Genetic diversity and population structure of Opisthopappus longilobus and Opisthopappus taihangensis (Asteraceae) in China determined using sequence related amplified polymorphism markers

The genetic diversity and structure of four Opisthopappus longilobus and nine Opisthopappus taihangensis populations from Mts. Taihang were analyzed using SRAP markers. The results showed that O. longilobus (PPB = 95.16%, H = 0.349, I = 0.517) and O. taihangensis populations (PPB = 94.58%, H = 0.332, I = 0.504) had high genetic diversity. The genetic diversity within populations varied according to two species. Low genetic differentiation was detected among O. longilobus (Φ_ST = 0.105) and O. taihangensis (Φ_ST = 0.188) populations, respectively. Significantly genetic variation was found between O. longilobus and O. taihangensis (Φ_ST = 0.232). The dendrogram generated from pairwise genetic distance among all populations showed two distinct clusters, each corresponding to one species. A Mantel test revealed insignificant positive correlation between genetic distances and geographic distances (r_{O. longilobus} = 0.3021; r_{O. taihangensis} = 0.3658; P > 0.05). Those results indicated that self-compatibility, effective gene flow, biological traits, and historical factors may be the main factors causing geographical differentiation in the structure of O. longilobus and O. taihangensis populations.     

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 diversity and structure of natural Pinus tabulaeformis populations in North China using amplified fragment length polymorphism (AFLP)

Chinese pine (Pinus tabulaeformis carr.), endemic to China, is a conifer species with extensive and fragmented distribution in North China. In this study, the genetic diversity and structure of 20 natural populations of this species were investigated using amplified fragment length polymorphism (AFLP) markers. A total of 445 fragments were revealed with 8 pairs of primers, 379 (85.17%) of which were polymorphic. A moderate level of genetic diversity was detected at the species level (Shannon's information index I = 0.356, Nei's gene diversity H_E = 0.271) and at the population level (I = 0.219, H_E = 0.206). Most of genetic variation was within populations while a considerable level of genetic differentiation was detected (G_ST = 0.352, Ф_ST = 0.304). The high differentiation could be attributed to the complex and fragmented habitats, and a limited gene flow among populations (N_m = 0.572). The Mantel test indicated that there was significant correlation (r = 0.455, P < 0.001) between Nei's genetic distance and geographical distance among all the populations. The results suggested that proper countermeasures should be taken to prevent the habitat further deterioration and maintain the genetic diversity of this species.     

Fragmented habitat drives significant genetic divergence in the Chinese endemic plant,Urophysa henryi (Ranuculaceae)

Urophysa henryi (Oliv.) Ulbr., endemic to China with small populations, is known as a medicinal plant. In this study, ISSR markers were used to assess the genetic diversity and population structure throughout its entire distribution areas. Twelve primers revealed high genetic diversity at the species level (PPB = 95.6%; H = 0.3441; I = 0.5111), as well as high level of genetic differentiation (F_ST = 0.659, p < 0.001; G_ST = 0.677) and restricted gene flow (Nm = 0.239) among populations. According to the UPGMA and PCoA analysis, the 9 populations were clustered into three main groups, which were roughly in accordance with their geographical regions. In addition, a significant correlation between the genetic difference and geographic distances among populations was detected from the IBD analysis (r = 0.516, p = 0.003). These results indicated that the habitat heterogeneity and physical barriers play important roles in the modern distribution pattern and population divergence of U. henryi. However, human activities have posed serious threat to its living environment and continued survival. It is necessary to adopt some measures to restrict anthropogenic disturbances and preserve the existing 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 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 variation and clonal diversity in populations of Nelumbo nucifera (Nelumbonaceae) in central China detected by ISSR markers

