Analysis of EST-SSRs in silver birch (<Emphasis Type="Italic">Betula pendula</Emphasis> Roth.)

Simple sequence repeats (SSRs) defined as sequence repeat units between 1 and 6 bp occur abundantly in both coding and non-coding regions in eukaryotic genomes and these repeats can affect gene expression. In this study, ESTs (expressed sequence tags) of Betula pendula (silver birch) were analyzed for in silico mining of EST-SSRs, protein annotation, open reading frames (ORFs), designing primers, and identifying codon repetitions. In B. pendula, the frequency of ESTs containing SSRs was 7.8 % with an average of 1SSR/4. 78 kb of EST sequences. A total of 188 SSRs was identified by using MISA software and di-nucleotide SSR motifs (65.9 %) were found to be the most abundant type of repeat motif followed by tri- (27.1 %), tetra- (4.8 %), and penta- (2.2 %) motifs. Based on ORF analysis, 175 of 178 sequences were predicted as ORFs and the most frequent SSRs were detected in 5′ UTR (58.43 %), followed by in ORF (31.46 %) and in 3′ UTR (8.43 %). 102 of 178 ESTs were annotated as ribosomal protein, transport protein, membrane protein, carrier protein, binding protein, and transferase protein. For a total of 102 SSRs (57.3 %) with significant matches, a set of 102 primers (100 %) with forward and reverse strands was designed by using Primer3 software. Serine (Ser, 19.6 %) was predominant in putative encoded amino acids and most of amino acids showed nonpolar (35.3 %) nature. Our data provide resources for B. pendula and can be useful for in silico comparative analyses of Betulaceae species, including SSR mining.     

马尾松表达序列标签多态性初步分析

遗传图谱是现代分子数量遗传学研究的一个基本平台 ,在过去的十几年中 ,林木遗传学家在几十个树种中构建了分子标记连锁图谱 ,并进行了一些重要数量性状的QTL分析。 (Bradshawetal.,1994 ;Ceveraetal.,2 0 0 1;Deveyetal .,1994 ;Echtetal .,1997;Grattapagliaetal.,1994 ;Muka     

表达序列标签技术及其应用

表达序列标签(Express Sequence Tags,以下简称为EST)是指表达基因一端或两端的部分DNA序列,能代表着某个表达基因的一段序列信息,平均长度为300~500 bp。EST是大规模获取基因功能的一种最为快捷、有效的研究手段,为寻找新基因、绘制遗传图谱、研究基因差异表达和比较基因组学及DNA芯片的制备等提供了大量的序列信息。综述了EST技术的原理、方法及其应用等方面的研究进展。     

Early performance of native birch (<Emphasis Type="Italic">Betula</Emphasis> spp.) planted on cutaway peatlands: influence of species,stock types and seedlings size

The poor reputation of birch in Ireland is gradually changing, and the interest shown in it by foresters is growing, as is the recognition of the many advantages that this genus offers, especially from an afforestation and ecosystem development point of view. The potential of native birch species was investigated on industrial cutaway peatlands in the Irish midlands. Field experiments were established to evaluate differences (in terms of survival, growth attributes and form) between B. pendula and B. pubescens, between bare-root and container planting, and between small and medium size seedlings. After five growing seasons, B. pendula was found to be the superior species especially on well drained and shallow peat sites. Bare-root B. pendula will grow faster with reasonable form but containerised birch may be favoured on more difficult sites (with deeper and wetter peat). Larger seedlings performed better, regardless of species. This study demonstrated good growth potential for planted birch on cutaway peatlands and that this species should be integrated in further planting programmes.     

