Assessing genetic diversity of populations of topmouth culter (Culter alburnus) in China using AFLP markers

Genetic diversity of five wild populations and a cultured population of topmouth culter (Culter alburnus) was investigated using amplified fragment length polymorphism (AFLP). A total of 373 reproducible bands amplified with seven AFLP primer combinations were obtained from 163 fish. The percentage of polymorphic loci ranged widely from 37.0% to 69.2% within distinct populations. The cultured population appeared to have a lower level of polymorphism (37.0%), gene diversity (0.121 ± 0.188) and Shannon's Information index (0.183 ± 0.263) than the wild populations. Analysis of molecular variance (AMOVA) revealed that average F_ST value overall loci was 0.2671, and the percentage of variation within population (73.29%) was larger than among populations (26.71%) (P < 0.01). The six populations were clustered into two major clades with UPGMA. The results from analysis of population pairwise gene flow indicated moderate gene flow among populations. Our study indicated that the genetic diversity of the cultured population was reduced compared with the wild populations. Geographic isolation, habitat, and artificial selection all may have played important roles in population differentiation. The information may be beneficial to future broodstock selection and defining conservation management for the different populations of topmouth culter.     

Genetic diversity in wild populations of Paulownia fortunei

The genetic diversities of 16 Paulownia fortunei populations involving 143 individuals collected from 6 provinces in China were analyzed using amplified fragment length polymorphism (AFLP). A total of 9 primer pairs with 1169 polymorphic loci were screened out, and each pair possessed 132 bands on average. The percentage of polymorphic bands (98.57%), the effective number of alleles (1.2138–1.2726), Nei’s genetic diversity (0.1566–0.1887), and Shannon’s information index (0.2692–0.3117) indicated a plentiful genetic diversity and different among Paulownia fortune populations. The genetic differentiation coefficient between populations was 0.2386, while the gene flow was 1.0954, and the low gene exchange promoted genetic differentiation. Analysis of variance indicated that genetic variation mainly occurred within populations (81.62% of total variation) rather than among populations (18.38%). The 16 populations were divided by unweighted pair-group method with arithmetic means (UPGMA) into 4 groups with obvious regionalism, in which the populations with close geographical locations (latitude) were clustered together.     

都支杜鹃遗传多样性的ISSR分析

通过ISSR分子标记对都支杜鹃(Rhododendron shanii)5个居群114个个体的遗传多样性进行了分析。8个引物共检测到69个位点,其中多态位点36个,多态位点百分率 （P） 为52.17%;物种水平的Shannon多样性指数（I）为0.2536,Nei指数（H）为0.1659;居群水平的P、I和H分别平均为32.46%、0.1955和0.1344;Nei’s基因分化系数GST=0.1845,基因流Nm=2.2104;遗传结构的AMOVA分析显示,总的遗传变异中88.3%存在于居群内,11.7%存在于居群间;PCA分析和Splite Tree构建的NJ树均显示居群间分化小;遗传距离与地理距离显著相关。较强的基因流、多年生木本及异交与分布区狭窄等可能是导致都支杜鹃遗传多样性较低的主要原因。目前该种的保护应以就地保护为主,尤其要注意对大居群的保护。     

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 analysis of Hepatacodium miconioides at different altitude in Tiantai Mountain, Zhejiang Province, China and its relationship with environmental factors