To obtain accurate estimates of population structure for purposes of conservation planning for wild lotus (Nelumbo nucifera Gaertn.) in central China, genetic diversity among and within six populations, and clonal diversity within another two populations of the species were analyzed. The genetic diversity was high (percentage of polymorphic bands, PPB = 90.0%; Shannon's information index, I = 0.383 ± 0.234) at the species level, but low within individual study populations (PPB = 35.8%; Shannon's information index I = 0.165 ± 0.241). The mean coefficient of gene differentiation (G_st) was 0.570, indicating that 43.0% of the genetic diversity resided within the population. Analysis of molecular variance (AMOVA) indicated that 50.47% of the genetic diversity among the study populations was attributed to geographical location while 12.3% was attributed to differences in their habitats. An overall value of mean estimated number of gene flow (N_m = 0.377) indicated that there was limited gene flow among the sampled populations. The level of clonal diversity found within the populations was considerably high (Simpson's diversity index, D = 0.985) indicating that clonal diversity contributes to a major extent to the overall genetic variation in the genetic structure of N. nucifera. On the basis of the high G_st and D values detected in this study we recommend that any future conservation plans for this species should be specifically designed to include those representative populations with the highest genetic variation for both in situ conservation and germplasm collection expeditions.     

Genetic diversity of Poa annua in western Oregon grass seed crops

The genetic diversity of Poa annua L.populations collected from western Oregon grass-seed fields was surveyed using 18 randomly amplified polymorphic DNA (RAPD) markers. Markers from 1357 individual plants from 47 populations collected at three sampling dates (fall, winter, and spring) for 16 sites were used to measure genetic diversity within and among populations. Site histories varied from low to high herbicide selection pressure, and some sites were subdivided by 3 years of differing post-harvest residue management. Gene diversity statistics, simple frequency of haplotype occurrence, and analysis of molecular variance (AMOVA) revealed the presence of significant variability in P. annua among sites, among collection dates within sites, and within collection dates. Nei gene-diversity statistics and population-differentiation parameters indicated that P. annua populations were highly diverse. Mean Nei gene diversity (h) for all 47 populations was 0.241 and total diversity (H_T) was 0.245. A greater proportion of this diversity, however, was within (H_S=0.209) rather than among (G_ST=0.146) populations. When populations were grouped by season of collection, within-group diversity was H_S=0.241, while among-group diversity was G_ST=0.017. When populations were grouped by site, within-group diversity was H_S=0.224, while among-group diversity was G_ST=0.087. The diversity among populations within season for fall, winter, and spring collections was G_ST=0.121, 0.142, and 0.133, respectively. Populations collected from fields with histories of high herbicide selection pressure showed low differentiation among collection dates, with G_ST as low as 0.016, whereas those collected from fields with low herbicide selection pressure showed greater differentiation among collection dates, with G_ST as high as 0.125. At high selection-pressure sites, populations were also lower in gene diversity (as low as h=0.155), while at low selection-pressure sites there was higher gene diversity (as high as h=0.286). The site to site variability was greater for the high selection-pressure sites (G_ST=0.107 or 69% of the total among-population variance), while the season of germination variability was greater at sites of low herbicide-selection pressure (G_ST=0.067, or 70% of the total among-population variance). High initial diversity coupled with a long-term re-supply of genotypes from the seed bank must have been factors in maintaining the genetic diversity of this weed despite the intensive use of herbicides. Knowledge of the genetic diversity of Willamette Valley P. annua should help in formulating more effective strategies for managing this weed. Received: 24 July 1999 / 11 November 1999     

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.     

白沙蒿不同地理种群遗传分化的ISSR分析

运用ISSR技术,对白沙蒿的5个种群进行遗传分化的分析。12个引物在108个个体中共扩增出222个位点,其中,多态位点为218个,多态位点百分率为98.20%,Shannon多样性指数为0.315 4,具有高的多态性。种群间的遗传分化系数（G_st）为0.076 7,与AMOVA分析的结果一致（Ф_st为7.96%）,表明绝大多数的遗传变异存在于种群内部。各种群间遗传一致度高达98%以上,遗传距离很小,基因流达3.008 2,均表现出白沙蒿各种群存在着广泛的基因交流,有着很小的遗传分化。     

Genetic variation and clonal diversity of the endangered aquatic fern Ceratopteris pteridoides as revealed by AFLP analysis

Ceratopteris pteridoides (Hook.) Hieron. is an endangered aquatic homosporous fern in China. Genetic diversity and structure of eight populations collected from the mid-lower reaches of Yangtze River were investigated using amplified fragment length polymorphisms (AFLPs). A low level of gene diversity was found at the population level (P_p = 17.4%, H_E = 0.039 and I = 0.063), which possibly resulted from its high degree of inbreeding, clonal growth and short life history of this species. C. pteridoides contained high clonal diversity (PD = 0.757, D = 0.992). High population differentiation was revealed by partitioning of genetic diversity (G_ST = 0.707), and the AMOVA analysis consistently showed that 72.3% of the total genetic diversity was attributable to among-population diversity. Based on the genetic information from UPGMA cluster and principal coordinate analysis, two management units have been identified, and translocation within each management unit is recommended.     

