Population genetic structure of three major river Populations of rohu,Labeo rohita (Cyprinidae: Cypriniformes) using microsatellite DNA markers

Determining the genetic structure is essential for developing conservation and stock improvement plans. Four dinucleotide microsatellite loci were analysed to reveal population genetic structure of the Indian major carp,Labeo rohita collected from three major rivers namely the Halda, the Jamuna, and the Padma in Bangladesh. The four loci were polymorphic (P ₉₅) in all the populations. The populations varied in the number and frequencies of alleles as well as heterozygosities in the loci analyzed. Population differentiation (F _ST) value between the Halda and the Jamuna population was significant (P<0.05). Relatively high level of gene flow and low level ofF _ST values were found between the Padma and the Jamuna population. The unweighted pair group method with averages (UPGMA) dendrogram based on genetic distance resulted in two clusters: the Halda population was alone in one cluster whereas the Jamuna and the Padma made another cluster. The results revealed a relatively low level of genetic variability in the river populations ofL. rohita in Bangladesh.     

Randomly amplified polymorphic DNA analysis of four different populations of the Indian major carp, Labeo rohita (Hamilton)

The level of genetic variation provides the raw material for selective improvement of a stock. Random amplified polymorphic DNA (RAPD) assay was used to assess the genetic variation in three rivers: the Halda, the Jamuna and the Padma as well as in one hatchery population of the commercially important Indian major carp, Labeo rohita. RAPD markers were amplified from DNA samples of 35 fish from each of the four populations using six decamer random primers. The polymorphic loci proportions were 0.33, 0.28, 0.28 and 0.26 and Nei's gene diversity values were 0.06, 0.07, 0.06 and 0.05 for the Halda, the Jamuna, the Padma and the hatchery populations, respectively. The pairwise population differentiation (F_ST) values indicated a low level of genetic differentiation between the population pairs. From the unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei's genetic distances a correlation between genetic affinities and geographical area was found. The populations were segregated into two groups: the Halda in one group and the Jamuna, the Padma and the hatchery in another group. Overall, the RAPD technique can be introduced as a tool in the population genetics of the rohu fish to provide information on their genetic stock structure.     

Genetic variation of wild and hatchery populations of the catla Indian major carp (Catla catla Hamilton 1822: Cypriniformes, Cyprinidae) revealed by RAPD markers

Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD) markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822) in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001) departure from homogeneity and the F(ST) values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA) dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.     

High levels of genetic variability and differentiation in hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) populations revealed by PCR-RFLP analysis of the mitochondrial DNA D-loop region

The hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) is an important anadromous clupeid species from the Western division of the Indo-Pacific region. It constitutes the largest single fishable species in Bangladesh. Information on genetic variability and population structure is very important for both management and conservation purposes. Past reports on the population structure of T. ilisha involving morphometric, allozyme and RAPD analyses are contradictory. We examined genetic variability and divergence in two riverine (the Jamuna and the Meghna), two estuarine (Kuakata and Sundarbans) and one marine (Cox's Bazar) populations of T. ilisha by applying PCR-RFLP analysis of the mtDNA D-loop region. The amplified PCR products were restricted with four restriction enzymes namely, XbaI, EcoRI, EcoRV, and HaeIII. High levels of haplotype and gene diversity within and significant differentiations among, populations of T. ilisha were observed in this study. Significant F(ST) values indicated differentiation among the river, estuary and marine populations. The UPGMA dendrogram based on genetic distance resulted in two major clusters, although, these were subsequently divided into three, corresponding to the riverine, estuarine and marine populations. The study underlines the usefulness of RFLP of mtDNA D-loop region as molecular markers, and detected at least two differentiated populations of T. ilisha in Bangladesh waters.     