The genetic diversity within and among populations of Hepatacodium miconioides collected at three different altitudes in Tiantai Mountain, Zhejiang Province and its relationships to environmental factors were analyzed by random amplified polymorphic DNA (RAPD) technique. Amplification using 12 random primers of 60 plants and 122 repetitive loci were produced. The percentage of polymorphic loci of three populations ranged from 18.85% to 23.77% with an average of 21.86%, indicating the relatively low genetic diversity of H. miconioides. The average Shannon index of phenotypic diversity (0.1329) and Nei index (0.0925) within populations were relatively low. A distinct genetic differentiation existed among populations of H. miconioides in spite of the relatively small geographical distribution. The average genetic diversity within populations of H. miconioides accounted for 33.58% of the total genetic diversity while the genetic diversity among populations accounted for 66.42% as estimated by the Shannon index of phenotypic diversity, The genetic differentiation among populations of H. miconioides was 0.6546, as estimated by Nei index. The gene flow estimated from G _ST was only 0.2656 and it indicated that gene flow among populations of H. miconioides was relatively low. The mean value of the genetic identity among populations of H. miconioides was 0.7126 and the average of genetic distance of H. miconioides was 0.3412. The genetic identity between populations at the elevation of 990 m and at the elevation of 780 m was the highest. The genetic identity between population at the elevation 500 m and other two populations was relatively low. The correlation analysis showed that the genetic diversity within populations was significantly related with the soil total nitrogen.     

珍稀濒危植物金毛狗的SRAP分析

利用SRAP分子标记技术,对7个居群79株金毛狗进行遗传多样性分析。结果表明:10对SRAP引物组合共得到107条扩增条带,多态性条带比率为85.98%,Nei’s基因多样性指数为0.229 6,Shannon’s多样性指数为0.358 6,表明金毛狗居群水平具有较高的遗传多样性;金毛狗7个居群的总基因多样度为0.229 6,居群内遗传多样度为0.135 4,居群间的遗传分化指数为0.410 6,表明有41.06%的变异存在于居群间,有58.94%的变异存在于居群内;居群间基因流为0.717 8,表明居群间基因交流频率较低;遗传一致度和UPGMA聚类分析结果显示,生境条件相似的居群优先聚集,说明金毛狗种质亲缘关系与地理分布相关性不显著。     

Analysis of genetic variability and population structure of the endemic medicinal Limonium sinense using molecular markers

Limonium sinense is an endemic medicinal herb used to treat fever, hemorrhage and other disorders. In the present study, population genetic diversity was elucidated using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) primers. Percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at species level. The analysis of molecular variance revealed that 69.88% (RAPD), 71.19% (ISSR) and 70.97% (AFLP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Gst (0.3849/0.3577/0.3670). Gene flow number (Nm) was 0.581/0.618/0.612, which indicated that there was a limited gene exchange between populations. The UPGMA clustering results showed that the genetic distance had no significant correlation with geographic distance. These results indicate that these markers were reliable tools for the differentiation and determination of the genetic diversity among the populations of L. sinense and the conservation of existing natural population is necessary.     

Genetic diversity analysis of Perinereis aibuhitensis based on ISSR and SRAP markers of Chinese coast populations

The objective of this study was to obtain an overview of the genetic relationships within Perinereis aibuhitensis using Inter-Simple Sequence Repeat (ISSR) and Sequence-Related Amplified Polymorphism (SRAP) markers that were derived from related populations residing in the Chinese coasts. The percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at the species level. The analysis of molecular variance revealed that 81.22% (ISSR) and 76.29% (SRAP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Nei's genetic differentiation (Gst) (0.2568/0.2876). The gene flow number (Nm) was 1.4470/1.2385, which indicated that there was limited gene exchange between populations. The phylogenetic tree of the ten P. aibuhitensis populations was separated into four major clusters using the neighbor-joining (NJ) method. These results provide a simple and useful basis for P. aibuhitensis germplasm research and aquaculture breeding.     

Genetic diversity and structure of the noxious alien grass Praxelis clematidea in southern China

Praxelis clematidea (Asteraceae), a plant species native to South America, is a noxious weed in southern China. We examined the genetic variation and population structure of 12 populations (76 individuals) of P. clematidea from Fujian, Guangdong, and Hainan Provinces in China using inter-simple sequence repeat (ISSR) analysis. From an initial set of 69 ISSR primers, 10 were selected which yielded 80 reproducible bands. Polymorphic bands (P) were 100%, Shannon's information index (I) was 0.4226, and Nei's gene diversity (H) was 0.2791. We infer that the high levels of genetic diversity exhibited by P. clematidea may have contributed to its invasiveness. Gene flow among populations was 2.4930, which has led to homogenization. The coefficient of population differentiation (Gst = 0.1671) indicated low levels of genetic variation among populations and high levels of genetic polymorphism within populations. There was a negative correlation between population elevation and genetic diversity, while there was a significant positive correlation between genetic distance and geographic distance based on a Mantel test (r = 0.5820, P < 0.01). Some populations from different provinces clustered together in principal coordinate and UPGMA analyses indicating that human-mediated events may have contributed to the dispersal of the species.     

