A preliminary study on the genetic structure of Northern European pinus sylvestris L. by means of neutral nuclear microsatellite markers

This paper aimed to investigate the genetic structure (GS) of Scots pine in the northern area of its distribution range by means of seven neutral nuclear microsatellite markers. In particular, the postglacial recolonization of these areas and possible different adaptation patterns in distinct refugia were studied. The GS and diversity were assessed with seven pairs of neutral nuclear microsatellite primers. A high genetic diversity was found in the Scots pine material tested, along with a shallow GS. This pattern is typical for recolonized areas and species with large population sizes, which are connected by pollen-mediated gene flow. A STRUCTURE analysis found two genetic groups to be the most likely, one south-eastern and one north-western group that meet in Fennoscandia. This indicates that Scots pine recolonization of Fennoscandia might have taken place from two different directions (south-west and north-east). Scots pine that recolonized the area originated in at least two different refugia during the last glacial maximum. The glacial survival in distinct refugia can have led to different adaptation patterns and growth optima in the different groups as reflected in the formation of latewood content, where lineage was a significant influencing factor.     

Genetic variability of Italian southern Scots pine (<Emphasis Type="Italic">Pinus sylvestris</Emphasis> L.) populations: the rear edge of the range

Understanding the genetic structure and diversity of edge populations can shed light on the role of peripheral populations and their relevance for conservation strategies. In this study, three fragmented and isolated Apennine populations of Scots pine (Pinus sylvestris L.) belonging to the rear edge of the species’ distribution were analyzed using both nuclear (nSSR) and chloroplast (cpSSR) microsatellites and were compared with an Alpine population belonging to the species’ main range. Although small population size and considerable isolation have probably reduced the genetic variability of Apennine populations, these fragmented populations maintain a high level of within-population genetic diversity. A significant among-population differentiation was found using both nSSR (F _ST = 0.08) and cpSSR markers (ρ = 0.14). Analysis of molecular variance (AMOVA) on the nSSRs attributed all variabilities to the among Apennine populations component supporting the theoretical predictions regarding fragmentation effects on genetic structure. On the other hand, AMOVA on the cpSSRs attributed all variances to the between-region component and no differentiation was found within region, among the Apennine populations. This result suggests the importance of pollen gene flow in homogenizing populations on this geographical scale. Our results confirm the genetic distinctiveness of Apennine populations and their possible derivation from different glacial refugia than those of the Alps. Considering their peculiarity and the high level of intrapopulation genetic diversity that they still retain, fragmented Apennine populations should be considered of high priority for conservation.     

Large-scale genetic structure and drought-induced effects on European Scots pine (Pinus sylvestris L.) seedlings

Seedlings of ten provenances of Scots pine (Pinus sylvestris L.) from the southwestern to the central part of the species distribution range were investigated in a greenhouse experiment under dry conditions compared to a well-watered control. We conducted an isozyme study and recorded phenology as well as growth traits during the first year of growth. Genetic variability and genetic diversity increased from the westernmost provenances to those central to the distribution. Provenances from the Apennines and Spain revealed the strongest genetic differentiation compared to all others, whereas populations from Germany, Poland and Bulgaria were found to belong to the same gene pool. Seedling development and bud set were faster in northern populations. Shoot length was highest for Polish and German provenances within both regimes, populations from France and Spain had the longest roots. Reduced soil moisture slowed later development stages and delayed bud set for all provenances by about 5 days. Shoot growth decreased considerably under the dry regime for all provenances. German provenances were the most sensitive to drought, whereas Spanish provenances showed adaptation to drought conditions indicated by the lowest reduction in shoot growth relative to optimum conditions. The results of this pilot study show that under more pronounced drought conditions with repeated drought events, the so far established superiority of northeastern provenances compared to southwestern ones could diminish in the future.     