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 diversity and population structure of the endangered species Psammosilene tunicoides revealed by DALP analysis

Psammosilene tunicoides W. C. Wu et C.Y. Wu (Caryophyllaceae) is a rare plant endemic to China. We used the direct amplification of length polymorphism (DALP) method to analyse the genetic diversity of 17 natural populations of this species from Yunnan, Sichuan and Guizhou provinces. The percentage of polymorphic bands (PPB) was 99.1% at the species level and 19.9% at the population level. The total genetic diversity (Ht) was 0.2827; the genetic diversity within populations (H_s) was 0.0594 and the coefficient of gene differentiation (G_st) was 0.7899. The results indicated low levels of genetic diversity within populations and extremely high genetic differentiation among populations. This pattern might be caused by genetic drift resulting from intensive harvesting and habitat fragmentation. It might also be a result of local adaptation. We further performed experiments on its breeding system and found a high rate of selfing in P. tunicoides, which may be partially responsible for its population structure.     

Genetic variation within the endangered mangrove species Sonneratia paracaseolaris (Sonneratiaceae) in China detected by inter-simple sequence repeats analysis

Sonneratia paracaseolaris, is a critically endangered mangrove species in China. Using inter-simple sequence repeats (ISSR) markers, we compared the genetic variation of introduced populations with that of natural populations to check whether the genetic diversity has been conserved. At the species level, genetic diversity was relatively high (P = 81.37%, He = 0.2241, and SI = 0.3501). Genetic variation in introduced populations (P = 75.78%, He = 0.2291, and SI = 0.3500) was more than that in natural populations (P = 70.81%, He = 0.1903, and SI = 0.2980). Based on Nei's G_ST value, more genetic differentiation among natural populations was detected (G_ST = 0.3591). Our data show that the genetic diversity of S. paracaseolaris was conserved in introduced populations to some extent, however, owing to the small natural populations and the threats they encountered, more plants should be planted to enlarge and restore the populations.     

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     

Genetic diversity of wild population of Pyropia haitanensis based on SSR analysis

Genetic diversity analysis was conducted on 80 individuals of 4 populations of non-bred Pyropia haitanensis by simple sequence repeat (SSR) method. Using 15 pairs of microsatellite primers, 37 polymorphic loci were amplified, representing 94.9% of all loci. At the population level, the percentage of polymorphic bands (P) and polymorphism information content (PIC) were 66.67–84.62% and 0.481–0.488, with average value at 73.72% and 0.483, respectively. Expected heterozygosity (H_e) and Shannon's information index (I) were 0.279 and 0.434, respectively, at the species level, and 0.233 and 0.356 at population level. According to the coefficient of gene differentiation (G_ST), a large proportion of genetic variance (83.6%) of P. haitanensis was among individuals within populations, only 16.4% genetic variance was among populations, which was identified with the moderate gene flow value (N_m = 2.542). UPGMA clustered the 4 populations into 3 groups, and no significant correlation was found between the genetic distance and the corresponding geographic distance among the populations.     

Assessment of genetic diversity and chemical composition among seven black locust populations from Northern China

