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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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Cowpea is a legume of great importance in the Brazilian nutrition, mainly in the Northeast region. Despite the low yield of Brazilian cowpea, the species presents a genetic potential to be explored. Thus, this work aimed to characterize the genetic diversity of cowpea genotypes by agronomic traits and select genotypes for possible crosses by multivariate analysis. Four value for cultivation and use tests were carried out with cowpea genotypes in 2005 and 2006, in the municipalities of Aquidauana, Chapadão do Sul, and Dourados, in the state of Mato Grosso do Sul. The experimental design was a complete randomized block with 20 genotypes and four replications. The evaluated traits were value for cultivation, plant lodging, pod length, grain weight of five pods, number of grains per pod, pod weight, severity of powdery mildew, and grain yield. To estimate the genetic diversity among the genotypes, the optimization methods of Tocher and UPGMA were used. The generalized distance of Mahalanobis was used as a dissimilarity measure. The clustering methods revealed genetic variability among the cowpea genotypes evaluated. The methods used formed a different number of groups for each environment. Genotypes TE97-309G-24, MNC99-542F-5, BRS Paraguaçu, BRS Paraguaçu, BR 17-Gurguéia, and CNC x 409-11F-P2 can be used to obtain promising combinations and high genetic variability.
O feijão-caupi é de grande importância na nutrição brasileira, principalmente na região Nordeste. Apesar do baixo rendimento do feijão-caupi no Brasil, esta leguminosa apresenta potencial genético a ser explorado. Dessa forma, o objetivo do trabalho foi caracterizar a variabilidade genética de caracteres agronômicos e estimar a divergência genética entre genótipos de feijão-caupi por meio de análise multivariada. Quatro ensaios de valor de cultivo e uso com genótipos de feijão-caupi foram conduzidos nos anos de 2005 e 2006, nos municípios de Aquidauana, Chapadão do Sul e Dourados. Os experimentos foram conduzidos em delineamento blocos casualizados, com 20 genótipos e quatro repetições. Os caracteres avaliados foram acamamento de plantas, comprimento de vagem, peso de grãos de cinco vagens, número de grãos por vagem, peso de vagem e produtividade de grãos. Realizou-se análise de variância individual e conjunta. Para estimar a diversidade genética entre os genótipos, foram utilizados o métodos de otimização de Tocher e UPGMA. A distância generalizada de Mahalanobis foi utilizada como medida de dissimilaridade. Foi possível detectar variabilidade genética entre os genótipos de feijão-caupi avaliados por meio dos métodos de agrupamento utilizados. Os métodos utilizados formaram números de grupos distintos para cada ambiente. Os genótipos TE97-309G-24, MNC99-542F-5, BRS Paraguaçu, BRS Paraguaçu, BR 17-Gurguéia e CNC x 409-11F-P2 podem ser usados para obter combinações promissoras e elevada variabilidade genética.
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Genetic Variation , Multivariate Analysis , VignaABSTRACT
Objective: To analyze the genetic diversity and relationship of Epimedium acuminatum from different habitats in Guizhou Province. Methods: PopGene 32 software and NTsys2.10e software was used to analyze the genetic diversity and phylogenetic relationship of five different habitats in Guizhou Province, and phylogenetic tree was constructed according to the UPGMA method. Results: A total of 13 polymorphic and clear bands were screened from 100 random primers showed that amplified 211 bands, of which 205 were polymorphic from the level of species, the percentage of polymorphic bands (PPB) was 97.16%. The Shannon’s information index (I) was 0.455 7; Nei’s gene diversity index (He) was 0.297 3; The effective number (Ne) of alleles was 1.490 2; The total genetic diversity (Ht) of five populations was 0.297 3, while the population genetic diversity within the group (Hs) was 0.207 5, indicated that the genetic variation mainly existed within populations, genetic differentiation within population than that of population between. The population genetic distance clustering was built by UPGMA. The results showed that five populations were divided into two branches, three populations from Anshun, Huaxi, and Gaopo clustered into one branch, and the other two populations from Longli and Leishan populations clustered into one branch. Conclusion: ISSR molecular marker technique can be used to analyze the genetic diversity and phylogenetic relationship of Epimedium acuminatum from different habitats in Guizhou Province.