Persistence of a biocontrol strain of Phlebiopsis gigantea in conifer stumps and its effects on within‐species genetic diversity

Fungal isolations and genetic fingerprinting were used to determine whether Phlebiopsis gigantea stump treatment against Heterobasidion annosum sl. using a single genotype (Rotstop) would affect the genetic diversity of P. gigantea populations. The survival time of P. gigantea was longer in Norway spruce (Picea abies) stumps compared to Scots pine (Pinus sylvestris) as no isolates were obtained from pine stumps 6 years after treatment, whereas in about half of the spruce stumps the fungus was still present. The usage of Rotstop did not seem to increase the occurrence of the fungus 5 years after the treatment in fresh (1‐year‐old) untreated stumps within the same forest stands. All the isolates from the 6‐year‐old treated spruce stumps were identical in genotype with the Rotstop‐strain, whereas all isolates from the fresh untreated spruce and pine stumps differed from it. Within the treated pine stand, the biocontrol usage seemed to have caused a slight reduction in genetic markers not related to Rotstop, but there were no statistically significant differences between the marker frequencies and the local natural population. Thus, Rotstop is not likely to cause any immediate threat to the genetic diversity of P. gigantea.     

Genetic diversity of Populus euphratica populations in northwestern China determined by RAPD DNA analysis

Five Populus euphratica Oliver populations in northwestern China were analyzed using RAPD DNA markers to determine genetic diversity among and within populations. One hundred-and-five polymorphic bands were observed, ranging in size from 250 bp to 1700 bp, using 10 primers. Only one population on the north side of the Tianshern Range had a unique band common to all individuals that was not found in individuals from populations in the Tarim River valley. Intra-population genetic diversity was high in two populations along the Tarim River and low in the other three populations. There was no significant correlation between genetic distances and geographic distances. The result of correspondence analysis shows that the individuals from the three populations with low genetic diversity are isolated from each other. The result of cluster analysis based on genetic distance shows that the population in the Tianshern Range is genetically distant from the other populations. These results suggest that the Tianshern Range population was genetically isolated from the other populations.     

Population management: potential impacts of advances in genomics

Even with advanced gene technologies continued population improvement remains a key foundation for future genetic gain in forest trees. Currently, this is served by maintaining genetic diversity while capturing genetic improvement, often through structuring populations into a genetic hierarchy, setting population sizes, and managing pedigrees and inbreeding. In the future, information from genomic technologies will complement classical approaches, such as common-garden field experiments, for characterizing the genetic base and measuring and monitoring genetic diversity. This will entail directly measuring DNA sequence diversity of both selectively neutral markers and functional genes. Calibrating neutral marker diversity against functional diversity will become easier with functional genomics. For maintaining pedigree and managing inbreeding, genomic information can be used to relax some traditional tenets of population management. With future knowledge of functional polymorphisms, the better understanding of the nature and origins of genetic variation should enhance management of populations to both conserve genetic diversity and exploit it by more efficient selection. Where fungal diseases threaten biotic crises, very large populations may be needed, the requisite sizes often being very uncertain. Gene discovery holds enormous promise, but depends heavily on comparative genomics, capitalizing on genomic information from Arabidopsis, Populus and Eucalyptus, and the increasing numbers of accessible ESTs. Much greater insights into non-codon mutational processes and rates should also guide population management. A key challenge, however, will be to utilize information and apply tools cost-effectively. Also, very detailed genomic information, exemplified by the poplar-genome sequencing, may allow earlier adaptation of technology and development of new information in angiosperms than in gymnosperms.     

Population biology of sugar pine (Pinus lambertiana Dougl.) with reference to historical disturbances in the Lake Tahoe Basin: Implications for restoration

Historical logging, fire suppression, and an invasive pathogen, Cronartium ribicola, the cause of white pine blister rust (WPBR), are assumed to have dramatically affected sugar pine (Pinus lambertiana) populations in the Lake Tahoe Basin. We examined population- and genetic-level consequences of these disturbances within 10 sugar pine populations by assessing current population structure and trends for 1129 individuals, genetic diversity for 250 individuals, and frequency of WPBR-resistance for 102 families. Logging had occurred in 9 of 10 sites and fire suppression was evident in all stands. High density of white fir (Abies concolor) is often an indicator of fire suppression and we found a negative relationship between sugar pine survivorship and white fir basal area (r² = 0.31). C. ribicola was present in 90% of stands (incidence range: 0-48%) and we found a significant relationship between mean host survivorship and disease incidence (r² = 0.46). We estimated population growth rates (λ) from size-based transition matrices. For six of 10 sugar pine populations λ was ?1.0, indicating that these populations appear to be stable; for four populations, λ was <1.0, indicating populations that may be in decline. A population specific drift parameter, c_i, which is a measure of genetic differentiation in allele frequencies relative to an ancestral population, ranged from 0.009 to 0.048. Higher values of c_i indicate greater genetic drift, possibly due to a bottleneck caused by historical logging, other agents of mortality or much older events affecting population sizes. Effects of drift are known to be greater in small populations and we found a negative relationship between sugar pine density and c_i (r² = 0.36). Allele frequency of the Cr1 gene, responsible for WPBR-resistance in sugar pine, averaged 0.068 for all populations sampled; no WPBR infection was found in one population in which the Cr1 frequency was 0.112. Historical disturbances and their interactions have likely influenced the population biology of sugar pine in the Tahoe Basin; for some populations this has meant reduced population size, higher genetic drift, and poor survival of small- and intermediate-sized individuals. Possible management strategies include restoring population numbers, deploying WPBR-resistance, treating stands to promote natural sugar pine regeneration, and enhancing genetic diversity.     

