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ABSTRACT: 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 fragments length polymorphism (AFLP) primers. Percentage of polymorphic bands, Nei's gene diversity and Shannon's information index reveald a high level of genetic diversity at species level. Analysis of molecular variance revealed that 69.88% (RAPD), 71.19% (ISSR) and 70.97% (AFLP) of variability was 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 limited gene exchange between populations. The UPGMA clustering results showed the genetic distance had no significant correlation with geographic distance. These results indicate that these markers were reliable tools for differentiation and determination of the genetic diversity among populations of L. sinense and the conservation of existing natural population is necessary.
Gene 03/2013; · 2.34 Impact Factor
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ABSTRACT: Phylogenetic relationship of Limonium and other genera of Plumbaginaceae in China were studied using the cp rbcL, matK and the intergene spacer of trnL-trnF. The analysis showed that Plumbaginaceae was strongly supported monophyletic group sister to Polygonacea, and two tribes were comfirmed by phylogenetic analysis in Plumbaginaceae. Preliminary genetic diversity of Limonium sinense in China was also analyzed in this study by nrDNA (ITS) and cp DNA (two regions of intergenic spacers, trnL-trnF and psbA-trnH). The results showed that the population genetic diversity was low perhaps for human activities and breeding system of this species. These results have been used to understand the evolutionary and demographic history of L. sinense, which is a requisite to establish efficient conservation measures for this species.
Gene 06/2012; 506(2):400-3. · 2.34 Impact Factor
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ABSTRACT: Eriocheir japonica sinensis has long been regarded as a fashionable dainty in China and other Asian countries for its good taste and rich nutrition.
The largest and most economically important mitten crab belongs to E. j. sinensis. But now, E. j. sinensis resource has been intermixed with E. j. hepuensis, which is similar to E. j. sinensis in morphology. In addition, the germplasm resource will be declining rapidly for the two subspecies’ intermixture. Development
of pure E. j. sinensis breed will be a dominant topic in future aquaculture. Molecular markers including DNA bar coding are stable and less affected
by external environment, and have been widely used for the discrimination of species or subspecies. In this study, single
nucleotide polymorphisms (SNPs) of two gene sequences were analyzed, and 17 stably variable sites were confirmed in Cytb and
11 sites in COI sequences, which might be used as the specific DNA bar coding of the two subspecies. Then, two pairs of diagnostic
primers (P1F/P1R, P2F/P2R) on stably variable sites were designed and proved to be valid in E. j. sinensis germplasm authentication for future aquaculture and could be extended for application of identification in food industry.
European Food Research and Technology 05/2012; 230(1):173-178. · 1.57 Impact Factor
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ABSTRACT: Mitten crabs (Eriocheir) were widely distributed in the West-Pacific Ocean. In response to change of temperature during the Pleistocene, they were forced into repeated cycle of glacial retreat and interglacial expansion. In the study, genetic diversity and phylogeographic structure of Eriocheir were analysed by mtDNA markers. All results supported the redivision of four geographic populations of mitten crabs corresponding to geographic distribution. And introgression of the sympatric populations might have happened for some shared haplotypes. Results of "star-like" network, unimodal curve of mismatch distributions and significantly negative values of neutral test suggested a recent population expansion.
Gene 05/2012; 503(1):126-30. · 2.34 Impact Factor
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ABSTRACT: Ten microsatellite loci of Helice tientsinensis (Brachyura: Varunidae) were isolated and characterized. Those loci were proved polymorphic by 21 individuals from coastal
wetland along West-Pacific. The number of observed alleles ranged from 5 to 17. Observed and expected heterozygosity was in
the range of 0.324–0.907 and 0.461–0.926 separately. In addition, those markers were tested polymorphic and suitable for further
assessing genetic diversity and population structure of Helice tientsinensis.
