Genetic diversity and relationship of endangered plant Magnolia officinalis (Magnoliaceae) assessed with ISSR polymorphisms

Twenty-eight populations of the rare medicinal plant Magnolia officinalis (Magnoliaceae) were sampled across its natural range, and inter-simple sequence repeats (ISSRs) markers were used to assess the genetic variation within and among populations. Twelve primer combinations produced a total of 137 unambiguous bands of which 114 (83.2%) were polymorphic. M. officinalis exhibited a relatively low genetic diversity at population level (the percentage of polymorphic loci PPB = 49.8%, Nei’s genetic diversity H = 0.194, Shannon’s information index I = 0.286). However, the genetic diversity at species level was relatively high (PPB = 83.2%; H = 0.342; I = 0.496). The coefficient of gene differentiation (G_ST, 42.8%) and the results of analysis of molecular variance (AMVOA) indicated that genetic differentiation occurred mainly within populations. The estimated gene flow (Nm) from G_ST was 0.669. It indicated that the fragmentation and isolation of populations might result from specific evolutionary history and anthropogenic activity. Genetic drift played a more important role than gene flow in the current population genetic structure of M. officinalis. Conservation strategies for this rare species are proposed based on the genetic data.     

Is the genetic diversity of small scattered forest tree populations at the southern limits of their range more prone to stochastic events? A wild cherry case study by microsatellite-based markers

Wild cherry (Prunus avium L.) is a widespread, partially asexual, noble hardwood European species characterized by a scattered distribution, small population sizes, and human exploitation for its valuable wood. These characteristics, especially at the southern limits of the species natural distribution where additional varying stresses may occur, render P. avium populations prone to potential stochastic, genetic, and demographic events. In this study, we used dominant inter simple sequence repeat (ISSR) and codominant simple sequence repeat (SSR) markers to infer the genetic structure of P. avium. Five populations from northern Greece were evaluated based on 46 ISSR and 11 SSR loci. Populations presented a relatively high level of genetic variation, with a mean genetic diversity of H _e?=?0.166 and H _e?=?0.740 regarding ISSR and SSR analysis, respectively. We observed moderate population differentiation for ISSR (G _ST?=?0.113) and SSR (F _ST?=?0.097) markers. AMOVA also detected significant differentiation among populations for ISSRs (?? _ST?=?0.338) and SRRs (?? _ST?=?0.162). According to linkage disequilibrium analysis, estimates of effective population size were generally sufficient for maintaining extant genetic variability and evolutionary potential. A possible bottleneck was detected for only one population. In general, it appears that despite the particular characteristics of the P. avium populations studied, genetic stochasticity events were not apparent. The studied populations, located at the rear edge of the species European distribution, reveal a wealth of genetic variation that is very valuable for the genetic conservation of local adaptive gene complexes, especially under contemporary climatic change scenarios.     

Lack of genetic variation of an invasive clonal plant Eichhornia crassipes in China revealed by RAPD and ISSR markers

Random amplified polymorphic DNAs (RAPDs) and inter-simple sequence repeats (ISSRs) markers were used to analyze genetic structure of six populations of invasive plant Eichhornia crassipes that were sampled from its introduced regions in Southern China. Using 25 RAPD primers and 18 ISSR primers, 172 RAPD bands and 145 ISSR bands were produced respectively. But no polymorphic band was detected either within population or among populations by both markers, indicating the genetic diversity of E. crassipes in Southern China is extremely low, and all populations most likely consist of the same genotype. This study suggested that some other adaptability related factors, other than the genetic diversity, are responsible to the E. crassipes rapid expansion in China.     