Distinction between cold-sensitive and -tolerant jute by DNA polymorphisms

Jute is the principal coarse fiber for commercial production and use in Bangladesh. Therefore, the development of a high-yielding and environmental-stress tolerant jute variety would be beneficial for the agro economy of Bangladesh. Two molecular fingerprinting techniques, random-amplified polymorphic DNA (RAPD) and amplified-fragment length polymorphism (AFLP) were applied on six jute samples. Two of them were cold-sensitive varieties and the remaining four were cold-tolerant accessions. RAPD and AFLP fingerprints were employed to generate polymorphism between the cold-sensitive varieties and cold-tolerant accessions because of their simplicity, and also because there is no available sequence information on jute. RAPD data were obtained by using 30 arbitrary oligonucleotide primers. Five primers were found to give polymorphism between the varieties that were tested. AFLP fingerprints were generated using 25 combinations of selective-amplification primers. Eight primer combinations gave the best results with 93 polymorphic fragments, and they were able to discriminate the two cold-sensitive and four cold-tolerant jute populations. A cluster analysis, based on the RAPD and AFLP fingerprint data, showed the population-specific grouping of individuals. This information could be useful later in marker-aided selection between the cold-sensitive varieties and cold-tolerant jute accessions.     

井冈山血水草种群遗传多样性的RAPD分析

采用RAPD技术对江西省井冈山5个血水草种群进行了遗传多样性研究。从50条随机引物中筛选出16条随机引物对血水草的90个个体进行了扩增,共得到180条可统计条带,其中156条为多态带,占总条带数的85.56%。根据Shannon指数和Nei’s遗传分化指数分析显示5个种群间的遗传多样性为31.50%、遗传分化系数为0.302 9,表明血水草大部分遗传变异存在于种群内,少部分存在种群间。血水草的基因流（Nm）为1.150 8。采用算数平均数的非加权成组配对法（UPMGA）对Nei’s的一致度进行的聚类分析结果显示梨坪种群和水口种群的遗传距离最近（0.120 9）,茨坪种群和荆竹山种群的遗传距离最远（0.234 9）。Mantel相关性分析结果显示血水草种群间的遗传距离不仅与海拔梯度有关,还与其生境有关。     

竹叶眼子菜居群遗传多样性和克隆结构

采用ISSR技术对长江中游南岸豹澥湖和大冶湖不同生境中的竹叶眼子菜(Potamogeton malaianus)居群的遗传多样性及克隆结构进行了研究.结果表明,在两居群的106株个体中,利用6条ISSR引物共得到40条符合3/N标准并无连锁不平衡的清晰位点,竹叶眼子菜具有较高的遗传多样性,其多态位点百分率为75.0％,Shannon多样性指数为0.3736, 两居群的遗传分化很小.竹叶眼子菜的克隆多样性很高(D=0.9917),两居群间的克隆分化很大,不具有共有的基因型.竹叶眼子菜的基株分布为游击型构型,位于湖心的大冶居群克隆距离(3.0～31.5 m)明显地大于湖岸豹澥居群(2.4～6.7 m).     

珍稀濒危植物天目木兰（Magnolia amoena）遗传多样性的RAPD分析

运用随机扩增多态DNA(RAPD)技术,对天目木兰(Magnolia amoena)居群的遗传多样性进行了研究．从40个10-mer随机引物中筛选出14个能得到清晰、稳定扩增带的引物进行扩增,14个引物共检测了94个位点,其中多态性位点为23,占24．4％,计算了12个居群之间的遗传相似度和遗传距离,并运用UPGMA法进行了聚类分析,结果显示相同严地个体间(居群内)的遗传距离较小,遗传多样性水平很低;不同产地个体间(居群间)遗传距离较大,遗传多样性水平较前者高,即天目木兰个体间遗传多样性水平与它的地理分布有关,天目木兰总体较低的遗传多样性是导致它濒危的原因之一。     

Genetic differentiation among Hemarthria compressa populations in south China and its genetic relationship with H. japonica

Within and among populations genetic variance of twelve Hemarthria compressa populations and one Hemarthria japonica population from China were analyzed using inter simple sequence repeat (ISSR). Twelve primers amplified a total of 165 genomic DNA fragments across a total of 148 individuals of which 156 were polymorphic (94.55%). 75.76% of the bands were unique to each species, while the average genetic distance (GD) between one population of H. japonica and twelve populations of H. compressa was 0.44, which suggest that there was distinct differentiation between these two species. In H. compressa, twelve primers produced 145 bands across 145 individuals. High genetic diversity was observed at species level. The percentage of polymorphic loci (P) was 86.21% and Shannon's information index of diversity (I) was 0.357. In contrast, there were relatively low levels of genetic diversity within population (P=32.93%, I=0.174). Analysis of molecular variance (AMOVA) showed that a considerable proportion of genetic variation (48.02%) resided among populations. The coefficient of gene differentiation (G(ST)=48.6%) also suggested that there was strong genetic differentiation among H. compressa populations in southern China. An indirect estimate of the number of migrants per generation (N(m)=0.264) indicated that gene flow was low among populations of this species. Relative high clonal diversity was found, and all local genotypes were found.     