A population genetic study in a scattered forest species, wild service tree [Sorbus torminalis (L.) Crantz], using RAPD markers

Wild service tree [Sorbus torminalis (L.) Crantz] is a forest tree widespread in Europe, characterized by a scattered distribution. Its hermaphroditic flowers are pollinated by insects, and outcrossing is the prominent mating system, also due to the presence of gametophytic self-incompatibility. Genetic diversity and differentiation of 22 populations from northwestern Italy were investigated by means of variation scored at 53 polymorphic RAPD (Random Amplified Polymorphic DNA) loci. Populations differed in genetic variation, with Shannon diversity index ranging from 0.166 to 0.469. According to Analysis of Molecular Variance (AMOVA), most of the genetic variation was found within populations (61.78%) with a significant proportion of variance attributable to genetic differences between regions (23.60%) and between populations (14.62%). Evidence for isolation by distance was found in the set of populations sampled. The effect of habitat fragmentation on genetic variation was also evaluated. The efficacy of RAPD markers in analysing genetic variation, and the contribution of the results in terms of the preservation of biodiversity are discussed.     

Advanced generation seed orchards’ turnover as affected by breeding advance,time to sexual maturity and costs,with special reference to Pinus sylvestris in Sweden

Abstract

The effect of various biological, genetic, economic and management factors relevant to advanced generation seed orchard establishment was investigated using numerical estimates for Scots pine (Pinus sylvestris L.) in Sweden. Factors considered were planting density, rate of genetic advance in the breeding population, timing of first seed collection, seed value, seed production cost (stratified to establishment, annual management, cone harvest and seed extraction), orchard rotation age and contamination level. The developed model demonstrated its utility in studying and evaluating various economic and biological options associated with advanced generation seed orchard establishment/turnover. Sensitivity analyses demonstrated the robustness of the developed model through various arbitrarily changes in genetic gain advances, establishment, management and seed production, particularly those associated with cone harvests from upper crown and costs. The Swedish Scots pine case study produced results supporting faster turnover of seed orchard generations (30 vs 40 years) with shorter orchard lifespan (early start of seed cone after 8 years vs 15 years) delivering higher gain through minimizing the genetic gain differential between the breeding and production populations and allowing the capture of this gain for inclusion in the seed orchards. Orchard planting densities of 400 and 600 grafts per hectare produced similar results with marginal differences, and the latter was recommended for future orchard establishment.     

Patterns of genetic diversity that result from bottlenecks in Scots Pine and the implications for local genetic conservation and management practices in Bulgaria

As one of the principal coniferous species of commercial importance in Bulgaria, Scots Pine has been subjected to strict management, which has posed a challenge for the conservation and management of its gene pool. In this study, we measured genetic diversity and population structure using 6 microsatellite loci in 12 populations from Bulgarian mountain ranges. Our analysis showed good intrapopulation divergence (18.22%; AMOVA) and genetic evidence of bottlenecks. “NJ-IAM” and “non-admixing” clusters divided the populations into 3 large groups. Our microsatellite analysis was consistent with the documented “mountain effect” influence on genetic diversity. Two methods—the Coalescent Bayesian model and M-stat analysis—implicated recent bottlenecks for all populations, suggesting that the genetic structure of Bulgarian Scots Pine was shaped over a long period (one thousand generations; i.e. 20,000 years) by the interaction of genetic and autoecological processes. Our results suggest that conservation and management practices should strive to maintain this genetic differentiation, specifically by emphasizing reforestation efforts with stocks from local provenances to avoid nonlocal introductions.     