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Objective: The genetic variation and relationship of 47 pieces of Gardenia jasminoides germplasms were analyzed by SCoT molecular markers. Methods: The genetic similarity coefficient was calculated by NTSYS version 2.1 software and the dendrogram was constructed by UPGMA method. Results: More than 20 polymorphic primers were screened from 36 primers and PCR amplificated to test materials. The primers generated totally 154 bands among which 120 bands were found to be polymorphic, with an average of 78.14%. The genetic similarity coefficient among the germplasms ranged from 0.655 8 to 0.980 5, and the average content was 0.784 1. The clustering results showed that the genetic diversity of G. jasminoides was rich and the genetic relationship was complex. Conclusion: SCoT markers were feasible and effective to analyze the genetic diversity of G. jasminoides germplasm resources. The results provide a reliable theoretical basis for breeding, classification, preservation and utilization of G. jasminoides.
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Objective In this paper, the genetic diversity of 64 samples of Tetrastigma hemsleyanum germplasm resources in Chinese was analyzed. Methods ISSR-PCR was firstly used to amplify, and then POPGENE 32 software and NTSYS software was used to analyze the genetic diversity and phylogenetic relationship of 64 samples of T. hemsleyanum germplasm resources, and phylogenetic tree was constructed according to the UPGMA method. Results Ten primers with clear and reproducible bands were screened from 30 primers and used for genomic DNA amplification of 64 sample materials. A total of 83 polymorphic locis were amplified, whose polymorphic percentages were 71.43%-100% and average polymorphism percentage was 94.31%. The amplification polymorphic locis of primer S17 were the most (11) and the amplification polymorphic locis of primer P6 were the least (5), the average amplified polymorphic locis of 10 primers were 8.3. Genetic diversity analysis showed that the average number of alleles (Na) of 64 samples was 1.943 1, the average effective allele number (Ne) was 1.381 08, the average Nei’s gene diversity index (H) was 0.242 98, and the average Shannon diversity index (I) was 0.385 83. The variation range of the genetic similarity coefficient of the 64 samples was 0.431 8-0.988 6. A total of 64 samples were divided to six groups by UPGMA clustering method according to the similarity coefficient matrix when the genetic similarity coefficient was 0.715 5, which showed the abundant genetic diversity and relative gene stability of T. hemsleyanum germplasm resources. In addition, amplification figures by primers ISSR20, UBC857, and S17 were screened based on amplification result of 10 ISSR primers, and DNA fingerprinting was constructed, which can be used to identify 64 samples of T. hemsleyanum tested. Conclusion There are abundant genetic diversity and relative gene stability in T. hemsleyanum germplasm esources in China. ISSR analysis can reveal the genetic relationship among T. hemsleyanum germplasm resources in China, and provide certain reference for the evaluation, identification and new variety breeding of T. hemsleyanum germplasm resources in China.
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Objective: To reveal the dynamic changing regularity of microflora in the fermentation process of Sojae Semen Praeparatum (SSP) and lay the foundation for revealing the mechanism of SSP processing by denaturing gradient gel electrophoresis (DGGE). Methods: The dynamic changes of microflora, both bacteria and fungi in fermentation process were monitored by PCR-denaturing gradient gel electrophoresis. According to the unweighted pair group method using arithmetic average clustering, the samples of SSP in various stages were analyzed. Results: Bacterial flora had diversity, and Aspergillus was the major fungus in the first stage called "yellow cladding". The major bacteria was Lactobacillus, while the major fungus was Cryptococcus at the "secondary fermentation" stage. The major microorganism was Bacillus subtillis and Pseudomonas putida on day 1, and Stenotrophomonas maltophilia, Sphingobacterium sp, and A. oryzae on day 3. Then on day 6, B. amyloliquefaciens, Aspergillus, and Trichosporon ovoides became the primary microorganisms. B. subtillis, T. ovoides, and A. niger were the major microorganism on day 3 of "secondary fermentation". On day 9 of this stage, the major strains were B. subtilis, L. concavus, L. nasuensis, and Cryptococcus randhawi. On day 15 of "secondary fermentation", they were B. subtilis, L. concavus, C. randhawi, Trichosporon, and two fungi cannot be cultured. Klebsiella oxytoca, B. subtilis, and L. concavus were dominant strains in the whole fermentation process. The composition of microflora in "yellow cladding" stage was different to that of the "secondary fermentation". The microbial community on day 3 and 6 was similar to 76.4%. While the lowest similarity between the samples on day 3 and 9, it was similar to 24.5% during samples on day 6 and 9 in "secondary fermentation" stage. The highest similarity of fungal composition was between day 3 and 6 samples, and the lowest one was between day 3 and 15 of "secondary fermentation", which was similar to 11.2% only. Conclusion: The results show that the unique flavor and function of SSP may be determined by the dynamic microbial communities and microbial flora in the fermentation process, and the secondary fermentation is proved to be irreplaceable from the microbiological point of view.
