastern and north-eastern Europe, indicating that pines from that area may not have participated in the most recent colonisation of the British Isles.     

Spring phenology shows genetic variation among and within populations in seedlings of Scots pine (Pinus sylvestris L.) in the Scottish Highlands

Background: Genetic differentiation in phenotypic traits is often observed among forest tree populations, but less is known about patterns of adaptive variation within populations. Such variation is expected to enhance the survival likelihood of extant populations under climate change.

Aims: Scots pine (Pinus sylvestris) occurs over a spatially and temporally heterogeneous landscape in Scotland. Our goal was to examine whether populations had differentiated genetically in timing of bud flush in response to spatial heterogeneity and whether variation was also maintained within populations.

Methods: Two common-garden studies, involving maternal families of seedlings from 21 native pinewoods, were established and variation in the trait was measured at the beginning of the second growing season.

Results: Populations showed genetic differences in the trait correlated with the length of growing season at their site of origin, but the majority of variation was observed within populations. Populations also differed in their levels of variation in the trait; a pattern that may be influenced by spatial variation in the extent of temporal climate variability.

Conclusions: Our findings suggest that populations have adapted to their home environments and that they also have substantial ability to adapt in situ to changes in growing season length.     

Electrophoretic analysis of genetic linkage in Scots pine (Pinus sylvestris L.)

Eighty megagametophytes from each of 24 Scots pines (Pinus sylvestris L.) were subjected to horizontal starch gel electrophoresis. The trees were from crosses among widely separated provenances, and each was polymorphic for 8 to 14 loci. Evidence for linkage among 275 two-locus combinations was tested using chi-square analysis. Data from different trees were pooled to calculate map distances for the species. Nineteen of the twenty-nine loci tested were linked in one of six groups; the groups varied in size from two to seven loci. Similarities in linkage relationships among Scots pine, other pines, and other species within the Pinaceae support karyological research that suggests extensive conservation of the conifer genome.     

Cryptic genetic variation and adaptation to waterlogging in Caledonian Scots pine,Pinus sylvestris L.

Local adaptation occurs as the result of differential selection among populations. Observations made under common environmental conditions may reveal phenotypic differences between populations with an underlying genetic basis; however, exposure to a contrasting novel environment can trigger release of otherwise unobservable (cryptic) genetic variation. We conducted a waterlogging experiment on a common garden trial of Scots pine, Pinus sylvestris (L.), saplings originating from across a steep rainfall gradient in Scotland. A flood treatment was maintained for approximately 1 year; physiological responses were gauged periodically in terms of photochemical capacity as measured via chlorophyll fluorescence. During the treatment, flooded individuals experienced a reduction in photochemical capacity, F_v/F_m, this reduction being greater for material originating from drier, eastern sites. Phenotypic variance was increased under flooding, and this increase was notably smaller in saplings originating from western sites where precipitation is substantially greater and waterlogging is more common. We conclude that local adaptation has occurred with respect to waterlogging tolerance and that, under the flooding treatment, the greater increase in variability observed in populations originating from drier sites is likely to reflect a relative absence of past selection. In view of a changing climate, we note that comparatively maladapted populations may possess considerable adaptive potential, due to cryptic genetic variation, that should not be overlooked.     

马尾松和黄山松两个核基因位点的群体遗传多样性和种间分化

利用两个核基因座位C3H和GI, 对重叠分布于中国东南部的两个松属(Pinus)物种马尾松(P. massoniana)和黄山松(P. hwangshanensis)的22个群体88个个体进行了遗传多样性和种间分化模式研究。在这两个核基因座位上, 两种植物都表现出较低的核苷酸多样性水平(马尾松π_sil = 0.001 71; 黄山松π_sil = 0.003 40), 但是马尾松要显著低于黄山松; 在种内分化水平上, 马尾松的种内遗传分化也明显低于黄山松(马尾松F_ST = 0.059; 黄山松F_ST = 0.339)。这可能是由于黄山松的海拔分布高于马尾松, 而高海拔分布使黄山松的分布区域更加片段化, 促使其形成较高的种内遗传多样性和遗传分化。分子变异分析(AMOVA)发现, 两物种基于两个核基因座位的种间差异为48.86%, 而GI基因座位上的种间差异明显高于C3H座位(GI: 77.24%, C3H: 20.48%), 同时, 基因谱系显示两物种的共享单倍型仅在C3H座位上存在。结合这两个基因的功能, 推测GI基因可能在物种形成过程中受到了一定的选择压力, 因为GI基因参与调控植物的开花时间, 而C3H与木质素表达水平的调控有关。不同的选择压力使得GI的进化速度相对较快, 从而加速了黄山松和马尾松的物种分化。     

Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice

Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of O. sativa and its close relatives (Oryza rufipogon and Oryza nivara), we investigated nucleotide diversity data from 10 unlinked nuclear loci in species-wide samples of these species. The results indicated that O. rufipogon and O. nivara possessed comparable levels of nucleotide variation ((sil) = 0.0077 approximately 0.0095) compared with the relatives of other crops. In contrast, nucleotide diversity of O. sativa was as low as (sil) = 0.0024 and even lower ((sil) = 0.0021 for indica and 0.0011 for japonica), if we consider the 2 subspecies separately. Overall, only 20-10% of the diversity in the wild species was retained in 2 subspecies of the cultivated rice (indica and japonica), respectively. Because statistic tests did not reject the assumption of neutrality for all 10 loci, we further used coalescent to simulate bottlenecks under various lengths and population sizes to better understand the domestication process. Consistent with the dramatic reduction in nucleotide diversity, we detected a severe domestication bottleneck and demonstrated that the sequence diversity currently found in the rice genome could be explained by a founding population of 1,500 individuals if the initial domestication event occurred over a 3,000-year period. Phylogenetic analyses revealed close genetic relationships and ambiguous species boundary of O. rufipogon and O. nivara, providing additional evidence to treat them as 2 ecotypes of a single species. Lowest linkage disequilibrium (LD) was found in the perennial O. rufipogon where the r(2) value dropped to a negligible level within 400 bp, and the highest in the japonica rice where LD extended to the entirely sequenced region ( approximately 900 bp), implying that LD mapping by genome scans may not be feasible in wild rice due to the high density of markers needed.     

Ectomycorrhizal development on Scots pine (Pinus sylvestris L.) seedlings in different soils

In the present study ectomycorrhizal development of Laccaria bicolor, Rhizopogon luteolus and Suillus bovinus associated with Scots pine (Pinus sylvestris) seedings was studied as affected by primary stand humus, secondary stand humus, podsolic sandy soil or peat in perspex growth chambers. After 9 weeks, ectomycorrhizal development with S. bovinus was significantly greater in peat and primary stand humus than in secondary stand humus or podsolic sandy soil. Ectomycorrhizal development with R. luteolus in secondary stand humus was higher than in primary stand humus. Degree of ectomycorrhizal development of L. bicolor, R. lutuelus and S. bovinus on Scots pine was related to potassium concentration, organic matter content and pH of the soils suggesting that chemical composition of the soils affects ectomycorrhizal development.     

Removal of nitrogen during needle senescence in Scots pine (Pinus sylvestris L.)

The concentrations of arginine, protein and total nitrogen (N) and the abundance of¹⁵N were measured in 3-and 4-year-old needles of Scots pine trees fertilized with either 0 (C), 36 (N1) or 73 (N2) kg N ha^-1 year^-1 annually for 22 years (average doses of N). Remaining green needles and needles that were shed were compared and removal of N from total, protein and arginine pools was calculated. Earlier investigations had shown that high arginine concentrations are found in needles of trees that have an excessive N supply (Näsholm and Ericsson 1990). This study aimed to elucidate the fate of the accumulated arginine during needle senescence. It was speculated that a low removal of arginine during senescence would implicate that the primary function of arginine is in N detoxification and not in N storage. Moreover, litter quality would be altered if needles are shed with high concentrations of arginine and this might affect the turnover of N in forest ecosystems. In remaining green needles, the concentration of total N increased with increasing N supply. Protein N concentrations were higher in fertilized trees, but did not differ between the two N treatments. Arginine N was low in C and N1 trees but high in N2 trees. Senescent needles from C and N1 trees had about equal total N concentrations while in N2 trees this concentration was significantly higher. Protein N in senescent needles did not differ between treatments. Arginine N, however, was less than 0.1 mg g^–1 dw in C and N1 trees but was higher than 1.5 mg g^–1 dw in N2 trees. Removal of N was highest in N1 trees followed by C trees while N2 trees removed least N from senescing needles. The high concentration of total N in senescent needles from N2 trees was to a great extent explained by a high arginine concentration.The ¹⁵N value of remaining, green needles was higher (less negative) in N2 trees than in C and N1 trees. The same pattern was found for senescent needles. Comparisons of ¹⁵N values between remaining, green and senescent needles within each treatment showed a significant increase in ¹⁵N for all treatments during senescence possibly indicating losses of N as NH₃ (g) from needles during senescence. It is concluded that arginine, accumulated in response to high N supply, is retranslocated only to a small extent during needle senescence. The ecological and physiological implications of this finding are discussed.     

Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris

Forest tree species provide many examples of well-studied adaptive differentiation, where the search for the underlying genes might be possible. In earlier studies and in our common conditions in a greenhouse, northern populations set bud earlier than southern ones. A difference in latitude of origin of one degree corresponded to a change of 1.4 days in number of days to terminal bud set of seedlings. Earlier physiological and ecological genetics work in conifers and other plants have suggested that such variation could be governed by phytochromes. Nucleotide variation was examined at two phytochrome loci (PHYP and PHYO, homologues of the Arabidopsis thaliana PHYB and PHYA, respectively) in three populations: northern Finland, southern Finland and northern Spain. In our samples of 12-15 sequences (2980 and 1156 base pairs at the two loci) we found very low nonsynonymous variation; pi was 0.0003 and 0.0002 at PHYP and PHYO loci, respectively. There was no functional differentiation between populations at the photosensory domains of either locus. The overall silent variation was also low, only 0.0024 for the PHYP locus. The low estimates of silent variation are consistent with the estimated low synonymous substitution rates between Pinus sylvestris and Picea abies at the PHYO locus. Despite the low level of nucleotide variation, haplotypic diversity was relatively high (0.42 and 0.41 for fragments of 1156 nucleotides) at the two loci.     

Bacterial endobionts in the big non-mycorrhizal roots of Scots pine (Pinus sylvestris L.)

Subsurface bacterial growth occurred in an N-free medium inoculated with interior tissues of big non-mycorrhizal roots (7 to 8 mm diameter) of 15-20 years-old Scots pine (Pinus sylvestris L.) growing on sand dunes at the Baltic Sea of Poland. The bacteria were not N2 fixers as determined by the acetylene reduction method. Light microscopic and scanning electron microscopic observations revealed massive bacterial clusters residing in the cortical cells underlying epidermis and parenchyma. The bacteria produced yellow-green pigments on King's medium, which fluoresced under ultraviolet (UV) irradiation at 366 nm wavelength, and could be a siderophore-producing Pseudomonas.     

The effects of UV-B radiation on epidermal anatomy in loblolly pine (Pinus taeda L.) and Scots pine (Pinus sylvestris L.)

The effects of enhanced UV‐B radiation on the needle anatomy of loblolly pine (Pinus taeda L.) and Scots pine (Pinus sylvestris L.) were studied in the field under supplemental UV‐B radiation supplied by a modulated irradiation system. The supplemental UV‐B levels were designed to simulate either a 16 or 25% loss of stratospheric ozone over College Park, Maryland. Enhanced UV‐B radiation caused different responses in these two species. The needles of loblolly pine had larger amounts of tannin in the lumen of epidermal cells and more wall‐bound phenolics in the outer epidermal walls of UV‐B‐treated needles, whereas the most pronounced effect on Scots pine needles was increased cutinization. In both species, the outer epidermal cell walls thickened and the needle cross‐sectional and mesophyll areas decreased (statistically significantly only in Scots pine). This suggests that more carbon may have been allocated to the protection mechanisms at the expense of photosynthetic area. The difference in response between these species suggests that the response to UV‐B radiation is not mediated by a single mechanism and that no generalization with regard to the effects of UV‐B on conifers can be made.     