RAPD Marker Diversity Within and Among Natural Populations of the Clonal Tree Cryptomeria japonica D. Don.

Abstract

The Japanese cedar, Cryptomeria japonica D. Don., is one of the most important endemic species in Japan. A long history of heavy logging has resulted in natural populations being discontinuously distributed and scattered among small, restricted areas. An understanding of the patterns of genetic variability among and within populations of C. japonica is important for conserving the genetic resources of this economically important species. We studied genetic variation by random amplified polymorphic DNA (RAPD) markers in C. japonica of Kyoto prefecture, western Japan. A total of 398 plants sampled from six natural populations were analyzed by ten arbitrarily chosen decamer primers, resulting in 50 highly reproducible RAPD bands. Analysis of molecular variance partitionated the RAPD variation into the among- and within population components. The within-population component accounted for 93.75% of the variation. The among-population component accounted for only 6.25%. Indirect estimates of gene flow indicated that the average number of migrants exchanged among six populations per generation was 3.72. A Mantel test for each population did not yield significant correlations between geographic and genetic distances. The extent and distribution of C. japonica diversity in the Kyoto prefecture is in agreement with the conclusion that long-lived, wind-pollinated, out-crossing species with wide ranges retain a considerable amount of genetic diversity within populations and exhibit little genetic differentiation among populations.     

Quantifying the effect of pine mistletoe on the growth of Scots pine

Mistletoe infection results in substantial growth losses in mistletoe‐infected forests. This study reports and evaluates the results of retrospective analyses of radial growth of Scots pine (Pinus sylvestris) in relation to the level of infection of pine mistletoe (Viscum album ssp. austriacum). A total of 43 Scots pine trees were destructively sampled from different sites. Of these trees, 14 were uninfected and 29 were infected. Infection classes were determined using six‐class dwarf mistletoe rating system (DMRS). All needle and mistletoe biomass were removed completely and weighed for each sampled tree. Subsamples from needles and all mistletoe biomass were taken to the laboratory for oven‐dried weight determinations. Five‐cm‐thick wood discs were cut from the stem at the breast height (1.3 m) to determine annual basal area increment for the last 25 years. In addition to DMRS, new infection classes were created using mistletoe‐to‐needle biomass (MB/NB) ratio. The results showed that the radial growth losses could be as much as 41% to 64% at different infection levels. The rate of growth loss in relation to DMRS and MB/NB ratio was similar, but with a larger variability in DMRS values. The results showed that both DMRS rating and MB/NB ratio seem to be important for quantifying growth loss on Scots pine trees infected with mistletoe. The results of this study can also be invaluable in modelling the effects of mistletoe on the growth of Scots pine trees.     

Genetic diversity and differentiation of yellowwood [<Emphasis Type="Italic">Cladrastis kentukea</Emphasis> (Dum.Cours.) Rudd] growing in the wild and in planted populations outside the natural range

Yellowwood (Cladrastis kentukea) grows in small, widely scattered populations in the wild, but is also a popular ornamental tree that thrives when planted in urban areas outside its natural range. Since the small native populations of yellowwood in several states are considered at risk of extirpation, the cultivated population could serve as an ex situ repository of yellowwood genetic diversity that could be used to restore lost local populations of the species. The potential value of cultivated yellowwood for conservation depends on the genetic diversity among cultivated trees compared to natural populations. Using nuclear microsatellite markers, we genotyped 180 yellowwoods from natural populations in Indiana, Missouri, Arkansas, and Kentucky, along with 61 trees from urban parks and landscapes in Indiana, Ohio, and Missouri. We found that, even when statistics were adjusted based on population size, the urban “population” had higher genetic diversity than any of the wild populations sampled, indicating that commercially-grown yellowwood is most likely a mixture of genotypes from isolated wild populations. We observed strong genetic differentiation among wild populations, and evidence for inbreeding in at least one of the wild populations.     