Genetic diversity of endangered Manglietia patungensis assessed by inter simple sequence repeat and sequence-related amplified polymorphism markers

Manglietia patungensis Hu is an endangered plant native to China. Knowledge of its genetic diversity and structure would aid its conservation. This study assessed nine natural populations of M. patungensis using two methods: inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Using 10 ISSR primer pairs, 334 bands were generated, and 10 SRAP primer pairs generated 276 bands. The percent of polymorphic bands (91.32% and 93.48%), Nei's genetic diversity (0.3448 and 0.3323), and Shannon's information index (0.5075 and 0.4935) revealed a high level of genetic diversity at the species level. Total heterozygosity was 0.3439 by ISSR and 0.3281 by SRAP. The mean heterozygosity was 0.2323 by ISSR and 0.2521 by SRAP. The coefficient of genetic differentiation among natural populations was 0.3245 by ISSR and 0.2316 by SRAP. These data indicated higher levels of genetic diversity of M. patungensis within, rather than among, populations. Estimates of gene flow among natural populations were 1.0411 and 1.0589, which implied a certain amount of gene exchange among populations. A Mantel test revealed no significant correlation between genetic and geographic distance. ISSR and SRAP markers are both effective for genetic diversity research in M. Patungensis. Based on these results, conservation of M. patungensis should be performed both in situ and ex situ.     

濒危植物三棱栎遗传多样性的RAPD分析

用随机扩增多态DNA (RAPD)标记对 5个三棱栎 (Trigonobalanusdoichangensis)居群共 99个个体进行遗传多样性和居群遗传结构分析。 16个引物共检测到 15 7个位点 ,其中多态位点 83个 ,占 5 2 87%。物种水平Shannon多样性指数I =0 2 4 31,Nei基因多样度h =0 15 95 ,种内总遗传变异量Ht=0 16 0 0 ,居群内遗传变异量Hs =0 0 74 9,居群间变异量大于居群内变异量 ,表明三棱栎的遗传变异主要存在于居群之间。与同科植物相比 ,三棱栎遗传多样性较低 ,遗传分化系数Gst =0 5 32 0 ,说明居群间的遗传变异占 5 3 2 0 % ,居群间已出现强烈的遗传分化。当地人的强烈活动造成的生境破碎化和居群隔离 ,以及三棱栎演化过程中的地史变化对其种群发展的影响等 ,可能是造成其居群间强烈的遗传分化和较低遗传多样性的原因。基于本研究结果 ,提出了三棱栎遗传多样性的保护策略。     

Genetic diversity and population structure of spottedtail goby (Synechogobius ommaturus) based on AFLP analysis

Larval dispersal may have an important impact on genetic structure of benthic fishes. To examine population genetic structure of spottedtail goby Synechogobius ommaturus, samples from five different locations of China and Kunsan population in Korea were analyzed by using amplified fragment length polymorphism (AFLP) technology. A total of 253 bands were identified from 91 individuals by 5 primer combinations and the percentage of polymorphic bands was 43.87%. The average gene diversity was 0.0794 ± 0.1470 and Shannon’s information index was 0.1279 ± 0.2138. The pairwise F_st values ranged from 0.022 to 0.201. The results of AMOVA analysis indicated that 90.54% of the genetic variation contained within populations and 9.46% occurred among populations. The gene flow estimates (Nm) demonstrated that different gene flow existed among populations from 0.994 to 11.114. No significant genealogical branches or clusters were recognized on the UPGMA tree. The results support the hypothesis that larval dispersal ability can be responsible for the genetic diversity and population structuring.     