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Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3–14 and the major allele frequency was distributed from 0.17–0.96. The values of observed and expected heterozygosity ranged from 0.00–0.76 and 0.07–0.90, respectively. The polymorphic information content value ranged from 0.07–0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.
Subject(s)
Alleles , Breeding , DNA , Gene Frequency , Genetic Linkage , Genetic Variation , Genome , Lentinula , Methods , Microsatellite Repeats , Shiitake MushroomsABSTRACT
RESUMO:O presente trabalho foi conduzido na unidade experimental da Empresa Mato-Grossense de Pesquisa, Assistência Técnica e Extensão Rural (Cáceres-MT) e teve como objetivo determinar a variabilidade genética existente entre 40 acessos tradicionais de Phaseolus vulgaris L. do banco ativo de germoplasma da região de Cáceres-MT. Foi utilizado um delineamento de blocos ao acaso com três repetições e analisadas onze características morfoagronômicas. Os dados obtidos foram submetidos à análise de variância, foi estimada a variabilidade genética entre os acessos empregando-se análise multivariada com base na distância generalizada de Mahalanobis, realizando as análises de agrupamento. Houve diferenças significativas a 1% de probabilidade para todas as características avaliadas. A maior distância genética foi encontrada entre os acessos 13 e 20 (D2ii'=364,99), e a menor distância entre os acessos 13 e 26 (D2ii'=2,23). Os métodos de Tocher e UPGMA ordenaram os acessos mais divergentes em grupos distintos, evidenciando a existência de variabilidade, podendo ser inclusos em programas de melhoramento com enfoque regional.
ABSTRACT:The present research was conducted at the experimental unit of the Empresa Mato-Grossense de Pesquisa, Assistência e Extensão Rural-EMPAER (Caceres-MT) and aimed to determine the genetic variability that exaist among 40 accesses from active germplasm bank of Phaseolus vulgaris L. of the region Caceres-MT. It was used a random blocks design with three replications and analyzed eleven agronomic characteristics. Data were submitted to analysis of variance, it was estimated the genetic variability among the accessions through multivariate analysis based on Mahalanobis distance, performing cluster analysis. There were significant differences at 1% probability for all the characteristics evaluated. The largest genetic distance was found between accessions 13 and 20 (D2ii'=364.99), and the smallest distance between accessions 13 and 26 (D2ii'=2.23). Methods of Tocher and UPGMA ordered the most divergent accessions into distinct groups, showing the existence of variability and can be included in breeding programs with a regional focus.
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Aims: Investigate the degree of polymorphism using 41 ISSR (Inter-simple sequence repeat) markers in 50 sorghum accessions from 11 different regions in Sudan and Republic of South Sudan. Study Design: UPGMA cluster analysis using STATISTCA- SPSS software Ver. 9. Place and Duration of Study: Department of Molecular Biology, Commission for Biotechnology and Genetic Engineering, National Center for Research, Khartoum, Sudan (2010-2012). Methodology: 50 sorghum accessions with important agronomic traits, representing 11 regions in Sudan and Republic of South Sudan were assayed for polymorphism using Inter-simple sequence repeats (ISSRs). Seven primers out of 41 tested (807, 808, 810, 814, 848, 872 and 879) showed high polymorphism among the Sorghum accessions. Results: The results indicated 75 polymorphic bands out of 78 bands with percentage of polymorphic bands of 97%. UPGMA analysis showed ISSR distance matrix ranged between (0.04-0.47) which reflected high genetic diversity. The ISSR UPGMA dendrogram showed high molecular variance within regions. Based on the results of this study ISSR technique showed differences among closely related accessions of sorghum. Also it proved to be useful technique to study genetic variation among the Sudanese Sorghum accessions. Conclusion: Sorghum accessions from Sudan exhibits high genetic variation within and among regions. ISSR marker technique used in this study proved that it is efficient and could be very useful for breeders and researchers community in various fields of sorghum improvement in Sudan.
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Randomly amplified polymorphic DNA (RAPD)-PCR was applied with ten random 10-mer primers to examine the molecular diversity among methicillin resistant Staphylococcus aureus (MRSA) strains in the hospitals and to investigate the epidemiological spread of these strains between different hospitals. The main objective of the study was to identify appropriate primers, which successfully established the clonality of MRSA. Three of the primers yielded particularly discriminatory patterns and they were used to perform the RAPD analysis which revealed different bands ranging from 200 to 1500 bp. Dendogram was created by the un-weighted pair group method using arithmetic (UPGMA) average clustering and it was constructed based on the combination results of the new primers (S224, S232 and S395) which represented a novel approach for rapid screening of the strains and also provided the opportunity for monitoring the emergence and determining clonal dissemination of MRSA strains between the hospitals. Dendogram generated two main groups (Group I and II) with three clusters (A, B and C) and indicated that the strains isolated from the same hospital were closely related and they placed together in the same group. This technique could be of attractive use in controlling the sources and routes of transmission, tracking the spread of strains within hospital and between the hospitals, and especially preventing the nosocomial infections caused by the MRSA.
