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.     

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.     

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 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.     

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.     

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 RAPD Mark for Natural Davidia involucrata Populations

The genetic diversity and genetic variation within and among populations of five natural Davidia involucrata populations were studied from 13 primers based on random amplified polymorphic DNA (RAPD) analysis. The results show that natural D. involucrata population has a rich genetic diversity, and the differences among populations are significant. Twenty-six percent of genetic variation exists among D. involucrata populations, which is similar to that of the endangered tree species Liriodendron chinense and Cathaya argyrophylla in China, but different from more widely distributed tree species. The analysis of the impacts of sampling method on genetic diversity parameters shows that the number of sampled individuals has little effect on the effective number of alleles and genetic diversity, but has a marked effect on the genetic differentiation among populations and gene flows. This study divides the provenances of D. involucrata into two parts, namely, a southeast and a northwest provenance. Translated from Scientia Silvae Sinicae, 2004, 40(4) (in Chinese)     

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.     

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.     

Genetics of red alder (Alnus Rubra Bong.) populations in British Columbia and its implications for gene resources management

The genetic structure of 19 red alder (Alnus rubra Bong.) populations representing the natural range of the species in British Columbia was investigated at 19 allozyme loci. The estimated average number of alleles per locus (1.79), percentage of polymorphic loci (52.6), and total expected genetic diversity (0.113) were all lower than those reported for most long-lived woody species but comparable to early successional species. About 8% of the total genetic variation was attributable to among-population differentiation, the majority being detected at the Aat-2 locus between the Mainland and the Islands regions. Phylogenetic analysis grouped the 19 populations into two distinct clusters that perfectly coincided with their geographical arrangement. Genetic differentiation between populations within both the Mainland and the Islands regions was very weak, accounting for about 3% of the total genetic variation within each region. Red alder is predominantly an outcrossing species with an average outcrossing rate of 0.85. The rate of outcrossing also varied widely among populations, ranging from 0.56 to 0.98. Practical implications of these findings with respect to tree improvement and in situ gene conservation are discussed.     

花吊丝竹居群遗传多样性的ISSR分析

[目的]研究花吊丝竹居群遗传多样性和遗传结构,为种质资源有效利用和良种选育提供理论指导。[方法]利用12条ISSR引物对48份种质(共3个居群)花吊丝竹居群进行遗传多样性和遗传距离分析。[结果]共检测到124个位点,其中,多态性位点为102个,种质和居群水平上的多态位点百分比(PPB)分别为82. 26%和50. 27%,Ne’基因多样性指数(He)分别为0. 220 4和0. 206 6,Shannon’s信息指数(I)分别为0. 349 4和0. 300 5,表明花吊丝竹居群间存在中等水平的遗传变异。根据Nei’s遗传多样性计算出不同居群间分化水平(Gst)=0. 163 3,表明16. 33%的遗传变异存在于居群间,居群内的遗传变异为83. 67%。居群间的基因流Nm为2. 562 1,表明花吊丝竹居群间存在较大基因流,很大程度减少居群间遗传差异。基于遗传距离的UPGMA聚类结果表明,48份种质可分为3组,3个居群可分为2组,居群间地理距离与亲缘关系无显著相关性。[结论]虽然花吊丝竹主要靠营养生殖来繁衍后代,其居群遗传多样性较丰富,且居群内遗传多样性大于居群间。此外,福建居群遗传多样性明显高于广西和广东地区居群。     

Low genetic diversity and high genetic differentiation among severely fragmented populations of the critically endangered tree Talbotiella gentii (Fabaceae)

The genetic diversity among 17 populations (including 10 newly discovered) of Talbotiella gentii (Fabaceae, Caesalpinioideae), a rare tree species endemic to Ghana, was assessed using random amplified polymorphic DNA (RAPD). A total of 80 polymorphic bands were generated from eight primers and analysed by cluster and correspondence analysis. This showed a clear distinction between populations, with two major groups associated with geographical origin. AMOVA analysis showed that 94.05% of the genetic variation was partitioned among populations, while only 5.95% was found within populations suggesting little gene flow between populations. Possible reasons for the high population genetic differentiation and the low levels of genetic variation within populations are inbreeding and genetic drift. Of a total of 26 known populations, 14 are now extinct, five during the course of this study. Action to prevent complete extinction of the species is therefore urgent.     

