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ObjectiveTo analyze the sequence variation and genetic diversity of 47 Isatis indigotica germplasm materials， and carry out the study on the genetic differentiation and structure. MethodGenomic DNA of 47 I. indigotica germplasm materials were extracted by kit extraction method. Two chloroplast DNA （cp DNA） sequences and five inter-simple sequence repeat （ISSR） primers were used for amplification and sequencing. Chromas， Mega 7.0， DanSP5， and GenALEx were used to calibrate， splice， and analyze the sequence characteristics. PERMUT and PopGen 1.31 were used to analyze the genetic diversity parameters and genetic structure， and NTSYS was used to obtain the unweighted pair-group method with arithmetic means（UPGMA） clustering tree plot of 47 I. indigotica germplasm materials. ResultA total of 129 samples from 47 I. indigotica germplasm materials were successfully amplified and sequenced. The length of 2 cp DNA sequences after spliced was 1 412 bp， and there were 377 polymorphic variation loci， and 36 haplotypes. Fu and Li's D* test was significant （P<0.01）. The values of Pi， HS， and HT based on cp DNA were 0.119 89， 0.787， and 0.891， respectively. The genetic differentiation coefficients of gene differentiation coefficient（Gst）， nucleotide differentiation coefficient（Nst）， and fixation index（Fst） were 0.117， 0.468， and 0.488， respectively， and the gene flow （Nm） was 0.615. The mean values of PPB， Shannon information diversity index（I）， Nei's genetic diversity index（H）， and Gst based on ISSR were 78.85%， 0.334 8， 0.218 6， and 0.754 4， respectively， and the Nm value was 0.162 8. ConclusionI. indigotica has high genetic diversity and abundant haplotypes at the species level， with abundant haplotypes. Genetic differentiation among different germplasm materials is obvious， and gene exchange is not frequent. Genetic variation mainly exists among populations. The population has accumulated various low-frequency gene mutations recently， suggesting that it has experienced significant regional expansion in the history.
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ObjectiveTo analyze the sequence variation and genetic diversity of 47 Isatis indigotica germplasm materials， and carry out the study on the genetic differentiation and structure. MethodGenomic DNA of 47 I. indigotica germplasm materials were extracted by kit extraction method. Two chloroplast DNA （cp DNA） sequences and five inter-simple sequence repeat （ISSR） primers were used for amplification and sequencing. Chromas， Mega 7.0， DanSP5， and GenALEx were used to calibrate， splice， and analyze the sequence characteristics. PERMUT and PopGen 1.31 were used to analyze the genetic diversity parameters and genetic structure， and NTSYS was used to obtain the unweighted pair-group method with arithmetic means（UPGMA） clustering tree plot of 47 I. indigotica germplasm materials. ResultA total of 129 samples from 47 I. indigotica germplasm materials were successfully amplified and sequenced. The length of 2 cp DNA sequences after spliced was 1 412 bp， and there were 377 polymorphic variation loci， and 36 haplotypes. Fu and Li's D* test was significant （P<0.01）. The values of Pi， HS， and HT based on cp DNA were 0.119 89， 0.787， and 0.891， respectively. The genetic differentiation coefficients of gene differentiation coefficient（Gst）， nucleotide differentiation coefficient（Nst）， and fixation index（Fst） were 0.117， 0.468， and 0.488， respectively， and the gene flow （Nm） was 0.615. The mean values of PPB， Shannon information diversity index（I）， Nei's genetic diversity index（H）， and Gst based on ISSR were 78.85%， 0.334 8， 0.218 6， and 0.754 4， respectively， and the Nm value was 0.162 8. ConclusionI. indigotica has high genetic diversity and abundant haplotypes at the species level， with abundant haplotypes. Genetic differentiation among different germplasm materials is obvious， and gene exchange is not frequent. Genetic variation mainly exists among populations. The population has accumulated various low-frequency gene mutations recently， suggesting that it has experienced significant regional expansion in the history.