Effects of log storage and drying on birch (<Emphasis Type="Italic">Betula pendula</Emphasis>) wood proanthocyanidin concentration and discoloration

In conventional drying, sawn birch (Betula sp.) timber darkens and reddens from the inside while the layer a few millimetres under the yellowish surface remains light in color. Lack of information concerning the chemical basis of the discoloration hinders the development of a reliable solution for this problem. In this study, the role of soluble proanthocyanidins in discoloration of birch wood was investigated because the polymerization and oxidation of these compounds are known to yield insoluble reddish compounds. Different periods of log storage affected the synthesis of soluble proanthocyanidins during conventional drying. Concentration of proanthocyanidins also correlated with changes in the color of birch wood. Discoloration appeared differently in conventionally dried and vacuum-dried wood, which indicates that the discoloration mechanism in these drying methods may differ chemically, and/or the compounds that take part in discoloration may be different at different drying temperatures.     

基于芭蕉属EST序列的地涌金莲SSR引物开发

对31 308条来自NCBI的芭蕉属(Musa)EST序列进行拼接得到全长为13.51 Mb的21 129条无冗余EST序列(含3 818条contigs及17 311条singletons),其中,4 944条(23.40%)EST序列含有5 416条SSRs,SSR的出现频率为25.63%,平均分布距离2.49 Kb,有234条(1.11%)含有1个以上的SSR。在所检测的SSR中,二、三、四核苷酸重复是主导重复类型,分别占EST-SSR总数的21.80%(1 181条)、52.55%(2 846条)和14.55% (788条)。AG/CT、AAG/CTT与AGG/CCT和AAAG/CTTT与AAAT/ATTT分别是二、三、四核苷酸的优势重复基元。随机设计了238对EST-SSR引物在24个地涌金莲个体中进行筛选,116对有扩增产物,其中,78对EST-SSR引物扩增出清晰稳定的目的片段,49对引物表现出多态性。本研究检测的15对引物扩增等位基因数范围是2~7个,平均3.067个;表观杂合度(Ho)范围是0.042 0.750,平均0.250;期望杂合度(He)范围是0.232~0.823,平均0.522。     

Analysis of EST-SSRs in silver birch(Betula pendula Roth.)

Simple sequence repeats(SSRs) defined as sequence repeat units between 1 and 6 bp occur abundantly in both coding and non-coding regions in eukaryotic genomes and these repeats can affect gene expression. In this study, ESTs(expressed sequence tags) of Betula pendula(silver birch) were analyzed for in silico mining of ESTSSRs, protein annotation, open reading frames(ORFs),designing primers, and identifying codon repetitions. In B.pendula, the frequency of ESTs containing SSRs was 7.8 %with an average of 1SSR/4. 78 kb of EST sequences. A total of 188 SSRs was identified by using MISA software and dinucleotide SSR motifs(65.9 %) were found to be the most abundant type of repeat motif followed by tri-(27.1 %),tetra-(4.8 %), and penta-(2.2 %) motifs. Based on ORF analysis, 175 of 178 sequences were predicted as ORFs and the most frequent SSRs were detected in 50 UTR(58.43 %),followed by in ORF(31.46 %) and in 30UTR(8.43 %). 102 of 178 ESTs were annotated as ribosomal protein, transport protein, membrane protein, carrier protein, binding protein,and transferase protein. For a total of 102 SSRs(57.3 %)with significant matches, a set of 102 primers(100 %) with forward and reverse strands was designed by using Primer 3 software. Serine(Ser, 19.6 %) was predominant in putative encoded amino acids and most of amino acids showed nonpolar(35.3 %) nature. Our data provide resources for B.pendula and can be useful for in silico comparative analyses of Betulaceae species, including SSR mining.     

