Genetic diversity of sea buckthorn (Hippophae rhamnoides) populations in northeastern and northwestern China as revealed by ISSR markers

As a N₂-fixing tree species, sea buckthorn (Hippophae rhamnoides) is well adapted to arid regions and is utilized for multiple purposes in China. Current knowledge of genetic variability of H. rhamnoides is limited in terms of rangewide distributions. Eleven natural populations of sea buckthorn in northeastern and northwestern China were analyzed to detect genetic variation among and within populations, by use of ISSR (inter-simple sequence repeats) markers. Using eight primers, 207 polymorphic loci were observed, ranging in size from 250 to 2500 bp. The coefficient of gene differentiation (Gst = 0.0679) showed that the total molecular variance of 11 populations was mainly existed within populations. The genetic variation within and among the 11 populations was 93.21 and 6.79%, respectively. No significant correlation between genetic and geographic distances of the populations was found using ISSR markers. Our study provides a population-level genetic profile for further investigation and conservation of genetic diversity of sea buckthorn.     

Effect of fluoride pollution on genetic variability of <Emphasis Type="Italic">Larix gmelinii</Emphasis> (Pinaceae) in East Siberia

The genetic variability of four natural populations of Larix gmelinii from East Siberia was determined and compared by RAPD analysis. Comparison of the RAPD profiles provided an estimation of variability in 193 RAPD fragments. More than 89% of these fragments were found to be polymorphic. The main genetic variability parameters of the two populations from Central Yakutia, a region free of fluoride pollution, had considerably higher values than those from East Transbaikalia, a region potentially affected by fluoride pollution (FLU, near a fluorite quarry growing on soils with a high natural content of fluorides). AMOVA revealed that 72.94% of the variation was within populations, while only 7.05% of the variation was between populations within geographical regions. The genetic diversity of the FLU fluoride-tolerant population was the lowest, but only slightly lower than that of a fluoride non-tolerant population from Chita, 50 km distant from FLU. Although this study demonstrates the absence of fundamental alterations of genetic structure within the populations of L. gmelinii growing on soils with a high content of fluorides, it is presumed that the reduction of genetic diversity was the genetic response of the FLU population to such an environmental stress as a constantly high concentration of fluorides within the soil.     

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.     

Assessment of morphological and genetic diversity in <Emphasis Type="Italic">Gmelina arborea</Emphasis> Roxb.

Gmelina arborea is an important timber-yielding tree that grows naturally in the tropical and subtropical regions of Southeast Asia and has also been introduced as a plantation species outside these regions. Genetic diversity in this tree species was observed in stone/seed-related traits and in vitro responses of cultured nodal segments from plants of eight different populations representing natural forests, fragmented forests and plantations. Variance analysis showed significant differences between populations for these traits. However, it was not possible to separate the different populations using these traits by multivariate analysis, even after environmental variation was reduced over six subcultures. Genetic diversity was therefore analysed using molecular markers. Inter-simple sequence repeat (ISSR) primers yielded 95% polymorphic loci among the eight populations and UPGMA analysis enabled separation of these populations on the basis of their genetic distances. Diversity was also analyzed using population genetics parameters like Nei’s genetic diversity and gene differentiation. Nei’s genetic diversity was 0.29 between populations and 0.11 within populations. AMOVA analysis indicated 41 and 59% within- and between-population genetic diversity, respectively. Mantel test suggested that genetic differentiation between six Indian populations was positively correlated to geographic distance (r = 0.626, P = 0.029). Assessment of the genetic variation in G. arborea populations is an important step in selection of conservation strategies for this species since diversity forms the basis for species adaptation.     

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.     

RAPD标记研究马褂木地理种群的遗传分化

利用RAPD标记对马褂木全分布区 15个种群的遗传多样性进行了分析。研究发现 ,马褂木具有丰富的遗传多样性 ,但东部种群因现有种群小 ,其遗传多样性明显地低于西部种群。种群遗传学研究揭示 ,由于小种群效应 ,以及缺乏有效的基因流和特有的致濒机制 ,马褂木种群间的遗传分化巨大 ,30 %以上的遗传变异存在于种群间。但在不同的地理区域 ,种群间的遗传分化程度不同。在西部分布区 ,地域上相距不远的种群其遗传距离较小 ,而在东部即使两个相邻的种群 ,其遗传距离也非常大。使用Nei’s遗传距离进行算术平均数的非加权成组配对法分析 (UPGMA) ,其聚类结果可以很好地将马褂木划分为西部和东部两个种源区 ,而西部种源又可再划分为西南亚区和华中亚区     

Genetic structure of plantations and the conservation of genetic resources of Brazilian pine (Araucaria angustifolia)