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Objective To provide the experimental basis for the subsequent genetic diversity research through establishing and optimizing the inter-simple sequence repeat PCR (ISSR-PCR) reaction system of Gnaphalium affine. Methods The single-factor experimental method and full experimental method were used to optimize the ISSR-PCR reaction system of Gnaphalium affine. Under the optimal system, after screening primers and corresponding annealing temperatures, the systematic feasibility was verified. Results The optimal ISSR-PCR reaction system was consisted of 10 μl Premix Taq DNA polymerase, 0.3 μmol/L primer, 10 ng DNA template, and sterilized water added to 20 μl. Finally, 10 primers were screened from 100 universal primers, and verification results indicated the system had high stability, good reproducibility, and the selected primers had good polymorphism. Conclusion The ISSR-PCR amplification system of Gnaphalium affine was established for the first time and the primers with appropriate annealing temperatures were filtered out, which provided a reference for the subsequent genetic diversity research of Gnaphalium affine.
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ABSTRACT: Poultry meat is a major source of animal protein in the world. Research indicates a high inbreeding rate derived from a relative absence of heterozygous subpopulations of chicken from different suppliers. Molecular markers can provide information for the genetic basis of chicken consumed in rural areas and help establishing a chicken database for product quality and warranty. The bibliometric research, comprises between 1994 and 2018, from five previously selected databases: Google Scholar, PubMed, ScienceDirect, Scopus and Web of Science, using the following descriptors: 'microsatellites', 'SSR', 'ISSR', 'genetic variability' and 'genetic diversity', all of them coupled to 'chicken' and/or 'birds' results in 66 scientific publications. The publications were then categorized according to their titles to the use of ISSR or SSR markers. They were also addressed by countries according first author cited. The publications data appointed that countries with the height production of poultry meat and hens are the most interested in the genetic diversity study of these species. The SSR markers, due to its more specific characteristic, are more frequently applied to genetic diversity assignment, compared to ISSR.
RESUMO: A carne de frango é uma das principais fontes de proteína animal do mundo. Pesquisas indicam uma alta taxa de endogamia derivada de uma relativa ausência de subpopulações heterozigotas de frango de diferentes fornecedores. Marcadores moleculares podem fornecer informações para a base genética de frango consumido em áreas rurais, e ajudar a estabelecer um banco de dados de frango para qualidade e garantia do produto. A pesquisa bibliométrica compreende entre 1994 e 2018, a partir de cinco bancos de dados selecionados anteriormente: Google Scholar, PubMed, ScienceDirect, Scopus e Web of Science, usando os seguintes descritores: 'microssatélites', 'SSR', 'ISSR', 'variabilidade genética' e 'diversidade genética', todos eles associados a resultados de 'galinha' e / ou 'aves' o que resultou em 66 publicações científicas. As publicações foram então categorizadas de acordo com seus títulos para o uso de marcadores ISSR ou SSR. Eles também foram abordados pelos países, segundo o primeiro autor citado. Os dados das publicações obtidas apontam que os países com grande produção de carnes de frangos são os mais interessados no estudo da diversidade genética dessas espécies. Os marcadores SSR, devido à sua característica mais específica, são frequentemente aplicados à atribuição de diversidade genética, em comparação com o ISSR.
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Objective:To explore genetic relationship and population structure of Turpinia arguta in six locations of Jiangxi province by inter-simple sequence repeat （ISSR） molecular marker technique， and to provide theoretical basis for the protection and utilization of this medicinal material resource. Method:A total of 22 samples from six locations in four counties in Jiangxi province were collected， and genomic DNA was extracted by kit method. Polymerase chain reaction （PCR） amplification was performed using sixty-four universal ISSR molecular marker primers， and the products were detected with polyacrylamide gel electrophoresis （PAGE）. NTsys 2.10e software was selected to calculate the genetic similarity coefficient by unweighted pair group method with arithmetic mean （UPGMA） and cluster analysis. Population genetic structure was analyzed by Structure 2.1 software. Result:A total of forty-eight ISSR primers were amplified to obtain the product， the percent of polymorphic bands ranged from 45.45% to 100%. UPGMA cluster analysis showed that these plant individuals could not be clustered according to their respective executive locations. Analysis of population genetic structure showed that 22 samples of T. arguta could be divided into three populations. Conclusion:There is gene exchange among the populations of T. arguta in Jiangxi province， and it can affect the genetic structure of germplasm resources from different geographical sources.