Genetic diversity of Betula luminifera populations at different elevations in Wuyi Mountain and its association with ecological factors

The random amplified polymorphic DNA (RAPD) technique was used to evaluate the genetic diversity and population structure of 91 genets from four wild populations of Betula luminifera at different elevations in the National Nature Reserve of theWuyi Mountain, Fujian Province, China. Eighteen random primers (from 139 primers) produced a total of 199 scorable amplified fragments, of which 174 (87.44%) were polymorphic across all individuals. The genetic diversities of B. luminifera at the population level and species level were PPL = 60.05%, h = 0.2242, I = 0.3181 and PPL = 87.44%, h = 0.3442, I = 0.4899, respectively. The value of differentiation (G _st= 0.3486) and analysis of molecular variance (AMOVA) indicated that there was a relatively high genetic differentiation among populations, and about one-third of the genetic variation occurred among populations. Pearson correlation analysis further revealed that the genetic diversity within populations had significant or very significant correlation with the elevation, climatic factors (annual average temperature and annual precipitation) and soil nutrient factors (total nitrogen, C/N ratio and organic matter). Mantel tests show that there was a significant correlation between the genetic distances among populations and the distance of elevation, and the divergence of soil nutrient factors. The results of the present study suggested that the relatively high genetic differentiation among populations of B. luminifera at different elevations might be caused by ecological factors and gene flow. __________ Translated from Scientia Silvae Sinicae, 2008, 44(3): 50–55 [译自: 林业科学]     

Molecular characterization and marker based chemotaxonomic studies of Podophyllum hexandrum Royle

Detailed chemical studies and RAPD analysis were done in different populations of Podophyllum hexandrum collected from high altitude regions of North Western Himalayas. Random amplified polymorphic DNA (RAPD) analysis revealed a high degree of genetic diversity among the 12 collected accessions, attributed to their geographical and climatic conditions. HPLC analysis also revealed variation in the concentration of two major marker compounds which lead to the identification of a chemotype. The study demonstrated that RAPD and chemical markers are very useful tools to compare the genetic relationship and pattern of variation among such prioritized and endangered medicinal plants.     

Genetic diversity of Quercus glandulifera var. brevipetiolata populations in three forest communities with different succession stages

In order to understand the relationship between population succession and its genetic behavior, random amplified polymorphic DNA (RAPD) technique was used to analyze the genetic diversity of Quercu glandulifera var. brevipetiolata populations in three forest communities with different succession stages (coniferous forest, coniferous and broad-leaved mixed forest, evergreen broad-leaved forest). The results showed that 145 repetitive loci were produced in 60 individuals of Q. glandulifera using 11 primers, among which 120 loci were polymorphic, and the total percentage of polymorphic loci was 82.76% with an average of 64.14%. Estimated by the Shannon information index, the total genetic diversity of the three populations was 0.4747, with an average of 0.3642, while it was 0.3234, with an average of 0.2484, judged from the Nei index. Judged from percentage of polymorphic loci, Shannon inform at ion index and Nei index, the genetic diversity followed a decreasing order: coniferous forest > broad-leaved mixed forest > evergreen broad-leaved forest. Analysis of molecular variance (AMOVA) showed that 69.73% of the genetic variance existed within populations and 30.27% of the genetic variance existed among populations. The coefficient of gene differentiation (GST) was 0.2319 and the gene flow (N _m) was 1.6539. The mean of genetic identity among populations of Q. glandulifera was 0.8501 and the mean of genetic distance was 0.1626. The genetic identity between the Q. glandulifera population in the coniferous forest and that in the coniferous and broadleaved mixed forest was the highest. UPGMA cluster analysis based on Nei’s genetic distance showed that the population in the coniferous forest gathered with that in the coniferous and broad-leaved mixed forest firstly, then with that in the evergreen broad-leaved forest. The genetic structure of Q. glandulifera was not only characteristic of the biological characteristics of this species, but was also influenced by the microenvironment in different communities. __________ Translated from Journal of Northwest Forestry University, 2008, 23(1): 18–22 [译自: 西北林学院学报]     