Black locust (Robinia pseudoacacia L.) is one of the important biomass sources used to produce bioenergy and bioethanol. In this study, we examined variations in chemical composition as well as genetic diversity and differentiation among 165 black locust plants from seven populations in five provinces (Beijing, Hebei, Gansu, Shanxi, Shandong) of Northern China using microsatellite markers(SSR). The contents of cellulose, hemicellulose, lignin varied widely among seven populations. Of the microsatellite markers analysed, 14 showed polymorphisms, and 45 alleles were identified. The polymorphism information content (PIC) ranged from 0.2885 (Rops4) to 0.6837 (Rp200), and most of the microsatellite loci had PIC values > 0.5. Expected heterozygosity (He), observed heterozygosity (Ho), and Shannon's information index (I) detected relatively high genetic variation among populations. The percentage of polymorphic loci in three populations was 100%, and the average among all populations were 95.92%. Analysis of molecular variance (AMOVA) indicated that the degree of genetic differentiation among the seven populations was low (G_ST = 0.058; N_m = 4.05), and chemical compositions had no relationship with genetic or geographic distance. This study demonstrates that microsatellite markers efficiently assess of genetic diversity and genetic differentiation in black locust populations, and all seven populations exhibit high genetic diversity. The population from Feixian has the potential to be lingo-cellulosic biomass for bioenergy and bioethanol.     

Population structure and genetic diversity of Stipa grandis P. Smirn,a dominant species in the typical steppe of northern China

Random amplified polymorphic DNA (RAPD) markers were used to characterize genetic heterogeneity within and among five populations of Stipa grandis in the Xilingol Plateau. Estimates of the percentage of polymorphic bands, Shannon's diversity information index and Nei's gene diversity index were comparatively high in the five populations, and the Population GSM was found to have the highest genetic diversity among all populations. An analysis of molecular variance indicated that the majority of variation existed within populations (74.12%), and that there was significant differentiation among populations (Φ_ST = 25.88%, P < 0.001). Genetic distance (Φ_ST) ranged from 0.198 to 0.310 and the differentiation between pair-wise populations was significant when individual pairs of populations were compared. Based on the Φ_ST values, gene flow (Nm) was estimated and was found to vary from 0.556 to 1.013 between pair-wise populations and 0.7412 among populations. The results of UPGMA cluster analysis and nonmetric multi-dimensional scaling analysis indicated that most variation occurred within populations and that genetic differentiation had happened between populations. These findings are important for a better understanding of the adaptive strategy of S. grandis in northern China and will be useful for conservation managers to work out an effective strategy to protect this important species.     

Genetic diversity and population structure of Swertia tetraptera (Gentianaceae), an endemic species of Qinghai-Tibetan Plateau

Swertia tetraptera Maxim is an annual alpine herb endemic to the Qinghai-Tibetan Plateau (QTP). Its populations are locally scattered as isolated patches throughout this region. Genetic variation within and among thirty-four populations of this species was assessed using ISSR fingerprinting with 10 primers. High levels of genetic diversity exist within species (P = 98.9%, I = 0.3475; He = 0.2227), while the within-population diversity is low (P = 32.7%, I = 0.177; He = 0.12). High levels of genetic differentiation were detected among populations based on various statistics, including Nei’s genetic diversity analysis (G_ST = 0.4608), Bayesian analysis (θ^B = 0.476) and AMOVA (F_ST = 0.57). That is, populations shared low levels of genetic identity (I = 0.2622–0.0966). This genetic structure was probably due to severe genetic drift, breeding system and limited gene flow. The observed genetic structure of the populations implies that different populations across the distribution range of the species should be sampled to maintain high genetic diversity when a conservation strategy is implemented.     

Genetic diversity and relationships among wild and cultivated Stenocereus queretaroensis populations in western Mexico

Stenocereus queretaroensis is an endemic, chiropterophilous, columnar cactus of economic importance in Mexico. To investigate the effect of artificial selection on genetic diversity, inter-simple sequence repeat (ISSR) markers were used to estimate the genetic variation of wild, orchard, and backyard populations of S. queretaroensis from two regions in western Mexico. Six primers were used to generate 62 bands, of which 39 were polymorphic (62.9%). The total genetic diversity was similar in the wild (H_T = 0.296) and orchard (H_T = 0.291) groups, and slightly lower in the backyard group (H_T = 0.281). Wild populations (F_ST = 0.13) were less differentiated than backyard (F_ST = 0.17) and orchard (F_ST = 0.21) populations. The wild and backyard groups were genetically closer (0.015) than the wild and orchard (0.018) groups. A Mantel test revealed a positive correlation between genetic and geographic distances (r = 0.433, p = 0.002). In conclusion, gene flow and the prevailing management system have efficiently maintained genetic diversity and facilitated inter-population differentiation in S. queretaroensis.