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@#This research used inter simple sequence repeat(ISSR)markers to analyze the genetic diversity of Hedyotis diffusa Willd. from different origins. A total of 23 samples of Hedyotis diffusa Willd. in the Guangxi Zhuang Autonomous Region, Guangdong, Hunan, Zhejiang, Fujian, Jiangxi and Anhui, respectively were collected. 150 ISSR primers were used to amplify PCR and then POPGENE1. 32, NTSYS2. 10 software were used to analyze genetic diversity. 11 primers were screened, 115 polymorphic bands were amplified, the polymorphism ratio was 85. 22%, the number of alleles(Na)was 1. 852 2, the effective allele(Ne)was 1. 543 4, Neis gene diversity index(H)was 0. 316 5 and Shannon′s information index(I)was 0. 470 0. The results of cluster analysis show that the Hedyotis diffusa can be divided into three clades. The conclusion is that ISSR molecular markers can provide a insight for the identification of Hedyotis diffusa Willd. .
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Background: Penthorum chinense Pursh (P. chinense) is a well-known traditional Chinese medicine (TCM) plant, which has long been used for the prevention and treatment of hepatic diseases. This study aimed to genetically characterize the varieties of P. chinense from different geographic localities of China by random amplification of polymorphic DNA (RAPD)-PCR technique and verified with inter-simple sequence repeat (ISSR) markers. Results: The P. chinense samples were collected from nine different geographic localities. Previously improved RAPD and ISSR markers were utilized for genetic analysis using DNA amplification. The genetic relationship dendrogram was obtained by conducting cluster analysis to the similarity coefficient of improved RAPD and ISSR markers. Improved RAPD yielded 185 scorable amplified products, of which 68.6% of the bands were polymorphic, with an average amplification of 9.25 bands per primer. The ISSR markers revealed 156 alleles with 7.8 bands per primers, where 59.7% bands were polymorphic. Furthermore, the similarity coefficient ranges of RAPD and ISSR markers were 0.710.91 and 0.660.89, respectively. Conclusions: This study indicated that improved RAPD and ISSR methods are useful tools for evaluating the genetic diversity and characterizing P. chinense. Our findings can provide the theoretical basis for cultivar identification, standardization, and molecular-assisted breeding of P. chinense for medicinal use.
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Plants, Medicinal/genetics , Magnoliopsida/genetics , Polymorphism, Genetic , Genetic Variation , Genetic Markers , China , DNA, Plant/genetics , Random Amplified Polymorphic DNA Technique , Microsatellite Repeats , Medicine, Chinese TraditionalABSTRACT
Purpose: To establish a new genotyping method for Vibrio cholerae and compare it with other methods. Materials and Methods: In the current study, a modified inter simple sequence repeat-polymerase chain reaction (MISSR-PCR) system was developed via several rounds of optimisation. Comparison study was then conducted between MISSR-PCR and three other methods, including enterobacterial repetitive intergenic consensus sequences-based PCR (ERIC-PCR), randomly amplified polymorphic DNA (RAPD) and 16S rRNA evolutionary clock, for the detection and genetic tracing of Vibrio cholerae isolated from seafood in China. Result: The results indicated that the MISSRPCR system could generate the highest polymorphic fingerprinting map in a single round PCR and showed the best discriminatory ability for Vibrio cholerae genotyping by clearly separating toxigenic/nontoxigenic strains, local/foreign strains, and O1/O139/non-O1/non-O139 serogroup strains, comparing to ERIC-PCR, RAPD and 16S rRNA evolutionary clock. Moreover, the MISSR-PCR is superior to previously described traditional simple sequence repeat based PCR method on genotyping by more clearly separating different clusters. Conclusion: To the best of our knowledge, this is the first head-to-head comparison of four detection and genotyping methods for Vibrio cholerae. The MISSRPCR system established here could serve as a simple, quick, reliable and cost-effective tool for the genotyping and epidemiological study.