内蒙古小花棘豆遗传多样性的ISSR分析

应用ISSR分子标记对内蒙古西部地区小花棘豆（Oxytropis glabra DC.）6个地理种群进行了遗传多样性研究.结果表明：小花棘豆具有较高的遗传多样性;14个引物共扩增出327个位点,物种水平上Nei＇s基因多样性指数为0.1972,Shannon多样性指数为0.3287;种内总基因多样性为0.1976,种群内基因多样性为0.1653,83.67%的遗传变异存在于种群内,16.33%的遗传变异存在于种群间,种群间的遗传分化系数为0.1633,基因流为2.5613,6个种群间有一定遗传分化,但遗传漂变不会引起遗传分化.UPGMA遗传距离聚类结果表明,生态地理条件相似的种群优先聚集.     

Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species

Genetic variability in the wild genotypes of Dendrobium nobile Lindl. collected from different parts of Northeast India, was analyzed using a Start Codon Targeted (SCoT) marker system. A total of sixty individuals comprising of six natural populations were investigated for the existing natural genetic diversity. One hundred and thirty two (132) amplicons were produced by SCoT marker generating 96.21% polymorphism. The PIC value of the SCoT marker system was 0.78 and the Rp values of the primers ranged between 4.43 and 7.50. The percentage of polymorphic loci (Pp) ranging from 25% to 56.82%, Nei's gene diversity (h) from 0.08 to 0.15 with mean Nei's gene diversity of 0.28, and Shannon's information index (I) values ranging from 0.13 to 0.24 with an average value of 0.43 were recorded. The gene flow value (0.37) and the diversity among populations (0.57) demonstrated higher genetic variation among the populations. Analysis of molecular variance (AMOVA) showed 43.37% of variation within the populations, whereas 56.63% variation was recorded among the populations. Cluster analysis also reveals high genetic variation among the genotypes. Present investigation suggests the effectiveness of SCoT marker system to estimate the genetic diversity of D. nobile and that it can be seen as a preliminary point for future research on the population and evolutionary genetics of this endangered orchid species of medicinal importance.     

珍稀濒危植物长叶红砂种群遗传多样性的ISSR分析

采用ISSR分子标记技术,对濒危小灌木长叶红砂(Reaumuria trigyna) 集中分布的5个种群的遗传多样性水平和遗传结构进行了研究。14条引物共检测到114个位点,其中99个为多态位点,多态位点比率为86.84％,长叶红砂种群具有较高的遗传多样性。物种水平上Shannon多样性指数(I)为0.468 8,Nei基因多样性指数(H)为0.308 4;种群水平上,多态位点比率P为77.89%,I为0.410 6,H为0.260 9,基因分化系数Gst为0.106 9,揭示了长叶红砂种群遗传变异多存在于种群内,种群间的遗传分化较小,占10.69%。 基因流(Nm)为4.178 7＞1,说明种群间的基因交流,防止了由于遗传漂变导致的遗传分化。聚类分析表明长叶红砂种群遗传距离与地理距离之间无显著的相关性。研究结果说明遗传多样性水平与物种本身特性和所处不同群落有关,濒危植物并不一定表现为遗传变异水平的降低。     

Comparative Estimate of the sheep breed gene pools using ISSR-analysis

Using the ISSR-PCR technique, the genetic structure of nine sheep breeds (Ovis aries) bred on the territories of Russia and Mongolia was examined. Species-specific and breed-specific DNA fragments were identified. For the first time, data on the genetic diversity of Telengit and Buubey sheep breeds were obtained. The main parameters of the genetic diversity and the breed structure were assessed, and the phylogenetic relationships and genetic distances between the studied breeds were determined. Using the method of hierarchical frequency averaging, the prototypal sheep gene pool was reconstructed. The three-tiered analysis of diversity based on the ISSR fingerprinting data showed that 15.8% of variability was found between the breeds, 31.4% of variability was found between the populations within the breeds, and the diversity among the individuals within the populations constituted 52.8%.     