七子花种群遗传多样性的RAPD分析

按胸径将浙江省天台山天然七子花划分为大树、中树、小树和幼树 4个大小级种群 ,利用RAPD分子标记技术对 4个大小级种群共 4 5株个体的遗传多样性及遗传分化进行了比较分析 ,结果表明 :通过 12种随机引物扩增共检测到 6 4个可重复的位点 ,4个大小级种群的多态位点百分率高低为大树 >中树 >小树 >幼树。Shannon信息指数估计七子花 4个大小级种群的遗传多样性高低为大树 >中树 >小树 >幼树 ,大小级种群内的遗传变异占总变异的 5 4 4 1% ,大小级种群间的遗传变异占总变异的 4 5 5 9% ,表明不同大小级种群内、大小级种群间个体均存在一定的遗传分化 ,但大小级种群内的遗传分化比大小级种群间高。Nei指数估计的七子花不同大小级种群的基因多样性的高低与Shannon指数估计的一致 ,大小级种群内的遗传分化高于大小级种群间 ,大小级种群间的基因分化系数为 0 3939。不同大小级种群间的遗传相似度以大树与中树最高 ,大树与幼树最低。聚类分析显示大树与中树先聚成一组 ,小树与幼树再聚成一组 ,最后 2组聚在一起     

天然珙桐群体的RAPD标记遗传多样性研究

利用RAPD技术 ,通过 13个引物对 5个天然珙桐种群的遗传多样性、种群内和种群间的遗传变异进行了研究。结果表明 :珙桐天然种群具有丰富的遗传多样性 ,但群体间的差异明显 ,2 6 %的遗传变异存在于群体间 ,与我国濒危树种马褂木和银杉等相似 ,而与广布性树种相异。取样方法对遗传多样性参数的影响分析表明 ,有效等位基因数和基因多样度受取样个体数的影响较小 ,群体间的分化系数和基因流的估算受取样个体数的影响较大。研究还将珙桐划分为东南部和西北部两大种源区。通过珙桐遗传多样性的研究 ,为今后有效保存和合理利用珙桐种质资源提供了理论依据     

Comparing genetic diversity in agroforestry systems with natural forest: a case study of the important timber tree Vitex fischeri in central Kenya

It is possible that current tree domestication practices undertaken by farmers reduce the genetic base of tree resources on farms, raising concerns regarding the productivity, sustainability and conservation value of agroforestry ecosystems. Here, we assessed possible changes in genetic variation during domestication in the important and heavily utilised timber species, Vitex fischeri Gürke (syn. Vitex keniensis), by comparing geographically proximate forest and farm material in central Kenya. Employing RAPD analysis, a total of 104 polymorphic markers revealed by five arbitrary primers were scored in a total of 65 individuals, 32 from forest and 33 from farmland. Despite concerns of possible genetic erosion, forest and farm stands did not differ significantly in levels of genetic variation, with H values of 0.278 and 0.269, respectively. However, Mantel tests did reveal greater geographically related associative genetic structure among individuals in farm rather than forest material, with r _M values of 0.217 and 0.114, respectively. A more detailed analysis of structure suggested this could be due to local variation in origin of some on-farm trees. Implications of data for the genetic management of V. fischeri stands during farmer-led tree domestication activities are discussed. At present, there appears little reason to reject on-farm V. fischeri as a source of germplasm for future on-farm planting or for conservation purposes, although this situation may change and will require monitoring.     