Genetic diversity of Lavandula multifida L. (Lamiaceae) in Tunisia: implication for conservation

The genetic variation within and among eight Tunisian natural populations of Lavandula multifida L., from different bioclimatic zones was assessed using random amplified polymorphic DNA (RAPDs). Of a total of 97 generated bands from seven selected primers, 84 bands were polymorphic. The genetic diversity within a population was high and varied according to the populations (0.308 < H’ < 0.459) without relationships to altitudes or pluviothermic indices of sites. The genetic differentiation among populations was high (G_ST = 0.395 and Φ_ST = 0.318). All population pairs were significantly differentiated. Among populations, within ecological groups genetic structure was high (0.219); whilst among them it was low (Φ_CT = 0.049; P < 0.05). The correlation between Φ_ST and geographic distance matrices among pairs of populations was not significant, suggesting that genetic connectivity between populations has a stochastic component at all spatial scales. The neighbour‐joining cluster analysis showed that individuals from each population clustered together. UPGMA cluster analysis showed that population groupings are not strictly in accordance with bioclimates or geographic location. The genetic differentiation in L. multifida could have occurred at local scales because of genetic drift. Efforts should be made to protect all populations. The maintenance of substantial population size should be initiated via fencing and controlling collection to restore the regeneration of populations.     

Molecular diversity and genetic relationships in <Emphasis Type="Italic">Secale</Emphasis>

The objective of this study was to quantify the molecular diversity and to determine the genetic relationships among Secale spp. and among cultivars of Secale cereale using RAPDs, ISSRs and sequence analysis of six exons of ScMATE1 gene. Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD and 16 ISSR primers. A total of 435 markers (242 RAPDs and 193 ISSRs) were obtained, with 293 being polymorphic (146 RAPDs and 147 ISSRs). Two RAPD and nine ISSR primers generated more than 80% of polymorphism. The ISSR markers were more polymorphic and informative than RAPDs. Further, 69% of the ISSR primers selected achieved at least 70% of DNA polymorphism. The study of six exons of the ScMATE1 gene also demonstrated a high genetic variability that subsists in Secale genus. One difference observed in exon 1 sequences from S. vavilovii seems to be correlated with Al sensitivity in this species. The genetic relationships obtained using RAPDs, ISSRs and exons of ScMATE1 gene were similar. S. ancestrale, S. kuprijanovii and S. cereale were grouped in the same cluster and S. segetale was in another cluster. S. vavilovii showed evidences of not being clearly an isolate species and having great intraspecific differences.     

采用RAPD和ISSR标记研究古尔班通古特沙漠东南缘梭梭种群的遗传结构

梭梭(Haloxylon ammodendron(CA Mey.)Bunge)是一种沙漠旱生优势树种,具有重要的生态和经济价值,然而,我们对梭梭种群的遗传多样性和遗传结构所知甚少.本文采用RAPD和ISSR标记对来自古尔班通古特沙漠东南缘的4个天然梭梭种群的遗传多样性和遗传结构进行了检测.5个RAPD引物和8个ISSR引物分别扩增出61和195条带,多态性位点比率分别为83.6%和89.7%,Shannon信息指数分别为0.333和0.367,RAPD和ISSR分析均表明梭梭种群的遗传多样性水平较高.利用分子方差分析(AMOVA)研究梭梭种群的遗传结构,结果表明,大部分遗传变异存在于种群内,通过RAPD分析发现138.2%的遗传变异发生在种群内;通过ISSR分析发现89.4%的遗传变异发生在种群内;而种群间的遗传分化很小.通过RAPD标记没有检测到种群间的遗传分化,ISSR分析表明10.6%的遗传变异发生在种群内.我们推测梭梭种群较高的遗传多样性水平可能源于对异质、高胁迫环境的长期适应,但还需要进一步的研究加以证实.种群间遗传分异低的主要原因是种群间存在强大的基因流.     

Genetic Diversity and Population Structure of Teucrium polium (Lamiaceae) in Tunisia

Random amplified polymorphic DNA markers were used to assess the genetic diversity within and among seven Tunisian diploid and polyploid populations of Teucrium polium L. from five bioclimatic areas. Out of the 141 bands generated from eight selected primers, 124 were polymorphic. The genetic diversity within a population (Shannon’s index) was high and varied according both the ploidal levels and bioclimatic zones. The genetic differentiation among populations assessed by G _ST and Φ_ST statistics was high, suggesting a low level of gene flow among them. The major proportion of the variation was attributable to individual differences within populations. The UPGMA analysis based on Nei and Li’s coefficient showed that individuals from each population clustered together. In a dendrogram using the Φ_ST distance matrix, population grouping is concordant with bioclimates and cytotypes. Conservation strategies should take into account the level of the genetic diversity of the populations according to their bioclimate and ploidal levels.     