Diversity and genetic structure of teak (<Emphasis Type="Italic">Tectona grandis</Emphasis> L.f) in its natural range using DNA microsatellite markers

Teak (Tectona grandis L.f.) is considered to be an extraordinarily durable building timber with a worldwide reputation. Its widespread use has entailed the over-exploitation of natural forests and a large reduction in natural diversity. Fifteen microsatellite markers were used to study the genetic variability and structure of 166 teak trees distributed over the whole natural area of teak. Analysis showed that in the teak natural area there were four main centers of genetic variability. Two clusters were in India and could be considered as main centers of genetic diversity in teak. The third cluster mainly consisting of populations in Thailand and Laos was genetically very distinct from the Indian populations but presented only half as much allelic variability. A fourth cluster from Central Laos showed even less genetic variability. The use of SSR markers for conservation of teak forest diversity is discussed.     

Genetic and environmental control of seasonal carbohydrate dynamics in trees of diverse Pinus sylvestris populations

We explored environmental and genetic factors affecting seasonal dynamics of starch and soluble nonstructural carbohydrates in needle and twig cohorts and roots of Scots pine (Pinus sylvestris L.) trees of six populations originating between 49 degrees and 60 degrees N, and grown under common garden conditions in western Poland. Trees of each population were sampled once or twice per month over a 3-year period from age 15 to 17 years. Based on similarity in starch concentration patterns in needles, two distinct groups of populations were identified; one comprised northern populations from Sweden and Russia (59-60 degrees N), and another comprised central European populations from Latvia, Poland, Germany and France (49-56 degrees N). Needle starch concentrations of northern populations started to decline in late spring and reached minimum values earlier than those of central populations. For all populations, starch accumulation in spring started when minimum air temperature permanently exceeded 0 degrees C. Starch accumulation peaked before bud break and was highest in 1-year-old needles, averaging 9-13% of dry mass. Soluble carbohydrate concentrations were lowest in spring and summer and highest in autumn and winter. There were no differences among populations in seasonal pattern of soluble carbohydrate concentrations. Averaged across all populations, needle soluble carbohydrate concentrations increased from about 4% of needle dry mass in developing current-year needles, to about 9% in 1- and 2-year-old needles. Root carbohydrate concentration exhibited a bimodal pattern with peaks in spring and autumn. Northern populations had higher concentrations of fine-root starch in spring and autumn than central populations. Late-summer carbohydrate accumulation in roots started only after depletion of starch in needles and woody shoots. We conclude that Scots pine carbohydrate dynamics depend partially on inherited properties that are probably related to phenology of root and shoot growth.     

毛红椿天然群体遗传多样性及取样策略探讨

[目的]研究毛红椿天然群体遗传多样性取样策略,为其种质资源收集、保存和遗传多样性保护等提供参考依据。[方法]利用8对微卫星分子标记进行毛红椿天然群体遗传多样性和空间自相关分析,综合制定其天然群体合理取样策略。[结果]毛红椿天然群体等位基因数平均为7.5个,期望杂合度(H_e)和多态性信息指数(PIC)均值分别为0.643 7和0.636 0,基因分化系数(G_(ST))均值为0.290 7。在遗传多样性取样策略方面,提出了根据毛红椿群体基因分化系数来确定取样群体遗传变异所占总变异比例的运算公式为1-(G_(ST))~(n-1),其中,n为取样群体的数量。当取样群体达到4个时,基本上能包括该树种97.5%的遗传变异;同时确定了目标群体的选择方法,应选择与其它群体间基因分化系数均值较大的4个群体,即贵州册亨(CH)、浙江遂昌(SC)、浙江仙居(XJ)和云南师宗(SZ)。通过构建云南宾川(BC)、云南师宗(SZ)和江西宜丰(YF)群体内取样单株数量与基因多样性和等位基因之间的捕获曲线,确定了群体内取样单株数量应达到15个以上;毛红椿天然群体内300～520 m范围内的单株间存在相似关系,超出此范围个体间差别较大,说明在进行群体内单株取样时,单株间距应大于520 m。[结论]取样群体数量、群体间遗传分化系数、群体内单株数量以及单株间距离等影响了毛红椿取样群体的遗传多样性。毛红椿天然群体遗传多样性取样策略为取样群体4个、每个群体最少取样15个单株,单株间距大于520 m。     

Structure and abundance of arachnid communities in Scots and lodgepole pine plantations