With growing concern about maintenance of genetic variation and conservation of gene resources, the question arises on the extent to which a planted population should be considered a resource able to preserve the gene pool of a species. In this study, levels of genetic diversity were assessed in natural and planted populations of Araucaria angustifolia using AFLPs and nuclear microsatellites, in order to assess the usefulness of planted forests in programs of species’ genetic resource conservation. In general, the genetic structure of the plantations was not strongly differentiated from the natural populations. For microsatellites, gene diversity (H) and allelic richness were significantly higher in plantations, while inbreeding was not different between planted and natural populations. For AFLPs, no significant difference was found between groups in the measures of genetic diversity. In the cluster analysis based on microsatellite data, plantations and natural populations from Santa Catarina State were grouped together, suggesting that plantations preserved genetic information very similar to natural populations. The cluster analysis of populations based on AFLP data differentiated plantations from natural populations. This pattern may be a result of genetic hitchhiking of AFLP fragments with genes under selective pressure due to plantations establishment and management. We suggest that the moderate to high level of genetic diversity retained in A. angustifolia populations after the intense fragmentation of the natural forest has the potential to supply plant material with sufficient genetic diversity for the species conservation through the establishment of planted forests. A sustainable management of the extant forest remnants and forestation/reforestation enterprises should additionally attend to trends revealed in previous studies concerning population structure and gene flow.     

Small-scale genetic diversity in oneseed hawthorn (<Emphasis Type="Italic">Crataegus monogyna</Emphasis> Jacq.)

We have examined the pattern of random amplified polymorphic DNA (RAPD) variation among six populations of Crataegus monogyna from northern Italy, extending over an area of about 20,000 km². The aim was to evaluate local differentiation in relation to geographical distance. Of the 73 loci analysed, 65 were polymorphic, and there were no bands at complete fixation at the population level. The mean genetic diversity was 0.291, with the values for individual populations ranging between 0.252 and 0.333. According to the analysis of molecular variance most of the genetic variation was found within populations (about 80%), with a significant proportion being attributable to genetic differences between populations. No evidence for isolation by distance was found in the set of populations sampled. The efficacy of RAPD markers in analysing genetic variation, and the contribution of the results in terms of the preservation of biodiversity and defining the most appropriate strategies for collecting forest reproductive material, are discussed.     

An analysis of the pattern of genetic variation in Vitellaria paradoxa using RAPD markers

Vitellaria paradoxa C.F.Gaertn. is one of the most economically and socially important tree species in the Sudano-Sahelian region. Little is known of the pattern of variation within its natural range. Eight populations covering most of the natural range from Senegal to Uganda were sampled and leaves of 118 individual trees were collected. An analysis of molecular diversity was carried out using random amplified polymorphic DNA (RAPD) markers. Fifteen random primers generated 67 polymorphic and 15 monomorphic RAPD loci ranging from size 1670 bp to 280 bp. Shannon's diversity index varied from Central Africa/Ndele (0.374) to Uganda/Amoya (0.350) but the differences between populations were smaller than the population standard errors. Correspondence analysis of unrooted neighbour-joining trees suggested that genetic distances between populations were correlated with geographic distances. This trend was confirmed by a Mantel test giving a coefficient of correlation between genetic and geographic distances of R = 0.88 (P = 0.0001). Result of AMOVA (analyses of molecular variance) showed that 14.8% (P = 0.002) of the RAPD variation was distributed among populations. Nested analysis of variance indicated that variance between the western and eastern groups of population represented 8.7% (P = 0.001) of the total variation and the variation amongst populations within group was 9.5% (P = 0.001). Eighty two percent of the variation was explained by variation amongst individuals within populations. The origin of genetic structure and level of diversity may be explained by the glacial refugia, the biological traits of Vitellaria paradoxa and by the impact of semi-domestication. Based on these results, sampling options of the natural populations are suggested for in or ex situ conservation. For the development of Vitellaria paradoxa breeding population, the sampling should consist of many individual trees selected within a few populations to capture a large proportion of variation.This revised version was published online in November 2005 with corrections to the Cover Date.     

Effect of Regeneration Method on RAPD-Based Genetic Variation of Cyclobalanopsis glauca (Fagaceae)

Cyclobalanopsis glauca is a dominant species of evergreen broad-leaved forests in mainland China. This study compares the genetic variation of an artificially regenerated population with its donor population and two other wild populations, by using RAPD markers. A total of 74 clear, reproducible bands were scored for 12 RAPD primers; 72 were polymorphic (P = 97.3%). AMOVA revealed that most genetic variation was within populations and only 10.35% was among populations. Various measures indicated that there is no difference in genetic diversity between the planted and the original populations. Φ_ST between the planted offspring population and the donor population was larger than those between the planted and other two natural populations, indicating that artificial regeneration might lead to biased genetic composition, given that temporal differentiation is usually lower than spatial differentiation. This divergence may be due to unequal seed production among the maternal individuals and viability differences among seeds.     