Genetic diversity within and among populations of the endangered species Taxus fuana (Taxaceae) from Pakistan and implications for its conservation

The West Himalayan yew, Taxus fuana Nan Li & R.R. Mill (Taxaceae), is an endangered species endemic to the Western Himalayas. An investigation of the genetic diversity of wild populations of T. fuana in Pakistan was undertaken. The genetic diversity and genetic structure was quantified using random amplified polymorphic DNA (RAPD) variation in 219 individuals of the 10 populations. Of the 32 universal primers screened 16 produced highly reproducible, clear RAPD bands. Using these primers, 193 discernible DNA fragments were generated, of which 164 (84.97%) were polymorphic. The statistical results indicated that there was a relatively low genetic diversity within populations (with percentages of polymorphic bands, PPB, ranging from 29.53 to 50.26%, with an average of 38.34% and a Nei's genetic diversity index (H_E) of 0.1165), and a high genetic differentiation among populations (G_ST = 0.5842, Φ_ST = 0.5685) within these populations. The gene flow (N_m) was low with only 0.3558.     

Genetic diversity of Astragalus nitidiflorus, a critically endangered endemic of SE Spain,and implications for its conservation

Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population structure in five populations of Astragalus nitidiflorus, a critically endangered species endemic to southeast Spain. Eight primers amplified 78 bands with 40 (51.3%) being polymorphic. Statistical results indicated a low genetic diversity at the population and species level, with percentages of polymorphic bands (PPB) ranging from 28.2 to 37.2% (an average of 31.8%), and means of gene diversity (H_E) of 0.129 and 0.171 respectively. The Shannon’s index (SI) ranged from 0.160 to 0.214 at the population level and was 0.260 at the species level. A low level of genetic differentiation among populations was detected, based on the Shannon’s information index (0.297), the coefficient of genetic differentiation between populations (G_ST = 0.2418) and AMOVA analysis (Φ_ST = 0.255). The estimated gene flow (Nm) was 0.789. The high genetic connectivity found among populations of A. nitidiflorus is an evidence of a recent habitat fragmentation. In addition, a bottleneck event in the past has been revealed, with a subsequent reduction of population size and a loss of genetic variation. Based on these results, the conservation strategy of A. nitidiflorus was proposed.     

Genetic differentiation between clone collections and natural populations of European black poplar (<Emphasis Type="Italic">Populus nigra</Emphasis> L.) in turkey

The European black poplar (Populus nigra L.) is an ecologically and economically important tree species for Turkey. The important and major genetic resources of species for future breeding and ex situ conservation purposes have been archived in a clone bank in Ankara by selecting clones from natural populations and old plantations throughout Turkey. There is no study to date assessing genetic composition these materials. Two-hundred-thirty-three P. nigra clones from six geographic region of Turkey (clone collection populations), and 32 trees from two natural populations (Tunceli and Melet) were genotyped by using 12 nuclear microsatellite DNA markers. There were nine clones which duplicated in various frequencies. The analysis carried out with removal of the duplicated clones revealed a moderately high genetic diversity in studied populations. The observed heterozygosities ranged from 0.59 in Tunceli natural to 0.69 in Central Anatolia clone collection populations. In general, there was excess of heterozygosity in the studied populations. Populations composed of clone collections were significantly differentiated from natural populations (F _ST = 0.17), while there was little differentiation among those populations in the clone collection (F _ST = 0.03). Two distantly located natural populations with small sizes also differed from each other (F _ST = 0.17). Genetic structure analysis revealed two distinct groups (clone collection vs natural populations) with very high membership values (>92%). Clone collection populations had high level of admixture while natural populations had homogenous genetic structure. The presence of large number of clonal duplication, reduced genetic differentiation, and high level of admixture in clone collection populations indicate that genetic resources of European black poplar were highly degraded through genetic erosion and pollution caused by intensive cultural practices and extensive dispersal of clonal materials. To understand genetic diversity and its structural pattern thoroughly in the six clone collection populations, a further study with extensive and systematic sampling of European black poplar populations in major river ecosystems in Turkey will be useful.     