Competition as a predisposing factor of crown dieback in a secondary forest of <Emphasis Type="Italic">Betula maximowicziana</Emphasis> in Hokkaido,northern Japan

We analyzed the probability that Betula maximowicziana Regel (monarch birch) would suffer crown dieback (crown-dieback probability) and the basal area growth rate (GB), which was found to be a predisposing stress factor making birch trees susceptible to crown dieback. First, we analyzed the relationship between the probability that birch trees would suffer from crown dieback in 1999 and GB from a period prior to the occurrence of crown dieback (1985–1987), using a data set of repeated measurements on 217 trees. Logistic regression analysis revealed that monarch birch had a larger crown-dieback probability when GB was low in the preceding period. Hence, there were predisposing stress factors that reduced GB and continued to affect trees for at least a decade. Next, we analyzed GB in the same period in relation to symmetrical and asymmetrical competition between trees and found that GB was reduced by symmetrical competition, suggesting that this was one of the predisposing factors for crown dieback. Based on these results, we used selected models for crown-dieback probability and GB to calculate crown-dieback probabilities for individuals with different initial basal areas and experiencing different intensities of symmetrical competition. The predicted crown-dieback probability decreased with decreasing symmetrical competition between trees. We discuss a possible process of crown dieback to death for monarch birch and the use of thinning as a method to reduce the risk of crown dieback.     

Additive tree biomass equations for <Emphasis Type="Italic">Betula platyphylla</Emphasis> Suk. plantations in Northeast China

Key message

A new system of additive tree biomass equations was developed for juvenile white birch plantations based on tree diameter at breast height (DBH) and tree height (HT). Compared with previous equations developed for natural white birch forests, the new system included one more biomass component and provided more accurate predictions.

Context

Accurate estimates of tree component and total biomass are necessary for evaluating alternative forest management strategies for biomass feedstock, carbon sequestration, and products. Previous biomass equations developed for white birch trees in natural stands provided substantially biased predictions for white birch plantations.

Aims

A new system of additive tree biomass equations was developed for juvenile white birch plantations in the northeastern China.

Methods

With destructive biomass sampling data from 501 trees sampled from white birch provenance and family trails at ages 7, 9, 10, and 13 in three provinces, a system of nonlinear additive tree biomass equations based on DBH and tree height was developed using the nonlinear seemingly unrelated regressions (NSUR) approach.

Results

Compared with previously published equations developed for natural white birch forests, the new system provided more accurate predictions of white birch tree component and aboveground and total biomass, especially of branch, foliage, and root biomass.

Conclusion

The new system extended the applicability of biomass equations to white birch plantations in the northeastern China.

     

EST-SSRs development and paternity analysis for <Emphasis Type="Italic">Liriodendron</Emphasis> spp

Liriodendron are ideal plants for research on mating system, systemic evolution and population genetics. Here we report the development and application of a set of simple sequence repeat (SSR) markers derived from expressed sequence tags (ESTs) of L. tulipifera. In total, 176 primer pairs were developed and yielded 132 EST-SSR markers that amplified clear SSR bands with genomic DNA of L. tulipifera. Transferability of these EST-SSR markers to related species and genera was further examined. Twelve highly informative loci screened from 132 EST-SSR markers were applied to explore the effective pollen dispersal patterns and male reproductive success of Liriodendron. A provenance trial population of Liriodendron comprised 12 L. chinense (Hemsl.) Sarg provenances and 5 L. tulipifera provenances. The four maternal trees were randomly sampled as tested maternal trees in the population. Paternities of 220 open-pollination progenies from 4 maternal trees above were potentially identified by means of paternity analysis, of which 138 progenies (accounting for 62.7%) were assigned to 49 male parents at the 95% confidence level. The cumulative exclusion probability of 12 EST-SSR loci was 98.5%. The average effective pollen dispersal distance of pollen donors ranged from 15 to 35 m, with the maximum dispersal distance of 77 m. There were obvious male reproductive success differences among individuals, ranging from 0 to 10.9%. The cumulative male reproductive success of individuals within 35 m radius around the known maternal trees reached 51.4%. Diversiform mating patterns, including selfing, intra-species mating and interspecies mating, coexisted in the occasion of open-pollination in Liriodendron.     