Conservation Genetics Resources 04/2012; 1(1):321-323. · 0.49 Impact Factor
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ABSTRACT: The adapter ligation-mediated allele-specific amplification (ALM-ASA) has been applied to authenticate three valuable Dendrobium species (Dendrobium aphyllum, Dendrobium devonianum and Dendrobium officinale) and their corresponding “Fengdou” foods samples. Three species-specific primers and a universal primer were designed. By
using these primers, three amplification products are 198bp (D. aphyllum), 250bp (D. devonianum) and 310bp (D. officinale) in length, which were clearly distinguishable on a 2.0% agarose gel. In addition, no band was observed with other 17 allied
Dendrobium species of “Fengdou”. The results showed that ALM-ASA could be used to authenticate not only the three valuable Dendrobium species but related food products such as “Fengdou” foods by simultaneous detection of three-site nucleotide difference on
rDNA internal transcribed spacer region.
European Food Research and Technology 04/2012; 229(1):1-7. · 1.57 Impact Factor
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ABSTRACT: Mitochondrial control region was called "A + T-rich" region in invertebrate. In the study, the general organization of control region in mitten crab was divided into two major domains: high variable segment and conserved segment. Four conserved blocks (CSB1, CSB2, CSB3 and CSB4) and two tandem repeat sequences (RT1 and RT2) were defined in control region. There were 116 polymorphic sites and 84 parsimony information sites in 571 aligned sites of the high variable segment adjacent "tRNA-Gln", in which 58 stable variable sites were defined between E. j. sinensis and E. j. hepuensis. Conserved domain contained more than two similar repeat units, and length polymorphism of control region was due to the number difference between the two repeat units (RT1 and RT2). And length polymorphism was a common phenomenon for tandem repeat in control region in the study. Furthermore, a novel result showed the core nucleotide of RT2 in control region tandem repeat was C in E. j. hepuensis, but G in E. j. sinensis. It might be a rapid and cost-effective measure of seedlings differentiation in aquaculture.
Molecular Biology Reports 12/2010; 38(8):4935-40. · 2.93 Impact Factor
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ABSTRACT: Dendrobium officinale is a rare and endangered herb with special habitats and endemic to China. Genetic diversity was examined within and among nine natural populations using inter-simple sequence repeat (ISSR) and random amplified polymorphic (RAPD) for conservation. Both molecular markers revealed a high percentage (>89%) of polymorphic bands and ISSR markers detected more diversity than RAPD markers. Analysis of molecular variance (AMOVA) revealed that 78.84% (ISSR) and 78.88% (RAPD) of variability was partitioned among individuals within populations. This genetic structure was probably due to severe genetic drift resulting from habitat fragmentation and human overexploitation since 1950s. Moreover, there is a lack of significant association between genetic and geographic distances (r = 0.276; p > 0.05) in the populations of D. officinale. From the conservation point of view, populations GL, GS and GSD with higher genetic diversity should be protected firstly to maintain the species potential for evolutionary change and population YG with lower diversity but representing a novel evolutionary unit should also be paid more attention to during D. officinale conservation practice.
Genetika 04/2009; 45(3):375-82. · 0.44 Impact Factor
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ABSTRACT: Dendrobium officinale (Orchidaceae) is used for traditional medicine and is critically endangered in China. To investigate the genetic structure
of this species and to offer some advice on conservation strategies, 84 individuals from nine wild populations of D. officinale were analyzed using the method of sequence-related amplified polymorphism. A high level of genetic diversity was detected
(PPB = 88.07%, H
E = 0.2880) at the species level. However, the genetic diversity at the population level was lower (PPB = 51.68%, H
E = 0.1878) in comparison with other species with similar life history characteristics. Based on analysis of molecular variation,
there was moderate variation between pairs of populations with Φ
ST values ranging from 0.1327 to 0.4151 and on average 27.05% of the genetic variation occurred among populations. Two main
clusters were shown in UPGMA using TFPGA, which is consistent with the result of principal coordinate analysis using NTSYS.
In situ conservation is the first advocated and and ex situ should be proposed at the same time to protect the endangered
plant and to preserve germplasm resources.