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。     

Genetic diversity analysis of Sinojackia microcarpa,a rare tree species endemic in China,based on simple sequence repeat markers

Although most Sinojackia species are endangered, they contribute greatly to the biodiversity of local ecosystems. Sinojackia microcarpa, an endangered species, is distributed only in three provinces of eastern China. Determining the genetic diversity of S. microcarpa provides key information for germplasm evaluation and species conservation. Here we used simple sequence repeat (SSR) markers to investigate the genetic diversity of eight natural populations of S. microcarpa. Leaf samples were collected from 144 individuals in 8 wild populations. The 156 bands were generated from 14 pairs of informative SSR primers, with an average percentage of polymorphic bands of 45.67%. The average values of Nei’s genetic diversity (He) and Shannon’s diversity index (I) were 0.1007 and 0.1658, respectively. The total genetic variation of S. microcarpa existed mainly within the eight populations, rather than among populations, and reached 86.41%. A cluster analysis showed that the eight wild populations of S. microcarpa could be classified into four groups, at a threshold of 4.0, based on an analysis of the SSR genotypes. Furthermore, there was a significant association between the phylogenetic relationships and the geographic locations of the S. microcarpa populations. In particular, populations from Fuyang, Jiande, and Lin’an in Zhejiang Province had close phylogenetic relationships and geographic distances. In addition, these three populations had the highest genetic diversity and the most individuals, suggesting that these three locations may be the S.microcarpa distribution center. This study serves as a model for studying the genetic diversity of endangered plant species.     

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.     

Genetic variation and divergence in Scots pine (Pinus sylvestris L.) within its natural range in Italy

Twenty-one populations of Scots pine sampled over the entire Italian range of the species were analysed for genetic variation scored at nine nuclear SSR markers. The main aim of the work was to find genetic features useful for conservation management, namely allelic composition, gene diversity and differentiation. High levels of intra-population variability were scored. The only population sampled in the Apennines gave the lowest values, confirming the genetic erosion undergone in the Scots pine remnants in this area. A low level of genetic variability was also scored for populations from the Po valley and hills of Piedmont. Most genetic diversity was found within populations, while only a small amount occurred among them (F _ST?=?0.058). Both Bayesian clustering and sPCA analysis showed a East–West subdivision, notwithstanding the unclear position of populations from the Po valley. The population from the Apennines was always clearly separated from the others. The results are discussed in terms of post-glacial recolonisation, as well as for defining genetically homogeneous regions for Scots pine in Italy. The management of genetic resources could benefit from the identification of such ‘gene zones’, thereby avoiding the use of non-local reproductive material for plantations, which can represent one of the most important reasons for failure of reforestation. In addition, the assessment of the biogeographic genetic structure by neutral markers is a prerequisite for disentangling the influence of selectively neutral and non-neutral processes on the distribution of adaptive genetic variability.     

云南松主分布区天然群体的遗传多样性及保护单元的构建

以20个云南松天然群体为对象,SSR分析表明云南松遗传变异主要存在于群体内,各群体间的遗传多样性水平差异不显著。基于SSR分子标记遗传多样性分析,根据Nei's遗传相似度,采用逐步聚类优先取样法,分别对初始群体、遗传多样性保护单元和剩余群体进行比较、t检验,以此评价遗传多样性保护单元的代表性。结果表明,利用该方法抽样的群体能很好地代表初始群体的遗传多样性,按30%的群体抽样,等位基因数、有效等位基因数、Shannon's信息指数和期望杂合度的保留率分别达到初始群体的98.03%、105.36%、103.99%和105.56%。保护单元的遗传多样性均高于剩余群体,抽样群体组成的遗传多样性保护单元的效果较好。     

Adaptive genetic diversity and population structure of the “algarrobo” [<Emphasis Type="Italic">Prosopis chilensis</Emphasis> (Molina) Stuntz] analysed by RAPD and isozyme markers

The “algarrobo” [Prosopis chilensis (Molina) Stuntz] is a tree species that represents an important natural resource in arid and semi-arid regions of Argentina. In this paper, we analysed and compared the variability of 46 RAPD (Random Amplified Polymorphic DNA) loci with previous estimates obtained from 12 isozyme markers in nine Argentinean populations of P. chilensis representative of the whole range of this species in Argentina. We evaluated the population structure and the existence of genetic variants associated with environmental variables. Expected heterozygosity (H _e) estimated from RAPD varied significantly among populations and regions. Hierarchical analysis of genetic variability (AMOVA) showed that most (88.1%) of the total diversity occurs within populations, the component among populations within regions (9.3%) was intermediate, while the between-region component was the lowest (2.6%). All three variance components were highly significant. The MDS plot from pair-wise Φ _ST matrix was consistent with the highly significant among-region differentiation indicated by the AMOVA. All 12 variable isozyme loci and 26 out of 46 RAPD loci showed significant or highly significant association with at least one geographic/climatic variable according to the stepwise multiple regression analysis. These results imply that the genetic differentiation among populations is better explained by environmental or biogeographical grounds than by geographical distances, suggesting gametic disequilibrium with loci responsible for the adaptation to particular environmental conditions. The information from RAPD markers would provide a relevant criterion to preserve genetic diversity in programmes for conservation and rationale use of this species.     