表达序列标签(EST)分析及其在林木研究中的应用

简要叙述了表达序列标签EST技术的原理和流程,综述了EST在研究林木木材形成和其它生物学过程时新基因的发现、基因表达分析和基因芯片方面的应用进展以及在开发林木单核苷酸多态性和简单序列重复等分子标记和构建遗传图谱方面的应用进展,并对其在林木基因组研究中的应用前景进行了展望。     

Effects of winter temperatures on two birch (Betula) species

In Massachusetts, low winter temperatures delay the onset of flowering in black birch (Betula lenta L.), but not in gray birch (B. populifolia Marsh.). During the winter of 2006, male inflorescences and twigs of black birch had higher water contents than those of gray birch, and the inflorescences of black birch experienced greater frost kill than those of gray birch. Vessels diameters were greater in black than in gray birch, a difference associated with a higher incidence of winter xylem embolism, as indicated by reduced xylem hydraulic conductance. In both species, recovery of hydraulic conductance in twigs that survived the winter coincided with the development of root pressure. Frost kill to male inflorescences or associated damage to plant tissues may account for the difference between species in the effect of winter temperature on the time of first flowering. In a comparison of 24 birch species, sensitivity of the first flowering date to temperature was also correlated with water content in male inflorescences.     

The effects of species mixture on the growth and yield of mid-rotation mixed stands of Scots pine and silver birch

The effect of tree species mixture on stand volume yield and on tree-species-specific diameter and height growth rates were analysed in managed mixed stands of Scots pine (Pinus sylvestris L.) and silver birch (Betula pendula Ehrn.).Data were obtained from 14 repeatedly measured stands located in Southern Finland on mineral soil sites with varying admixture of Scots pine and silver birch. Statistical analysis was carried out for studying the effect of species mixture on the development of stand characteristics. For the analysis, the plots were categorised into three groups (plot types) according to the species dominance. In order to analyse species-specific growth rates, individual-tree mixed linear growth models for tree diameter and height growth were developed for both tree species.The results clearly show that the yield of the managed mid-rotation, mixed stands was greater for stands dominated by Scots pine than for stands dominated by birch, and the stand volume increment decreased with an increasing proportion of silver birch. Analysis of diameter and height growth by tree species revealed that the main reason for this pattern is the negative impact of birch competition on the growth of pine trees. The increase in diameter of pine was clearly hampered if the proportion of birch was high. An abundance of birch also slightly decreased the growth in height of Scots pine, although the effect was less than on diameter growth. Species mixture did not affect the diameter growth of birch but did have a significant effect on height development. Height growth of birch was considerably greater in pine-dominated stands than in birch-dominated stands. In pine-dominated mixed stands, the height growth of birch was quite close to that of dominant pine trees, and birches can endure in competition with pines for light.The results apply for even-aged and single-storey managed stands, where stocking density and structure are controlled with pre-commercial and commercial thinnings. The results are not applicable to unmanaged mixed stands undergoing self-thinning. This study provides new information on mixed stands from a silvicultural perspective, which can be applied in decisions involving the management of mixed stands.     

Extraction of betulin from bark of Betula platyphylla by supercritical carbon dioxide extraction

Betulin, which is a medicinal pentacyclic triterpene, is abundant in the bark of white birch (Betula platyphlly). The bark of birch was collected at Tayuan Forest Farm of Jiagedaqi, Heilongjiang Province in September 2000. Supercritical fluid extraction (SFE) that is a new separation technology has been used for the processing pharmaceutical and natural products. In this paper, the extraction of betulin from the bark of birch by supercritical CO2 extraction was studied. The authors investigated and analyzed a few parameters such as modifier dosage, extraction pressure and extraction temperature. The optimal extraction conditions showed that the modifier dosage used for per gram bark powder was 1.5 mL, the extraction pressure was at 20 Mpa, and the extraction temperature was at 55 ℃. The velocity of flow of liquid CO2 was at 10 kg/h. The pressure and temperature in separation vessel were at 5.5 Mpa and 50 ℃, respectively.     