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 and Differentiation among Five Populations of Blunt Snout Bream (Megalobrama amblycephala) Revealed by SRAP Markers: Implications for Conservation and Management

The blunt snout bream (Megalobrama amblycephala) is an important freshwater aquaculture fish throughout China. Because of widespread introductions of this species to many regions, the genetic diversity of wild and natural populations is now threatened. In the present study, SRAP (sequence-related amplified polymorphism) markers were used to assess genetic diversity of blunt snout bream. Three natural populations (Liangzi Lake, Poyang Lake and Yuni Lake, one cultured population (Nanxian) and one genetic strain (‘Pujiang No. 1’) of blunt snout bream were screened with 88 SRAP primer combinations, of which 13 primer pairs produced stable and reproducible amplification patterns. In total, 172 bands were produced, of which 132 bands were polymorphic. Nei''s gene diversity (h) and Shannon''s information index (I) values provided evidence of differences in genetic diversity among the five populations (Poyang Lake>Liangzi Lake>Nanxian>‘Pujiang No. 1’>Yuni Lake). Based on cluster analysis conducted on genetic distance values, the five blunt snout bream populations were divided into three groups, Poyang Lake and Liangzi Lake (natural populations), Nanxian and ‘Pujiang No. 1’ (cultured population and genetically selected strain), and Yuni Lake (natural population). Significant genetic differentiation was found among the five populations using analysis of molecular variance (AMOVA), with more genetic divergence existing among populations (55.49%), than within populations (44.51%). This molecular marker technique is a simple and efficient method to quantify genetic diversity within and among fish populations, and is employed here to help manage and conserve germplasm variability of blunt snout bream and to support the ongoing selective breeding programme for this fish.     

短柄枹种群遗传多样性的ISSR分析

利用ISSR分子标记方法对分布在浙江省境内的7个短柄枹种群的遗传多样性和遗传分化进行了分析。从100个引物中筛选出12个用于正式扩增的ISSR引物,在7个种群140个个体中共检测到132个位点,其中多态位点118个,多态位点百分率(P)为89.39%,各种群P平均为58.87%。短柄枹总的Shannon信息指数(I)为0.493 3、Nei指数(h)为0.334 7,各种群I平均为0.336 2、h平均为0.229 1。P、I、h均显示云峰种群最高,天台山种群最低。AMOVA分子差异分析表明,67.97%的变异存在于种群内,32.03%的变异存在于种群间,种群间的基因分化系数(G_ST)为0.315 4。短柄枹种群间的基因流为(N_m)为1.085 3。7个种群的平均遗传距离为0.173 9。利用UPGMA法对7个种群进行聚类,结果显示天台山和雪窦山种群聚成一类,其它5个种群聚成另一类。     

Genetic diversity and structure among natural populations of Sindora glabra in Hainan Island,China as revealed by ISSR markers

Sindora glabra, one of the second-class national protective plants in China, has important ecological and commercial values. To understand the genetic diversity and structure of S. glabra, eleven natural populations from four areas of Hainan Island in China were analyzed by inter-simple sequence repeat (ISSR) markers. Thirteen primers were screened out and used to amplify 157 DNA samples. A total of 122 bands were obtained, among which 114 (93.4%) bands were polymorphic. Genetic parameters including average number of effective alleles (1.547), Nei's gene diversity (0.321), Shannon's information index (0.482), and gene differentiation coefficient (0.1944) revealed a high level of genetic diversity maintained in S. glabra populations. The variation within populations accounted for 85.6% of total variation based on analysis of molecular variance. Genetic distance analysis showed that 11 populations could be divided into three groups and populations from the same areas were classified as one group, suggesting that high genetic diversity of S. glabra was attributable to geographic isolation. Together, introduction of germplasm from distant natural distribution areas would be a sound strategy for germplasm resource conservation of S. glabra and selection of elite individuals from populations of far relationship for hybridization is of great importance for breeding improvement programs in future.