Plant Systematics and Evolution 11/2008; 276(3):149-156. · 1.34 Impact Factor
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ABSTRACT: Dendrobium officinale is commonly used as a traditional valuable Chinese tonic hygienic food. In order to authenticate the quality of hygienic
food in the market and geoherbalism in the process of GAP (good agriculture practice), sequences of chloroplast genes (matK
and rbcL), the nuclear rDNA ITS region and mitochondria gene nad1 intron2 were used to survey eight populations of D. officinale. No difference was found in sequences of matK, rbcL and nad1 intron2 between populations, except for nine single nucleotide
polymorphisms (SNPs) sites in rDNA ITS regions. Two pairs of allele-specific PCR primers based on SNPs were designed to authenticate
two genuine populations (GSG and FSC populations). The AS-PCR (allele-specific PCR) fragments of GSG and FSC populations are
about 600 and 560bp, and annealing temperatures are 55–57 and 58–60°C, respectively. Dried “Fengdou” food samples from genuine
populations could also be authenticated using two pairs of diagnostic primers. It is demonstrated that methods based on SNPs
of rDNA ITS region and AS-PCR are simple, practical and effective for genuine germplasm authentication of D. officinale during the process of GAP and hygienic food quality control.
European Food Research and Technology 07/2008; 227(4):1283-1286. · 1.57 Impact Factor
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ABSTRACT: Dendrobium officinale is a critically endangered perennial herb endemic to China. Determining the levels of genetic diversity and patterns of population genetic structure of this species would assist in its conservation and management. Data of 12 populations were used to assess its genetic diversity and population structure, employing the method of amplified fragment length polymorphism (AFLP). A high level of genetic diversity was detected (H (E) = 0.269) with POPGENE. As revealed by AMOVA analysis, there was moderate variation between pairs of populations with Phi(ST) values ranging from 0.047 to 0.578 and on average 26.97% of the genetic variation occurred among populations. Three main clusters were shown in UPGMA dendrogram using TFPGA, which is consistent with the result of principal coordinate ananlysis (PCO) using NTSYS. Keeping a stable environment is critical for the in situ conservation and management of this rare and endangered plant, and for ex situ conservation it is important to design an integrated germplasm bank.
Genetica 07/2008; 133(2):159-66. · 2.15 Impact Factor
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ABSTRACT: The aim of this study is to develop a convenient and effective method for the identification of heparin from pigs (include Sus scrofa domestica Brisson and Sus scrofa riukiuanus). Based on sequences of D-loop region of pigs and the other animals, two pairs of highly specific primers were designed for distinguishing heparin of pigs from other animals. The primers were employed to amplify D-loop region of DNA templates extracted from pig and seven other animal species that amounted to 49 samples. AS-PCR (allele-specific PCR) and ARMS (amplification refractory mutation system) were all suitable for fast identification of heparin from pig with anneal temperature at 54-56 degrees C in AS-PCR and with wider anneal temperature in ARMS,at 52-58 degrees C. An about 170 bp DNA fragments were amplified from separately pigs and whereas no DNA fragment was amplified from other samples under the same reaction condition.
Yao xue xue bao = Acta pharmaceutica Sinica 06/2008; 43(5):535-41.
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ABSTRACT: Dried stems of Dendrobium officinale have been used as crude drugs in traditional Chinese medicine (TCM) with good tonic efficacy. Sequences of chloroplast, nuclear and mitochondria genes and the method of genomic DNA (gDNA) suppression subtraction hybridization (SSH) were used to authenticate different populations during the process of good agriculture practice (GAP) and crude drug quality control. Six populations could be authenticated successfully by nine single sucleotide polymorphism (SNP) sites and six pairs of diagnostic primers for amplification refractory mutation system (ARMS) were also designed to identify six populations on the basis of single nucleotide polymorphism (SNPs). The remainder two populations (JSR, GGL) with the same sequences could be authenticated by SSH. One population-specific fragment was obtained by SSH and a pair of specific primers (SSH-JB01, SSH-JB02) on the specific sequence was designed to authenticate GGL population from the other populations tested. As the resultants were population-specific, the botanic origins of fifty "Fengdou" drug samples from markets could be classified. It is evident that the combined methods provide a high throughput and reliable approach for identification of D. officinale plants and "Fengdou" drugs.