Low Levels of Genetic Diversity within Populations of Hosta clausa (Liliaceae)

Abstract Genetic diversity of Korean populations in Hosta clausa was investigated using starch gel electrophoresis. Hosta clausa is widespread, grows only along streamsides, and has both sexual and asexual reproduction. Populations of the species are small and isolated. Thirty-two percent of the loci examined were polymorphic, and mean genetic diversity within populations (He_p=0.082) was lower than mean estimates for species with very similar life history characteristics (0.131), particularly for its congener H. yingeri (0.250). The mean number of multilocus genotypes per population was 8.7, and genotypic diversity index (D_G) was 0.84. Significant differences in allele frequencies among populations were found in all seven polymorphic loci (P < 0.001). About one-fifth of the total allozyme variation was among populations (G_ST=0.192). Indirect estimate of the number of migrants per generation (Nm=0.48, calculated from mean G_ST) and nine private alleles found indicate that gene movement among populations was low. The low levels of genetic diversity within populations and the relatively high levels of genetic diversity among populations suggest that strong moist habitat preferences, clonal reproduction, low level of gene flow among populations, genetic drift, and historical events may have played roles in the genetic structuring of the species.     

Genetic diversity within and among populations of the endangered and endemic species Primula merrilliana in China

Primula merrilliana Schltr. is an endangered and narrowly-distributed endemic species of southern Anhui Province in China. In this study, the level of genetic variation and the pattern of genetic structure in six natural populations of P. merrilliana were assessed by using ISSR (inter-simple sequence repeats) markers. Based on ten primers, 137 clear and reproducible DNA fragments were generated, of which 109 were polymorphic. The statistical results indicated that there was a relatively low genetic diversity within populations, and a high genetic differentiation among populations (G_ST = 0.53, Φ_ST = 0.49). The level of population genetic diversity was correlated to habitat type and the gene flow (N_m) was low with only 0.45. The unexpected genetic structure of P. merrilliana may be explained by limited gene flow that was caused by habitat fragmentation and limited seeds and pollen dispersal ability, self-compatible breeding system and biennial life form.     

Genetic variation within the sand-fixation species Caragana microphylla (Leguminosae) in Horqin sandy land detected by inter-simple sequence repeats analysis

Caragana microphylla is the most dominant and constructive shrub species in the Horqin sandy land in the northeast of China. We evaluated it's the level of genetic variation within and among populations sampled from two different populations types in Horqin sandy land by using inter-simple sequence repeat polymorphism (ISSR) molecular markers. The results showed that eight ISSR primers generated 106 bands, of which 87 were polymorphic. At the species level, genetic diversity was relatively high (P = 82.08%, h = 0.2831, I = 0.4233). Genetic variation in natural populations (h = 0.2152, I = 0.3169) was more than that in plantation populations (h = 0.2021, I = 0.3040). Based on Nei's G_ST value, more genetic differentiation among plantation populations was detected (G_ST = 0.7787). Six populations of C. microphylla clustered into two clades. These results have important implications for restoring and managing the degraded ecosystem in arid and semi-arid areas.     

Genetic variation in the endangered <Emphasis Type="Italic">Anisodus tanguticus</Emphasis> (Solanaceae), an alpine perennial endemic to the Qinghai-Tibetan Plateau

We used random amplified polymorphic DNA markers (RAPDs) to assess genetic variation between- and within-populations of Anisodus tanguticus (Solanaceae), an endangered perennial endemic to the Qinghai-Tibetan Plateau with important medicinal value. We recorded a total of 92 amplified bands, using 12 RAPD primers, 76 of which (P = 82.61%) were polymorphic, and calculated values of H_t and H_sp of 0.3015 and 0.4459, respectively, suggesting a remarkably high rate of genetic variation at the species level. The average within-population diversity also appeared to be high, with P, H_e and H_pop values of 55.11%, 0.1948 and 0.2918, respectively. Analyses of molecular variance (AMOVA) showed that among- and between-population genetic variation accounted for 67.02% and 32.98% of the total genetic variation, respectively. In addition, Nei’s coefficient of differentiation (G_ST) was found to be high (0.35), confirming the relatively high level of genetic differentiation among the populations. These differentiation coefficients are higher than mean corresponding coefficients for outbreeding species, but lower than reported coefficients for some rare species from this region. The genetic structure of A. tanguticus has probably been shaped by its breeding attributes, biogeographic history and human impact due to collection for medicinal purposes. The observed genetic variations suggest that as many populations as possible should be considered in any planned in situ or ex situ conservation programs for this species.     