珍稀濒危蕨类植物东方水韭的遗传多样性

采用ISSR分子标记对珍稀濒危蕨类植物东方水韭和中华水韭4个自然居群共72个样品进行了DNA多态性分析。从65个随机引物中筛选出11个有效引物,共产生98条DNA片段,其中68条为多态性条带,多态位点百分率(PPL)为66.33%。东方水韭两个居群的多态位点百分比率(PPL)较低(8.16%和7.14%)。中华水韭两个居群的PPL也较低(9.18%和23.47%)。中华水韭物种水平上的PPL(51.02%)高于东方水韭(9.18%)。AMO-VA分析结果表明,东方水韭遗传变异中主要存在于居群内(94.74%),而中华水韭绝大部分的遗传变异却存在于居群间(86.71%)。东方水韭和中华水韭个体间UPGMA聚类结果表明:同一物种的个体完全能聚在一起,中华水韭的两个居群也能明显分开,而东方水韭两居群的个体并不能完全聚在一起。探讨了可能造成上述居群遗传结构模式的主要因素,同时提出今后工作中需重点解决的问题。     

Allozyme,chloroplast DNA and RAPD markers for determining genetic relationships between Abies alba and the relic population of Abies nebrodensis

Allozyme, chloroplast (cpDNA) and random amplified polymorphic DNA (RAPD) markers have been used to estimate genetic and taxonomic relationships among different populations of Abies alba and the relic population of A. nebrodensis. Twelve isozyme gene loci, as well as restriction fragment length polymorphism (RFLP) at cpDNA spacer regions between t-RNA genes were analysed. Moreover, a set of 60 random sequence 10-mer primers were tested. Over all isozyme loci, evident differences in allele frequencies among A. nebrodensis and A. alba populations were found, particularly at 2 loci, phosphoglucose isomerase (Pgi-a) and shikimate dehydrogenase (Skd-a). More than 10% of the total genetic diversity was due to differences among populations. High values of genetic distances among populations were also found. Out of the 60 primers tested, 12 resulted in a polymorphic banding pattern both within and among populations. A total of 84 RAPD fragments were produced by the 12 selected primers. A phenogram of relationships among populations was constructed based on RAPD band sharing: the differentiation of the A. nebrodensis population was evident. The analysis of molecular variance (AMOVA) was used to apportion the variation among individuals within populations and among populations. There was considerable variation within each population: even so, genetic divergence was found among populations. This pattern of genetic variation was very different from that reported for inbred species. Identical cpDNA amplification and restriction patterns were observed among all the individuals sampled from the populations. Taken together, the results of allozyme and RAPDs show a clear differentiation among A. nebrodensis and A. alba populations and provide support for their classification into two different taxonomic groups.     

Length and restriction site heteroplasmy in the mitochondrial DNA of american shad (alosa sapidissima)

Restriction endonuclease analysis was used to assess mitochondrial DNA (mtDNA) variation in American shad (Alosa sapidissima) collected from 14 rivers ranging from Florida to Quebec. Two types of heteroplasmy were observed, one involving a major length polymorphism and the other a single restriction site. Shad mtDNA occurred in two principal size classes, 18.3 and 19.8 kb. Of 244 shad examined, 30 were heteroplasmic and carried both size classes of mtDNA in varying proportions; the remainder were homoplasmic for the smaller size class of mtDNA. The large mtDNA variant occurred most frequently at the southern end of the range, and except for two individuals from Nova Scotia, was not detected among shad from rivers north of the Delaware. In contrast, ten shad heteroplasmic for a SalI restriction site originated from rivers ranging from South Carolina to Nova Scotia. DNA mapping and hybridization experiments indicated that the length polymorphism is in the D-loop-containing region and consists of a tandemly repeated 1.5-kb DNA sequence occurring in two and three copies, respectively, in the two major size classes of shad mtDNA. Continuous length variation up to approximately 40 bp occurs among copies of the repeat both within and among individuals. Restriction site data support the conclusion that both forms of heteroplasmy in shad mtDNA have originated more than once.     