Genetic insights into the evolution of Scots pine,Pinus sylvestris L., in Scotland

Summary

Present day populations of native Scots pine contain a wealth of genetic variation. The arrangement of this variation within and among populations has been influenced by a number of processes in the past. These include patterns of recolonization of Scotland after glaciation, gene flow among populations, and natural selection acting at both a regional and local scale. By analyzing present day patterns of genetic variation, insights into past evolution can be obtained. Suitable analysis of genetic variation for monoterpenes, enzymes, mitochondrial DNA and quantitative characters such as growth rate and phenology in native pine indicate two origins for Scottish populations, substantial adaptive divergence from continental populations, and the presence of local adaptation within Scotland. The implications for conservation and future research are addressed.     

Ribosomal RNA genes in Scots pine (Pinus sylvestris L.): Chromosomal organization and structure

The nuclear 18S, 5.8S and 25S rRNA genes exist as thousands of rDNA repeats in the Scots pine genome. The number and location of rDNA loci (nucleolus organizers, NORs) were studied by cytological methods, and a restriction map from the coding region of the Scots pine rDNA repeat was constructed using digoxigenin-labeled flax rDNA as a probe. Based on the maximum number of nucleoli and chromosomal secondary constrictions, Scots pine has at least eight NORs in its haploid genome. The size of the Scots pine rDNA repeat unit is approximately 27 kb, two- or threefold larger than the typical angiosperm rDNA unit, but similar in size to other characterized conifer rDNA repeats. The intergenic spacer region (IGS) of the rDNA repeat unit in Scots pine is longer than 20 kb, and the transcribed spacer regions surrounding the 5.8S gene (ITS1 and ITS2) span a region of 2.9 kb. Restriction analysis revealed that although the coding regions of rDNA repeats are homogeneous, heterogeneity exists in the intergenic spacer region between individuals, as well as among the rDNA repeats within individuals.     

The postglacial history of Scots pine (Pinus sylvestris L.) in western Europe: evidence from mitochondrial DNA variation

The geographical structure of mitochondrial (mt)DNA variants (mitotypes) was investigated in 38 western European populations of Scots pine Pinus sylvestris using restriction fragment length polymorphism (RFLP) analysis of total DNA and a homologous cox1 probe. Three major mitotypes (designated a, b and d ) were detected. Within Spain all three major mitotypes were found, gene diversity was high, H_T = 0.586, and this diversity was distributed predominantly among rather than within populations (F_ST(M) = 0.813 for the seven Spanish populations). Mitotype d was present only in the most southerly population from the Sierra Nevada . Elsewhere in Europe, populations showed little or no mtDNA diversity within regions, but there were marked differences between regions. Italian populations were fixed for mitotype b ; populations from northern France, Germany, Poland, Russia and southern Sweden were fixed for mitotype a ; while populations in northern Fennoscandia were fixed for mitotype b . The isolated Scottish populations were predominantly of mitotype a , but mitotype b was present in three of the 20 populations scored. In Scotland, UK gene diversity (H_T = 0.120) and genetic differentiation among populations (F_ST(M) = 0.37) was much lower than in Spain. When interpreted in the light of complementary data from pollen analysis and nuclear genetic markers, the results suggest that present-day populations of P. sylvestris in western Europe have been derived from at least three different sources after glaciation.     

Daily dynamics in xylem cell radial growth of Scots pine (Pinus sylvestris L.)

Daily dynamics of radial cell expansion during wood formation within the stems of 25-year-old Scots pine trees (Pinus sylvestris L.), growing in field conditions, were studied. The samples of forming wood layers were extracted 4 times per day for 3 days. Possible variations in the growth on different sides of the stem, duration of cell development in radial cell expansion phase and dynamics of cell growth in this phase were taken into account. The perimeters of tracheid cross-sections as a reflection of primary cell wall growth were the criterion of growth in a radial direction. For the evaluation of growing cell perimeters a special system for digital processing and image analysis of tracheid cross-sections of the forming wood was used. Growth rate for certain time intervals was estimated by the change in the relation of the perimeter of each observed cell in each of ten tracheid rows in each of 12 trees to the perimeter of the xylem cell of the same row before the expansion. Temporal differences in average values of the relations were estimated by Analyses of Variance. The existence of daily dynamics of Scots pine xylem cell radial growth has been proved. Intensive growth of pine tracheids has been shown to occur at any time of the day and to depend on the temperature regime of the day and the night as well as water supply of stem tissues. Moreover, reliable differences (P = 0.95) in the increment of cell walls during tracheid radial expansion have been found. Pulsing changes of the water potentials both of the cell and the apoplast, as the reason for the fluctuations of radial cell growth rate, were discussed.     