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La fusariosis de la espiga de trigo es una importante enfermedad para la región pampeana Argentina; Fusarium graminearum es el principal patógeno asociado. Se estudió el polimorfismo del ADN de un conjunto de aislamientos utilizando las técnicas de IGS-RFLP e ISSR. La técnica de IGS-RFLP produjo 41 bandas, 30 de ellas fueron polimórficas. El análisis de los ISSR mostró 87 bandas con 47 bandas polimórficas. La primera de estas metodologías fue más eficiente, ya que detectó mayor promedio polimórfico (59,91%) que la segunda (44,11%). Los valores promedio del contenido de información polimórfica (PIC) fueron 0,211 y 0,129, respectivamente. Se identificaron 20 haplotipos por IGS-RFLP, mientras que el análisis de los ISSR reveló 15 haplotipos. La agrupación de genotipos obtenida en ambos dendrogramas fue diferente. Los grupos genéticos obtenidos por la técnica de IGS-RFLP mostraron una asociación parcial con el origen geográfico. Este es el primer reporte que analiza la variabilidad genética en poblaciones de F. graminearum de trigo empleando marcadores IGS-RFLP e ISSR en Argentina
Fusarium Head Blight is an important wheat disease in the Argentine Pampas region, being Fusarium graminearum the predominant pathogen. DNA polymorphism of the isolates was analyzed by IGS-RFLP and ISSR. IGS-RFLP and ISSR profiling were carried out using six endonucleases and eight primers, respectively. IGS-RFLP yielded 41 bands, 30 of which were polymorphic while ISSR produced 87 bands with 47 polymorphic bands. Both markers showed genetic variability among the analyzed isolates; however, IGS-RFLP was more efficient than ISSR, showing a higher polymorphic average (59.91%) than the latter (44.11%). The averages of polymorphic information content (PIC) were 0.211 and 0.129, respectively. Twenty haplotypes were identified by IGS-RFLP and 15 haplotypes by ISSR. Genotype clustering within dendrograms was different for both types of markers. The genetic groups obtained by IGS-RFLP showed a partial association to geographic origin. This is the first report on genetic variability of F. graminearum isolates from wheat in Argentina using IGS-RFLP and ISSR markers
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Genetic Variation , Triticum/microbiology , Fusariosis/microbiology , Fusarium/genetics , Fusarium/isolation & purificationABSTRACT
Background Angelica sinensis is a well-known traditional Chinese medicinal plant. We aimed to assess the genetic diversity and relationships in A. sinensis cultivars collected from different locations of China and also some other Angelica species. Results We employed an improved random amplified polymorphic DNA (RAPD) technique for the amplification of DNA materials from ten Angelica cultivars, and the results were verified by inter-simple sequence repeat (ISSR) analysis. Twenty six RAPD primers were used for RAPD, and the amplified bands were found highly polymorphic (96%). Each primer amplified 8-14 bands with an average of 10.25. The cluster dendrogram showed that the similarity coefficients ranged from 0.41 to 0.92. The similarity coefficients were higher among different cultivars of A. sinensis, and lower among different species. Twenty ISSR primers were used for the amplification, and each primer generated 6-10 bands with an average of 7.2 bands per primer. The cluster dendrogram showed that the similarity coefficients ranged from 0.35 to 0.89. Conclusions This study genetically characterized the Angelica species, which might have a significant contribution to the genetic and ecological conservation of this important medicinal plant. Also, this study indicates that the improved RAPD and ISSR analyses are important and potent molecular tools for the study of genetic diversity and authentication of organisms.