Genetic analysis and conservation of endangered medicinal tree species <Emphasis Type="Italic">Taxus wallichiana</Emphasis> in the Himalayan region

Taxus wallichiana is one of the most important medicinal tree species of the Himalayan region. Leaf and bark of the species yield an important drug called taxol, which is used for treatment of many types of cancer. There is a serious threat to the existence of the species due to over exploitation in its native habitat. Adequate information on the nature and the extent of genetic diversity in this important species is required for developing suitable strategy for its conservation. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) were used to assess genetic variation in nine natural populations of T. wallichiana from western part of the Himalayan ranges. Both the markers revealed low genetic diversity in these populations. Average heterozygosity for AFLP and RAPD were 0.3715 and 0.3072, respectively. Φ_ST values derived from molecular variance were 0.0855 and 0.1005 for AFLP and RAPD, respectively, whereas the corresponding G_ST values were 0.1796 and 0.2140. Most part of the genetic variation was present within the populations. However, between population variation was low but statistically significant, which suggested that the sampled populations might not constitute a single panmictic population. Cluster analysis and Mantel’s correlation revealed that genetic differentiation broadly followed geographic distribution of the populations. T. wallichiana thus urgently needs to be conserved using both in situ and ex situ conservation approaches.     

Genetic diversity in Nordic and Baltic populations of Chondrostereum purpureum: a potential herbicide biocontrol agent

We analysed genetic variation in the natural populations of a potential herbicide biocontrol agent, Chondrostereum purpureum, in Nordic and Baltic countries using random amplified microsatellite markers. The results showed high genetic diversity among the populations of this fungus, but almost a complete lack of local differentiation. The results implicate that any local strain from the area can be used as a biocontrol agent without a fear of introducing new genotypes to treatment areas.     

油橄榄品种表型和SSR标记的多样性及聚类分析

[目的]利用表型性状和分子标记,对我国油橄榄品种进行鉴定和遗传多样性研究,有利于种质资源保存和利用,对了解油橄榄品种的组成结构及未来的引种和育种工作都具有重要意义。[方法]以甘肃省陇南市17个油橄榄品种为研究材料,利用表型上15个数量性状、18个质量性状和8个SSR荧光标记分别进行多样性和聚类分析。[结果]各性状在品种间存在显著差异,数量性状和质量性状的表型多样性指数分别介于1.579 2.089和0.3621.091,8个SSR位点共检测到51个等位基因变异,平均每个位点等位基因数为6.375个,利用表型性状和SSR标记可以将17个品种完全区分开。[结论]17个油橄榄品种具有较丰富的表型和遗传多样性,基于表型数量性状、质量性状和SSR标记的聚类分析结果,判别品种间遗传关系的结果有一致的,也存在一定差异。对于表型性状相似的品种,需结合SSR标记进行品种鉴定。     

Evaluation Of Genetic Diversity Using Inter-Simple Sequence Repeat Markers And Effect On The Severity Of Leaf Blight Disease Of Teak (Tectona Grandis L.)

ABSTRACT

Leaf blight is an important disease of teak which reduces photosynthetic rate and ultimate timber yield in infected trees. Symptomatic leaf samples were randomly collected from three forest reserves, Onigambari, Olokemeji and Omo in Southwest Nigeria. Genomic DNA from the samples was extracted using Cetyl Trimethyl Ammonium Bromide (CTAB) method and amplified with Inter Simple-Sequence Repeat (ISSR) markers to evaluate genetic diversity. Dendrogram analysis using UPMA procedure separated the accessions into 12 major groups with bootstrap values ranging from 51 to 62. The constructed dendogram showed that accessions from Onigambari forest reserve were genetically similar to those from the two other reserves. Principal component analysis (PCA) showed that the first, second and third axes accounted for 79.19%, 85.41%, and 88.11%, respectively, of the total molecular variation. All the four ISSR markers showed 100% polymorphism which induced the amplification of 48 alleles across the 39 teak accessions evaluated. Polymorphic information content (PIC) obtained from ISSR markers ranged from 0.6038 to 0.8886, while genetic diversity varied from 0.6288 to 0.8947. The inter-population genetic diversity and allelic richness observed in the study could be employed in breeding for resistance against leaf blight disease of teak.