基于形态及分子标记的濒危植物夏蜡梅自然居群的遗传变异研究

比较了濒危植物夏蜡梅(Sinocalycanthus chinensis)大明山、大雷山、龙须山3个居群的果实与种子的形态变异,采用ISSR分子标记技术分析DNA序列的变异,综合评价夏蜡梅3个居群的遗传变异。结果如下:果实性状中,果柄长、果实长、果实重、每果种子数等指标均以大明山居群最大、大雷山居群次之、龙须山居群最小,它们之间差异显著(P<0.05)。种子重、种子长、种子宽、种子厚等指标均以大雷山居群最大,与大明山居群和龙须山居群差异显著(P<0.05)。基于果实形态特征的表型分化系数(VST)在0.5518—0.9750之间,平均为0.8930,所有果实形态指标的变异大部分存在于居群间。基于种子形态特征的VST在0.1669—0.8678之间,平均为0.6240,除种子长外,其他种子形态指标的变异也大部分存在于居群间。ISSR分析表明,3个居群的多态位点百分率、Shannon信息指数、Nei基因多样性均是大明山居群最高、龙须山居群次之、大雷山居群最低。居群间的遗传分化系数(GST)为0.6050。基于ISSR分子标记数据的聚类结果显示大明山居群先与龙须山居群聚在一起,再与大雷山居群相聚,这与基于种子性状特征的聚类结果相似,而与基于果实性状特征的聚类结果不同。3个居群的种子形态特征变异系数与遗传多样性水平具有显著的正相关,且基于果实形态特征估算的VST要高于GST,而基于种子形态特征估算的VST仅略高于GST,表明夏蜡梅不同居群间的种子形态变异主要由遗传变异所造成的,而环境因子在果实形态变异中起了重要作用。Mantel检验显示3个居群基于分子标记数据的遗传距离矩阵和基于果实及种子形态特征的欧氏距离矩阵之间的相关性不显著,表明果实与种子在居群间出现的表型分化除了受遗传因素影响外,还受到其它环境因子的强烈影响。     

Population structure of red-cockaded woodpeckers in south Florida: RAPDs revisited

Six south Florida populations of the endangered red-cockaded woodpecker (Picoides borealis) were sampled to examine genetic diversity and population structure in the southernmost portion of the species' range relative to 14 previously sampled populations from throughout the species range. Random amplified polymorphic DNA (RAPD) analyses were used to evaluate the populations (n= 161 individuals, 13 primers, one band/primer). Results suggested that south Florida populations have significant among-population genetic differentiation (F_ST= 0.17, P < 0.000), although gene flow may be adequate to offset drift (N_m= 1.26). Comparison of Florida populations with others sampled indicated differentiation was less in Florida (F_ST for all populations = 0.21). Cluster analyses of all 20 populations did not reflect complete geographical predictions, although clustering of distant populations resulted in a significant correlation between genetic distance and geographical distance. Overall, results suggest populations in south Florida, similar to the remainder of the species, have low genetic diversity and high population fragmentation. Exact clustering of distant populations supports the ability of RAPDs to differentiate populations accurately. Our results further support past management recommendations that translocations of birds among geographically proximate populations is preferable to movement of birds between distant populations.     