Subject(s)
Random Amplified Polymorphic DNA Technique , Microsatellite Repeats , Angelica sinensis/genetics , Plants, Medicinal , Genetic Variation , Genetic Markers , Cluster Analysis , China , Electrophoresis, Agar GelABSTRACT
OBJECTIVE:To compare genetic diversity of Spatolobi caulis from different areas of Guangxi by random amplified polymorphic DNA(RAPD)and inter-simple sequence repeat(ISSR). METHODS:Through using POPGENE 32 software,Ntsys software and SPSS 17.0 software,RAPD and ISSR methods were used to study genetic diversity of 9 samples of S. caulis from dif-ferent areas of Guangxi. RESULTS:After amplification of screened 3 RAPD primers and 4 ISSR primers,and there were 198 and 315 locus,and 37 and 80 polymorphism locus. Rates of polymorphism locus were 18.7% and 25.4%;the number of effective al-leles were 1.416 8 and 1.584 0;genetic diversity index were 0.269 4 and 0.351 3;Shannon diversity index were 0.431 6 and 0.529 9. All the values of ISSR marker were higher than RAPD marker. The average genetic similarity coefficient of ISSR and RAPD were 0.757 64 and 0.683 80,indicating ISSR was more sensitive for the detection of genetic diversity. The clustering result of them was close to each other. The correlation coefficient of them were 0.847,indicating very significant positive correlation at the level of 0.001. CONCLUSIONS:ISSR could reflect more information of genetic diversity than RAPD,and is more suitable for research of genetic diversity of S. caulis from different areas of Guangxi.
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Cassava serves as primary staple food of millions of people in the tropics and subtropics, and is used as a carbohydrate source in animal feed. Knowledge of agro-morphological characteristics and genetic relatedness is essential for an efficient recombination of varieties in a breeding program. The objective of the present study was to determine genetic relatedness and morpho-agronomic differentiation among Congolese cassava collection for breeding purposes. The morphological and agronomic characters were highly variable among accessions. Every accession could be differentiated from any other one. There were significant genotypes x location interactions for storage root yields. Root weights were positively correlated with the number of roots per plant. In general, all the improved varieties were tolerant or resistant to the Cassava Mosaic Virus (CMV) while the local (non-improved) varieties were susceptible. But the reaction to Cassava Bacterial Blight (CBB) confirmed that genetically improved accessions are susceptible and local varieties are resistant. Molecular analysis revealed that the accessions analyzed were genetically distant with 80% of genetic distance values estimated above 0.5. One local accession was an out-group that was separated from the main groupings with 100% degree of confidence. More importantly, there were no associations between genetic relationships and morphological similarities based on lobe shape, leaf colour, petiole colour, petiole orientation, and stem colour. Although the Congolese cassava genepool is small, there is enough variability to sustain a breeding program without new introductions of germplasms.
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Context: Survivors of the Bhopal gas disaster still suffer from various respiratory ailments. We examined the effects of exposures among a cross-section of current residents suffering from COPD by ISSR-PCR. Aims: Molecular screening of the gas-affected population of Bhopal with COPD for microsatellite instability due to exposure of MIC. Settings and Design: The isocyanate-exposed population of Bhopal city suffering from chronic obstructive pulmonary disorder. Materials and Methods: Inter-(SSR) analysis was used to characterize microsatellite instability in 52 MIC victims of Bhopal, suffering from COPD using (CA) 8 RG and (CA) 8 R[Y-Q] primer. Statistical Analysis Used: Association analyses were performed using regression analysis. Results: The study on the MIC-affected population in Bhopal showed weak association between microsatellite instability and age (r = + 0.37); exposure distance from site (r = −0.44); and smoking status(r = + 0.12); while regression analysis of the above parameters displayed supporting evidence. Conclusions: The high prevalence of smoking coupled with aging and poor living habits threatens, to further increase COPD incidences among this population, highlighting the need for enhanced screening efforts.