Habitat modelling of juvenile Hilsa Tenualosa ilisha (Clupeiformes) in the coastal ecosystem of the northern Bay of Bengal,Bangladesh

Hilsa shad Tenualosa ilisha comprises the largest and most valuable single fishery of Bangladesh. This study was conducted to identify suitable habitats for Hilsa juvenile in the northern Bay of Bengal along the coast of Bangladesh using Geographical Information Systems (GIS) based Multi-Criteria Evaluation (MCE) of water temperature, dissolved oxygen, pH, salinity, turbidity, current, depth and rainfall. Landsat imagery and 8 thematic layers were analyzed with ENVI and GIS capabilities, and developed as a series of GIS models to identify and prioritize the appropriate habitats for Hilsa juvenile. The study covered 29.484 km² water body and revealed that 56% (16.388 km²) is the most suitable, 21% (6.054 km²) is moderately suitable and 24% (7.042 km²) is not suitable which was consistent with field verification. The assemblage of marinebrackish-freshwater ecosystems with favourable ecological parameters and rainfall patterns are very much important for supporting juvenile Hilsa in the study area. The results are useful for habitat-specific sanctuary development as the efficient conservation may lead to higher production of adult Hilsa and increase the economic benefit to the fishers.     

安徽羽叶报春与毛茛叶报春的遗传多样性研究与新资源评估

采用RAPD方法对分布于安徽的珍稀濒危植物安徽羽叶报春(Primula merrilliana Schltr.)和毛茛叶报春(P．cicutariifolia Pax)的10个居群进行了DNA基因组多态性分析,从50条10碱基随机引物中筛选出14条能扩增出稳定性和重复性好的DNA片段的引物,共扩增出85条带,其中多态性带67条,占总数的78．8％。安徽羽叶报春与毛茛叶报春的多态位点分别达到71．6％与66．7％,因而推测主要致濒因素可能不是通常认为的低水平的遗传多样性。采用N—J法对遗传距离构建的树状图进行聚类分析,从分子角度证明了安徽羽叶报春与毛茛叶报春是2个自然的物种,同时也说明了它们的遗传多样性与生境多样性的密切相关性。由于这2个物种具有地处黄山风景区的地理优势和花朵多、花期长、花姿优美等观赏性特点以及遗传优势,如加以合理的开发与利用,可以作为观赏花卉新资源。     

Genetic Variation and Clonal Diversity of Psammochloa villosa(Poaceae) Detected by ISSR Markers

Genetic variation and clonal diversity of seven Psammochloavillosa(Poaceae) populations from northwest China were investigatedusing inter simple sequence repeat (ISSR) markers. Of the 84primers screened, 12 produced highly reproducible ISSR bands.Using these primers, 173 discernible DNA fragments were generatedwith 122 (70.5%) being polymorphic, indicating considerablegenetic variation at the species level. In contrast, there wererelatively low levels of polymorphism at the population levelwith the percentage of polymorphic bands (PPB) ranging from6.1 to 26.8. Analysis of molecular variance (AMOVA) showed thata large proportion of genetic variation (87.46%) resided amongpopulations, while only 12.54% resided among individuals withinpopulations. Clonal diversity was also high with 98 genets beingdetected from among 157 individuals using 12 ISSR primers. Theevenness of distribution of genotypes in P. villosa populationsvaried greatly, with all of the genotypes being local ones.No significant differences in genetic or clonal diversity werefound between populations in mobile or fixed dunes. The mainfactor responsible for the high level of differentiation amongpopulations and the low level of diversity within populationsis probably the clonal nature of this species, although selfingmay also affect the population genetic structure to some extent.The efficiency of ISSRs in identifying genetic individuals wasmuch higher than that of allozymes. An approximately asymptoticcorrelation was found between the number of genets detectedand the number of polymorphic loci used, suggesting that useof a high number of polymorphic bands is critical in genet identification.Copyright 2001 Annals of Botany Company Psammochloa villosa, ISSRs, genetic variation, clonal diversity     