Low genetic diversity and significant structuring in the endangered Mentha cervina populations and its implications for conservation

Eighteen populations of the endangered aromatic and medicinal plant Mentha cervina (Lamiaceae) were sampled across its natural range, in the western half of the Iberian Peninsula, and inter-simple sequence repeats (ISSRs) markers were used to assess genetic diversity and population structure. M. cervina populations exhibited a relatively low genetic diversity (percentage of polymorphic loci PPB = 14.2–58.3%, Nei's genetic diversity H_e = 0.135–0.205, Shannon's information index I = 0.08 − 0.33). However, the genetic diversity at species level was relatively high (PPB = 98.3%; H_e = 0.325; I = 0.23). The results of the analysis of molecular variance indicated very structured populations, with 50% of the variance within populations, 44% among populations and 6% between regions defined by hydrographic basins, in line with the gene differentiation coefficient (G_ST = 0.532). A Mantel test did not find significant correlation between genetic and geographic distance matrices (r = 0.064), indicating that isolation by distance is not shaping the present genetic structure. The levels and patterns of genetic diversity in M. cervina populations were assumed to result largely from a combination of evolutionary history and its unique biological traits, such as breeding system, low capacity of dispersion, small effective size and habitat fragmentation. The high genetic differentiation among populations indicates the necessity of conserving the maximum possible number of populations. The results also provide information to select sites for ex situ conservation. Optimal harvesting strategies, cultivation and tissue culture should also be developed as soon as possible to guarantee sustainable use of the species under study.     

Genetic Diversity and Population Structure of Alnus hirsuta (Betulaceae) in Korea

Alnus hirsuta in Korea was measured to estimate the amount and pattern of genetic diversity and population structure. The mean genetic diversity within populations was 0.166. Korean alder populations have slightly high levels of genetic diversity compared to those of two Canadian alder species. The genetic differentiation among populations accounted for 9% of the total variation. The rate of gene flow was estimated high (Nm=2.63). Analysis of inbreeding coefficient, calculated for all polymorphic loci in each population, showed a substantial heterozygote deficiency relative to Hardy-Weinberg expectations. The mean G _ST value of A. hirsuta in Korea was 0.087. The low value of G _ST in this species, reflecting little spatial genetic differentiation, may indicate extensive gene flow. A relationship between the mean heterozygosity and annual rainfall showed a positive relationship (r ²=0.54, F=4.67). Received 8 August 1998/ Accepted in revised form 7 July 1999     

High genetic differentiation and variation as revealed by ISSR marker in Pseudotaxus chienii (Taxaceae), an old rare conifer endemic to China

Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China, with a historically disjunct distribution pattern. Eleven populations sampled throughout its range were examined using inter-simple sequence repeats (ISSR) markers. Twenty primers generated 242 bands, and each detected polymorphic loci, with 73.14% of polymorphic loci overall. The estimate for θ^B was 0.5306, whereas G_ST and Φ_ST values were 0.6146 and 0.6401, respectively. 50.62% of the total diversity based on Shannon's index of phenetic diversity was attributed to among populations, which was consistent with the θ^B estimation. Compared with other conifers, remarkable genetic differentiation occurred among P. chienii populations. A Mantel test indicated that pairwise values of θ^B were significantly related with geographical distances between populations (r = 0.676, P = 0.001). In terms of the above results, conservation strategies and maintenance plans of P. chienii were recommended.     

Molecular characterization of Platonia insignis Mart. (“Bacurizeiro”) using inter simple sequence repeat (ISSR) markers

Platonia insignis Mart. (Clusiaceae) is widespread throughout the Amazon and adjacent areas. The fruits (known locally as “bacuri”) have significant commercial potential, but the species is under threat from agro-industrial expansion. The genetic variability within 72 genotypes of P. insignis belonging to ten populations collected in the Brazilian states of Maranhão and Piauí, and maintained in the germplasm collection of Embrapa Meio-Norte, has been determined, and the organization of genetic diversity within populations, between populations and among geographic groups verified. Eighteen selected inter simple sequence repeat primers allowed amplification of 236 loci of which 221 (93.64 %) were polymorphic, indicating a high level of genetic diversity. At the population level, the Shannon and Nei diversity indices ranged from 0.082 to 0.323 and from 0.120 to 0.480, respectively. The global coefficient of genetic differentiation (G _ST ) was 0.4730 indicating that differentiation between populations was significant, a finding that was confirmed by analysis of molecular variance (Φ _ST  = 0.28). UPGMA cluster analysis revealed that the genotypes could be stratified into groups that were well defined and consistent with those identified in the dendrogram constructed using pair wise Φ _ST values. The high genetic diversity established in this study may facilitate the management and conservation of the germplasm of P. insignis.