Species-specific spatial structure,species coexistence and mortality pattern in natural,uneven-aged Scots pine (<Emphasis Type="Italic">Pinus sylvestris</Emphasis> L.)-dominated forest

Complexity of uneven-aged forests results from the heterogeneity of their structure reflected among others by the spatial pattern of their components. Forest structure is usually modified by various processes operating at different scales and time. Structure and processes are not independent, and both are important drivers of forest dynamics. The impact of natural processes on forest structure manifested in the specific spatial pattern of trees can be quantified by point pattern analysis applied to long-term repeatedly measured stem-mapped plots. Such studies are relatively scarce in the literature although they provide better insight into the mechanisms affecting forest dynamics. Our study is focused on the spatiotemporal analysis of the structure of mixed uneven-aged Scots pine-dominated forest located at the Kampinoski National Park (Poland). Univariate analysis showed that the initial pattern of all live trees was initially random and it shifted toward more uniform with forest aging. Spatial patterns of individual tree species varied from that stated for all forest community. We observed changes in spatial pattern of Scots pine and common oak from random toward more clumped (pine) or uniform (oak) pattern. In case of black alder and common birch, the initial aggregated pattern was maintained over the examined 14-year period of the forest succession. Bivariate analysis showed that the most common interspecific association between pairs of tree species was spatial segregation (pine vs. alder, alder vs. birch and oak vs. birch) followed by spatial independence (pine vs. oak and oak vs. alder). The positive association was stated only for pine and birch and only for certain spatial scales (> 5 m). Simultaneously, at small distances they showed reciprocal repulsion. Changes in spatial relationships between tree species were negligible over 14-year period of forest succession. Our results confirmed the density-dependent mortality process in the uneven-aged Scots pine-dominated forest over 14-year period of forest development. Our study showed that spatial interactions between individuals along with species-specific ecological requirements should be incorporated into realistic models of forest development, helping to manage the forest ecosystems toward their greater structural complexity.     

黑河地区阔叶林和白桦落叶松林火烧迹地生物量动态变化的研究

采用空间序列代替时间系列的方法,对阔叶林和白桦落叶松林火烧迹地生物量变化进行研究的结果表明：在阔叶林和白桦落叶松林的火烧迹地中,总生物量随着火烧后时间的延长呈增长趋势;在中、重度火烧迹地中,草本生物量、灌木生物量占总生物量的比例在火烧后15年间波动比较大,15年后趋于稳定;在轻度火烧迹地中,火烧1年后波动趋于平缓。     

Photosynthetic utilization efficiency of absorbed photosynthetically active radiation by Scots pine and birch forest stands in the southern Taiga

Absorption and utilization of photosynthetically active radiation (PAR) were investigated in Scots pine (Pinus sylvestris L.) and birch (Betula pendula Roth.) stands that were 41 years old at the end of the experimental period. Canopy depth of the Scots pine stand was about half that of the birch stand (6.5 versus 11.0 m), but absorption of PAR was similar in the two stands. The Scots pine forest canopy, with a leaf area index of 8.9, absorbed 90% of the incoming PAR (APAR), whereas the birch forest canopy, with a leaf area index of 5.9, absorbed 92% of APAR. During maximum foliage development, the upper Scots pine canopy absorbed more PAR than the upper birch canopy (75 versus 66%). The upper, middle and lower layers of the Scots pine canopy contained 37, 48 and 15% of the total needle surface area, respectively. The corresponding distribution of foliage surface area in the three layers of the birch canopy was 50, 30 and 20%, respectively. Measurements of photosynthetic rate were combined with estimates of leaf area index and stand phytomass to determine rates of primary production on a sunny day, a cloudy day, and on an annual basis. The energy equivalents of short- and long-term carbon gain were used with determinations of APAR to calculate photosynthetic utilization efficiency. Throughout the growing season, photosynthetic utilization efficiency of APAR in the upper canopy layer of the Scots pine forest was almost twice that in the lower canopy layer. In the birch forest, photosynthetic utilization efficiency was greater in the lower canopy layer than in the upper canopy layer. In all cases, utilization efficiency was higher in the birch stand than in the Scots pine stand (52 versus 29 J kJ(-1)). Taking account of respiration of the non-photosynthetic parts of each stand (night respiration of needles or leaves; respiration of branches, trunk and roots), estimated utilization efficiency of APAR for net primary production was 11 J kJ(-1) for Scots pine and 19 J kJ(-1) for birch. Solar conversion ratios, expressed as whole-plant net primary productivity per unit of APAR for the growing season, were 0.81 g MJ(-1) for Scots pine and 0.93 g MJ(-1) for birch.     