乌龟遗传多样性的RAPD分析

运用RAPD技术对乌龟的遗传多样性进行了分析。用20个随机引物对24个个体的基因组DNA进行了PCR扩增,一共扩增出3288条DNA片段,平均每个个体扩增出137条带。在检测到的137个位点中,多态位点数为119个,占869%,标记的分子量在0.2kb-3kb之间。个体间最大的遗传距离为0467,个体间最小的遗传距离为0168。24个个体的平均遗传距离为0324+00631。表明乌龟的遗传多样性水平较高。采用类平均聚类法(NJTREE)构建了24个个体相互关系的分支图。24个个体被分为几个类群,显示种内遗传差异较大,可能存在不同种群。本研究为乌龟的种质保护、合理开发利用以及选择育种提供了新的分析参数。       

ISSR analysis of genetic diversity of the Qinghai-Tibet Plateau endemic Rhodiola chrysanthemifolia (Crassulaceae)

Inter-simple sequence repeat markers (ISSR) were used to estimate genetic diversity within and among 10 populations of Rhodiola chrysanthemifolia along Nianqingtangula Mountains and Brahmaputra, a species endemic to the Qinghai-Tibet Plateau and an endangered medicinal plant. Of the 100 primers screened, 13 produced highly polymorphic DNA fragments. Using these primers, 116 discernible DNA fragments were generated of which 104 (89.7%) were polymorphic, indicating substantial genetic diversity at the species level. Genetic diversity measured by the percentage of polymorphic bands (PPB) at the population level ranged from 21.97% to 48.8%. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly among populations (77.3%), but no regional differentiation was discernible. Variance within populations was only 22.7%. The main factor responsible for this high level of differentiation among populations is probably the historical geographical and genetic isolation of populations in a harsh mountainous environment. Concerning the management of R. chrysanthemifolia, the high genetic differentiation of populations indicates the necessity of conserving the maximum possible number of populations.     

日本落叶松群体的叶绿体SSR分析

利用叶绿体微卫星（cpSSR）分子标记对日本国内的7个日本落叶松（Larix kaempferi）群体遗传结构进行了研究。11对cpSSR引物中筛选出的3对多态性引物,共产生10个长度不同片段,在197个样品中组合出现10个不同的单倍型（haplotype）。各群体的单倍型差异较大。cpSSR基因座揭示了日本落叶松的遗传变异：平均等位基因数A=3.33,平均有效等位基因数NE=1.20,基因多样度HE=0.17,群体间变异占总群体变异的5.37%,遗传变异主要来自于群体内个体间。Abstract: Genetic structure of seven populations in Larix kaempferi in Japan was studied by use of cpSSR markers. Ten different length fragments in and ten different kinds of haplotypes were reduced in 197 samples based on 3 pairs of polymorphic primers screened from 11 pairs of primers. There were significant variant haplotypes among the populations. The genetic variation in the populations of Larix kaempferi was detected by using cpSSR with the number of average loci A=3.33, the number of average efficient loci NE=1.20, gene diversity HE=0.17 and 5.37% variation from different populations. The genetic variation was mainly from individuals in population.     

Genetic variability analysis of Giant river cattish (<Emphasis Type="Italic">Sperata seenghala</Emphasis>) populations from Indus river system by RAPD-PCR

The Giant river catfish, Sperata seenghala (Sykes) is commercially very important fish species of South Asia. Genetic variability between its populations collected from two rivers i.e. river Sutlej and river Beas of Indus river system in India were examined using randomly amplified polymorphic DNA analysis. Total 38 fish samples were collected from river Sutlej whereas 46 fish samples were collected from river Beas. Total 40 primers were screened, out of these 7 were selected for studying polymorphism which produced a total of 64 RAPD loci in two populations. Percentage polymorphic loci calculated following 95% criterion was 89.06 % for Beas population as compared to 95.31 % for Sutlej population. Moderate level of genetic divergence (genetic distance of 0.0486) between both the populations suggests distinct population substructure of giant river catfish in both the rivers.