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Adult , Aged , Aged, 80 and over , Female , Bhopal Accidental Release , Factor Analysis, Statistical , Genomic Instability/genetics , Humans , Male , Middle Aged , India , Isocyanates/adverse effects , Isocyanates/toxicity , Microsatellite Instability , Microsatellite Repeats/genetics , Population Groups/genetics , Pulmonary Disease, Chronic Obstructive/epidemiology , Pulmonary Disease, Chronic Obstructive/etiology , Pulmonary Disease, Chronic Obstructive/geneticsABSTRACT
Objective: In order to provide the foundation for the genetics and breeding of Trichosanthes kirilowii, the genetic diversity of T. kirilowii was analyzed. Methods: Studies on polymorphism and cluster on 34 T. kirilowii materials from different growing areas were done by inter-simple sequence repeat (ISSR). Results: The genetic polymorphism of T. kirilowii was up to 90% from different growing areas. According to the results of ISSR culster, the materials of T. kirilowii were divided into three classes: food seed, edible and medicinal, and wild types. Conclusion: There is higher genetic polymorphism among T. kirilowii materials, and no correlation to the growing areas.
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Brycon pesu is a small-sized fish distributed throughout the Amazon and Orinoco Basins and other coastal basins of northeastern South America. Brycon cf. pesu specimens from the Araguaia-Tocantins Basin are currently separated into two morphotypes, Brycon sp1 and Brycon sp2, owing to different coloration of their anal fin. Brycon sp2 has a reddish margin stripe on the anal fin which morphologically distinguishes it from Brycon sp1. In the present research, nuclear and mitochondrial markers were used to test the hypothesis that the Brycon sp1 and Brycon sp2 morphotypes are distinct species. Specimens from the two morphotypes were collected from the Lajeado Hydroelectric Plant and the Palmas River in the Araguaia-Tocantins Basin. Thirty-five loci obtained by the amplification of five inter-simple sequence repeat primers were analyzed but no species-specific bands were detected. Electrophoretic profiles obtained from 5S rDNA non-transcribed spacer amplification failed to show any differentiation in morphotypes. These results were corroborated by nucleotide sequence analysis of the mtDNA control region, in which 24 polymorphic nucleotide sites, representing a polymorphism rate of only 5%, were detected. The low rates of polymorphism detected by inter-simple sequence repeat, non-transcribed spacer and mtDNA D-loop markers strongly reject the hypothesis that the two morphotypes Brycon sp1 and Brycon sp2 represent distinct species within Brycon cf. pesu. Further studies are needed to obtain conclusive data on the notion that the coloration of the anal fin is an intraspecific polymorphism, possibly related to environmental factors.
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Animals , DNA, Intergenic/genetics , DNA, Mitochondrial/genetics , Genetic Variation , Fishes/genetics , /genetics , Base Sequence , Brazil , DNA , Genetic Markers , Genome , Geography , Microsatellite Repeats , Nucleic Acid Conformation , Polymerase Chain Reaction , Polymorphism, Genetic , Fishes/classification , Sequence Analysis, DNA , Species SpecificityABSTRACT
Objective A new breed of licorice seeds(Wuxin No.1) was selected from wild licorice,Glycyrrhiza uralensis.Methods Its germination rate,content of soluble protein,and peroxidase(POD) activities were investigated and compared with the wild licorice seeds(control group).The leaves of Wuxin No.1 were collected and its genetic polymorphism was analyzed by inter-simple sequence repeat technique(ISSR).Results The results suggested that the seed vitality in Wuxin No.1 was higher than that in the control group.The change of soluble protein and POD activity also demonstrated that the seeds in Wuxin No.1 have the higher vigor.ISSR Analysis showed that among 22 random primers used in this experiment,six primers generated different DNA band types,which meant that there was genetic polymorphism in Wuxin No.1.Conclusion All these changes indicate that Wuxin No.1 is a prospective domestication species of licorice and may be cultivated widely in the future.