Gene-pool variation in caledonian and European Scots pine (Pinus sylvestris L.) revealed by chloroplast simple-sequence repeats.

We have used polymorphic chloroplast simple-sequence repeats to analyse levels of genetic variation within and between seven native Scottish and eight mainland European populations of Scots pine (Pinus sylvestris L.). Diversity levels for the Scottish populations based on haplotype frequency were far in excess of those previously obtained using monoterpenes and isozymes and confirmed lower levels of genetic variation within the derelict population at Glen Falloch. The diversity levels were higher than those reported in similar studies in other Pinus species. An analysis of molecular variance (AMOVA) showed that small (3.24-8.81%) but significant (p < or = 0.001) portions of the variation existed between the populations and that there was no significant difference between the Scottish and the mainland European populations. Evidence of population substructure was found in the Rannoch population, which exhibited two subgroups. Finally, one of the loci studied exhibited an allele distribution uncharacteristic of the stepwise mutation model of evolution of simple-sequence repeats, and sequencing of the PCR products revealed that this was due to a duplication rather than slippage in the repeat region. An examination of the distribution of this mutation suggests that it may have occurred fairly recently in the Wester Ross region or that it may be evidence of a refugial population.     

Topographic influences on radial growth of Scots pine (Pinus sylvestris L.) at small spatial scales

Dendroecological and numerical methods were used to study the influence of topographic position on radial growth of Scots pine (Pinus sylvestris) stands exposed to soil dryness. The correlation structure of total tree-ring width and latewood width of eight scattered populations representing various topographic habitats (steep south-facing slopes, plateaus and hollows) within a rock-slide area (750 m a.s.l.) of about 1 km² was investigated by principal component analysis. Scatter plots of component loadings indicated that (i) total ring width and latewood width are influenced by various climatic factors, (ii) stands growing at similar topographic position show a high agreement in year-to-year variability of radial growth, and (iii) distinct effects of topographic features (slope aspect, slope magnitude) on tree growth are modified by local disturbances (erosion, grazing) and the age structure of stands. Furthermore, both the time series of component scores and non-metric multidimensional scaling of chronologies indicated years where extremely limiting or favorable climate conditions prevailed throughout the study area (pointer years). The influence of climate on tree growth in various topographic habitats was mediated through the influence of climatically stressful years. Because stands are located at sites with different levels of water stress, growth differences between chronologies are considered to be caused by site-specific susceptibility of tree growth to soil dryness. Significant correlations between precipitation in April to June and ring-width confirm that water availability is the primary growth-limiting factor within the study area. These small-scale variations in growth-climate relationships have significant implications for dendroclimatological studies. So paleoclimatic reconstructions based on tree rings will have to assure that an unbiased data set is used, which compensates for local growth-variabilities due to site related environmental stresses.     

Environmental factors and host genetic variation shape the fungal endophyte communities within needles of Scots pine (Pinus sylvestris)

To determine the role of environmental and host genetic factors in shaping fungal endophyte communities we used culturing and metabarcoding techniques to quantify fungal taxa within healthy Scots pine (Pinus sylvestris) needles in a 7-y old provenance-progeny trial replicated at three sites. Both methods revealed a community of ascomycete and basidiomycete taxa dominated by the needle pathogen Lophodermium seditiosum. Differences in fungal endophyte taxon composition and diversity indices were highly significant among trial sites. Within two sites, fungal endophyte communities varied significantly among provenances. Furthermore, the communities differed significantly among maternal families within provenances in 11/15 and 7/15 comparisons involving culture and metabarcoding data respectively. We conclude that both environmental and host genetic variation shape the fungal endophyte community of P. sylvestris needles.