Between April and September 1994, six plots within Aberfoyle Forest in Scotland, three of Scots (Pinus sylvestris) and three of lodgepole pine (Pinus contorta), were surveyed for spiders and harvestmen, as these are predators of several forest invertebrate pests.A total of 64 species of spider were trapped in Scots and lodgepole pine; 56 in Scots pine and 32 in Lodgepole pine. The most abundant spiders, both in Scots and Lodgepole pine, were Linyphiidae.Scots pine plots were floristically more diverse and structurally more complex than lodgepole pine plots. More species of spiders and harvestmen (midsummer only) were found at ground level in Scots pine than lodgepole pine plots. More species and a greater numbers of spiders were found in the canopy of Scots pine than in that of lodgepole pine. However, no differences in the abundance of harvestmen were found between the canopies of Scots and lodgepole pine. Spider species diversity was greatest in Scots pine.     

Variation in needle and cone traits in natural populations of Pinus yunnanensis

Pinus yunnanensis Franch. is a major component of coniferous forests in southwestern China. Little is known about its intraspecific variation. Morphological variations in needle and cone traits of P. yunnanensis were analyzed to quantify variability among and within natural populations.Seven traits were measured on 10 needles collected from 30 trees in each of the 18 sampled populations of P. yunnanensis. Four cone traits were measured in 221 individual trees from nine populations. The results showed that there were significant differences(p \ 0.01) both among populations and within populations in each needle and cone trait.The proportion of phenotypic variation of nearly all needle and cone traits was over 50 % within populations, which showed trees within populations accounted for a majority of the total variation. The needle traits showed higher variability within population than cone traits. Variability in theneedle traits was correlated with geo-climatic parameters(longitude, latitude, altitude, temperature, and precipitation).Needle length and the ratio of needle length to fascicle sheath length showed clinal variation in response to latitudinal and altitudinal gradients. A hierarchical classification of all populations based on needle traits led to the formation of four major groups. The findings provide important genetic information for the evaluation of variation. Moreover, it will assist in management of genetic diversity of P. yunnanensis.     

无患子天然居群遗传多样性研究

[目的]通过我国无患子主要分布区的居群样本,研究无患子天然居群的遗传多样性和遗传结构.[方法]采用ISSR分子标记技术,利用12条ISSR引物分析18个天然居群的265株个体样本.[结果]表明无患子遗传多样性水平较高,物种和居群水平上的多态位点百分率 (PPB)分别为95.37%和57.82%,Shannon's信息指数(I)分别为0.256 9和0.199 8,Nei's遗传多样性指数(H)分别为0.390 9和0.298 0.AMOVA分析表明,18个居群间出现一定程度的遗传分化,且遗传变异主要发生在居群内.UPGMA聚类和Mantel检验结果表明,18个天然居群可分为2大组群,且居群间的地理距离与遗传距离之间不存在显著相关性(r=0.066 7,P=0.541 7>0.05).[结论]无患子以自交为主,其天然居群遗传多样性丰富,居群内的遗传多样性高于居群间.研究结果可为无患子育种策略的科学制定和种质资源的有效保护及利用提供理论依据.     

燕山山脉西伯利亚杏的遗传多样性和遗传结构

以西伯利亚杏分布的核心区域燕山山脉地区的17个群体为材料,利用9对微卫星标记进行遗传多样性和遗传结构的分析。在533个个体扩增得到203个等位基因,每位点平均等位基因数为22.556个。分析表明燕山山脉西伯利亚杏群体具有较高的遗传多样性,每位点平均有效等位基因数(Ne)为5.714,多态位点百分率(P)为100%,期望杂合度(He)为0.788。根据有效等位基因数(Ne)、期望杂合度(He)和Shannon信息指数(I)3个遗传多样性参数,遗传多样性最高的群体为北京八达岭,其次为平泉榆树林子,而最低的群体为崇礼驿马图。群体间总的遗传分化系数FST为0.065,总的基因流Nm为3.836。分子方差分析(AMOVA)结果显示燕山山脉地区西伯利亚杏群体的遗传变异主要存在于群体内(95.62%)。Mantel检验发现遗传距离与地理距离呈显著相关性(r=0.5894,P<0.0001)。UPGMA聚类结果显示,地理距离接近的群体聚在一起,进一步验证了Mantel检验结果。基于上述分析结果,提出西伯利亚杏的种质收集策略。研究结果为西伯利亚杏可持续利用与保护提供一定的理论依据。