Über die Eignung von Phosphatase- und Esteraseaktivitätsbestimmungen an Fichtennadeln und Birkenblättern zum Nachweis „unsichtbarer physiologischer” Fluorimmissionsschädigungen

Measurement of phosphatase and esterase activity in Norway spruce needles and birch leaves to detect “hidden” F-injury . Potted Norway spruce and birch were exposed at various distances from an industrial fluoride source. The needles and leaves were analysed periodically during a year for their enzymatic activities. In contrast to phosphatase, increased esterase activities were found to be a possible indicator of “hidden” F-injury to the trees.     

Analysis of SSR loci and development of SSR primers in <Emphasis Type="Italic">Eucalyptus</Emphasis>

In this study, 28,691 genome sequences and 16,566 expressed sequence tags (ESTs) of Eucalyptus were derived from the GenBank database. A total of 2292 SSR loci were sought out from 1785 effective sequences. Through analyses of SSR loci information, the SSR motif length was negatively correlated with the abundance of the SSRs. In the EST sequences of Eucalyptus, triplet repeat motifs were the most abundant, and dinucleotide repeats motifs had the highest frequencies. Subsequently, 395 pairs of primers were designed based on the SSR loci. Using optimized SSR-PCR conditions, 340 pairs of primers were successfully screened, with a success rate of 86.1%. By construction of a maximum likelihood phylogenetic tree of six eucalypt species, represented by five species of the genus Eucalyptus and one of the genus Corymbia, the genetic relationships of Eucalyptus urophylla and E. camaldulensis suggested by this tree was found to differ from that suggested by traditional morphological taxonomy. The results provide insights for evaluating genetic diversity of Eucalyptus and analysis of Eucalyptus phylogenetics using SSR markers.     

Reforestation with native tree species using site preparation techniques for the restoration of woodlands degraded by air pollution in the Erzgebirge,Germany

Reforestation of woodlands with native species in the Erzgebirge, where large-scale deforestation has been caused by severe air pollution, was investigated. In an experiment, three tree species (Norway spruce, rowanberry, and birch) were studied with regard to fencing (no protection versus protection against game browsing) and site preparation techniques with eight levels: a control and seven amelioration techniques (soil cultivation, weed control, liming, and their combinations). Four criteria, survival, growth, production, and vitality, were used in assessing the success of the plantings. Repeated-measures analyses were performed to examine the development of the young plantations over an observation period of 7 years, and to determine whether this development was dependent on the experimental factors. Spruce showed high survival rates, reasonable growth and production, and good individual vitality. With the exception of survival, birch responded similarly to spruce. The low survival rate of birch resulted from the initial small size of the seedlings. By providing appropriate seedling material, both species could be used for reforestation. Seedlings of rowanberry were unsuccessful due to severe mouse damage, confirming the necessity of rodent control when planting cleared areas with this species is undertaken. Game browsing was not significant. None of the amelioration techniques had a major effect on the studied criteria of the three tree species. Slightly positive effects occurred only when spruce was limed and when birch received soil cultivation. Weed control by scything showed undesirable results, particularly for birch. For reasons of financial thriftiness, none of the amelioration techniques could be justified for the study area.