Biological & Pharmaceutical Bulletin 05/2008; 31(4):553-7. · 1.66 Impact Factor
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ABSTRACT: As a widely used medicinal plant, Dendrobium loddigesii Rolfe is always a possible target for fraudulent labeling. The identification of D. loddigesii is generally difficult from its morphological and chemical appearance only. In order to develop a convenient and efficient identification method for D. loddigesii, six pairs of diagnostic ARMS primers were designed based on nrDNA ITS sequences of D. loddigesii and eleven adulterants. The results showed that one diagnostic primer pair (FJB-04-forward, FJB-04-reverse) could be used to authenticate D. loddigesii by generating a fragment of 353 bp at annealing temperatures from 48 degrees C to 62 degrees C while the other diagnostic primer pair (FJB-03-forward, FJB-03-reverse) took on the same effect at annealing temperatures from 49 degrees C to 55 degrees C. This points out the potential of ARMS analysis for authentication of D. loddigesii.
Planta Medica 04/2008; 74(4):470-3. · 2.15 Impact Factor
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ABSTRACT: As a widely used medicinal plant, Alisma orientale is always a possible target for fraudulent labeling. The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA) of the six species of genus Alisma were sequenced, and two variant sites were found to be specific for A. orientale. Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis and amplification refractory mutation system (ARMS) analysis were applied to the ITS region for the identification of A. orientale. A restriction site for PSTI useful for PCR-RFLP analysis was detected and a pair of diagnostic primers DFZX-JB02S and DFZX-JB02X were designed for ARMS.
Planta Medica 02/2007; 73(1):67-70. · 2.15 Impact Factor
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ABSTRACT: Intersimple sequence repeats (ISSR) molecular fingerprinting markers have been employed to authenticate eight populations of Dendrobium officinale using 10 primers selected from 76 ISSR primers. A total of 127 DNA fragments were amplified, of which 115 were polymorphic (90.5% of all bands). Sixteen specific authentication markers have been found. To enhance the efficiency of authentication, ISSR fingerprinting codes have been constructed using six polymorphic bands for authenticating D. officinale populations. Eight wild populations of D. officinale have been authenticated accurately using ISSR.
Biological & Pharmaceutical Bulletin 04/2006; 29(3):420-2. · 1.66 Impact Factor
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ABSTRACT: To establish and optimize ISSR-PCR system of Dendrobiwn officinale according to the ISSR-PCR characters of D. officinale.
The effects of ISSR-PCRs was examined by selecting primers and designing different concentrations of the factors in the ISSR-PCRs, the reliable ISSR-PCR systems for D. officinale populations researching was established by analyzing the reasons for occurrence of differential bands and optimizing reaction conditions.
The optimal ISSR-PCR system in D. officinale was reported for the first time, and 25 15327012 microL ISSR-PCR system contained 10 x Taq buffer, 1.5 U Taq DNA polymerase, 1.2-1.8 mmol x L(-1) MgCl2, 80 micromol x L(-1) dNTP, 0.2 micro mol x L(-1) primer and 20 ng template DNA. The appropriate annealing temperature was among 52-60 degrees C. ISSR PCRs were significantly influenced by Taq DNA polymerase, template DNA quantity and annealing temperature, etc. The ISSR-PCR systems, which were established in this paper for studying D. officinale, could provide clear reliable abundant polymorphisms molecular markers and were proved suitable for studying population authentication and population molecular ecology of D. officinale.
Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica 03/2006; 31(4):291-4.
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ABSTRACT: Genetic diversity, relationship and molecular authentication of total 8 wild populations of Dendrobium officinale were investigated using RAPD markers.
10 random decamer primers were screened for Random Amplified Polymophic DNA (RAPD) fragments. A DNA molecular dendrogram was established based on cluster analysis by UPGMA (unweighted pair-group method with arithmetic average), and the relationship of the wild populations were analyzed, and all the wild populations were authenticated.
A total of 439 loci with an average of 43.9 loci per primer and 54.9 loci per population were amplified from 8 wild populations by 10 effective primers. In the total 104 amplified bands, 95 were polymorphic, corresponding to 91.35% genetic polymorphism. The genetic distances were 0. 590 to 0. 727, with an average of 0. 686.
Distinct genetic differences and extensive genetic diversity were presented among the wild populations. RAPD markers were an informative and useful tool for the genetic diversity, evaluation and authentication of wild populations of Dendrobium officinale. Primer S412 could be used to authenticate 8 wild populations completely.
Yao xue xue bao = Acta pharmaceutica Sinica 12/2005; 40(11):1028-32.