Genetic diversity of Lithocarpus harlandii populations in three forest communities with different succession stages

By using random amplified polymorphic DNA (RAPD) technique, this paper studied the genetic diversity and genetic differentiation of Lithocarpus harlandii populations in three forest communities (coniferous forest, coniferous and broad-leaved mixed forest, and evergreen broad-leaved forest) with different succession stages in Tiantai Mountain in Zhejiang Province. The results showed that a total of 173 repetitive loci were produced in 60 individuals of L. harlandii by 12 random primers, among which, 152 loci were polymorphic, and the total percentage of polymorphic loci was 87.86%. The average percentage of polymorphic loci of the populations was 65.32%, and their total genetic diversity estimated by Shannon information index was 0.4529, with an average of 0.3458, while that judged from Nei’s index was 0.3004, with an average of 0.2320. The percentage of polymorphic loci, Shannon information index, and Nei’s index of the populations were in the sequence of coniferous forest community > coniferous and broad-leaved mixed forest community > evergreen broad-leaved forest community. Analysis of molecular variance (AMOVA) showed that 72.85% of genetic variance was found within the populations, and 27.15% of genetic variance resided among the populations. The coefficient of gene diferentiation was 0.2277, and the gene flow was 1.6949. The genetic structure of L. harlandii was influenced not only by the biological characteristics of this species, but also by the microenvironment of different communities. The mean of genetic identity among three populations of L. harlandii was 0.8662, and the mean of their genetic distance was 0.1442. The genetic similarity between coniferous and broad-leaved mixed forest community and evergreen broad-leaved forest community was the highest, while that between evergreen broad-leaved forest community and coniferous forest community was the lowest. The unweighted pair group method with arithmeticmean (UPGMA) cluster analysis based on Nei’s genetic distance showed that conierous and broad-leaved mixed forest community first gathered with evergreen broad-leaved forest community, and then with coniferous forest community. __________ Translated from Chinese Journal of Ecology, 2007, 26(4): 509–514 [译自: 生态学杂志]     

红豆树优树子代遗传多样性及与生长相关性分析

[目的]研究红豆树优树自由授粉子代遗传多样性及其对生长的影响,比较天然居群子代和孤立木子代遗传多样性差异,揭示子代遗传多样性的变化规律及天然居群在子代遗传多样性维持中的作用,为红豆树遗传保育和优异种质挖掘提供科学依据。[方法]以来自浙、闽、赣、川等26个红豆树优树自由授粉家系为研究对象,利用11对SSR引物对765个子代群体进行遗传多样性评价,同时分析子代遗传多样性参数与种子、生长性状的相关性。[结果](1)红豆树优树子代群体具有较高的遗传多样性,有效等位基因数为7.766个,观测杂合度(H_O)和期望杂合度(H_E)分别为0.469和0.865。(2)除SSR8外,其余位点的观测杂合度均小于期望杂合度,表明子代群体绝大多数位点处于杂合子缺失状态。(3)红豆树不同家系的遗传多样性存在明显差异,12号家系的遗传多样性水平最高,8号家系则最低。(4)比较发现,天然居群子代的遗传多样性显著或极显著地高于孤立木子代。(5)F统计量和分子方差分析(AMOVA)均表明,红豆树优树子代群体的遗传变异主要存在于家系内,家系间的遗传分化相对较小。(6)相关性分析发现,子代遗传多样性参数与种子性状、子代年高生长量呈显著正相关(r=0.378~0.527)。[结论]较大的红豆树天然居群在维持其子代较高遗传多样性中发挥了重要作用,子代遗传多样性显著影响苗木生长,这为红豆树遗传保育和优良家系选择提供了理论依据。