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Objective: To study the germplasm resources of Anoectochilus roxburghii. and the genetic diversity of its spurious breed. Methods: By ISSR-PCR amplification, 24 samples were PCR amplified, and then electrophoresis detected. After marking the electrophoresis strips with "0" and "1" matrix, the genetic distances were calculated by NTSYSpc software, and the dendrogram was constructed by UPGMA. Results: A. roxburghii, A. formosanus, and A. sp. were identified. A. roxburghii with different geographical distribution and morphology had the close genetic relationship. Conclusion: The wild population of A. roxburghii resources have higher genetic diversity, witch could provide a great genetic library for varieties breeding.
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Background: The Bemisia tabaci is one of the most devastating pests of agricultural crops and ornamental plants worldwide. The genetic diversity and biotype status of the Bemisia tabaci in Pakistan was assessed by using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). A total 80 samples of B. tabaci collected from 14 districts of the Punjab province and 7 districts of the Sindh province were included. Results: All 10 primers screened in this study generated 151 scorable amplification products, of which 117 or 77 percent were polymorphic. Pairwise Nei and Lis similarity had ranged from 0.25 to 0.88 among all individuals analyzed. Based on Nei and Lis similarity coefficients Bemisia populations were grouped into 3 main clusters and clearly distinguished the non B biotype from the B biotype. Conclusion: The level of similarity among populations of same biotypes was high whereas between populations of non B and B biotypes appeared to be less closely related. This analysis showed that non B biotype is prevalent in both provinces however B biotype is restricted to few locations in Sindh. This monitoring of the spread of B. tabaci in Pakistan will assist in the establishment of appropriate management strategies.
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Animals , DNA , Genetic Markers , Genetic Variation , Hemiptera/genetics , Random Amplified Polymorphic DNA Technique , PakistanABSTRACT
Background: Cassava (Manihot esculenta Crantz) is a crop that is high in carbohydrates in the roots and in protein in the leaves, important for both human consumption and animal feed, and also has a significant industrial use for its starches. In this study we evaluated the genetic variability with molecular markers in different stages in micropropagated plants from somatic embryos of Venezuelan native clone 56. Results: Three markers were used: ISTR, AFLP and SSR, finding that ISTR showed the highest polymorphism among individuals tested. With AFLP a high similarity between the evaluated individuals was observed and with SSR total monomorphism was seen. Using cluster analysis it was found that individuals from an embryo labeled as fasciated at the beginning of the somatic embryogenesis process were grouped as independent of the other plants when analyzed at the acclimatization stage. The differences found with the different markers used are discussed. In field trials, micropropagated plants had a yield between 4 and 5 times the average yield of cassava in Venezuela. Conclusion: Despite variability in terms of DNA markers, somatic embryogenesis is suitable for mass propagation of highly performing cassava clones.
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Manihot/embryology , Manihot/genetics , DNA, Plant/genetics , Amplified Fragment Length Polymorphism Analysis , Biomarkers , Embryonic Development , Microsatellite RepeatsABSTRACT
With the purpose of isolating and characterizing free nitrogen fixing bacteria (FNFB) of the genus Azotobacter, soil samples were collected randomly from different vegetable organic cultures with neutral pH in different zones of Boyacá-Colombia. Isolations were done in selective free nitrogen Ashby-Sucrose agar obtaining a recovery of 40 percent. Twenty four isolates were evaluated for colony and cellular morphology, pigment production and metabolic activities. Molecular characterization was carried out using amplified ribosomal DNA restriction analysis (ARDRA). After digestion of 16S rDNA Y1-Y3 PCR products (1487pb) with AluI, HpaII and RsaI endonucleases, a polymorphism of 16 percent was obtained. Cluster analysis showed three main groups based on DNA fingerprints. Comparison between ribotypes generated by isolates and in silico restriction of 16S rDNA partial sequences with same restriction enzymes was done with Gen Workbench v.2.2.4 software. Nevertheless, Y1-Y2 PCR products were analysed using BLASTn. Isolate C5T from tomato (Lycopersicon esculentum) grown soils presented the same in silico restriction patterns with A. chroococcum (AY353708) and 99 percent of similarity with the same sequence. Isolate C5CO from cauliflower (Brassica oleracea var. botrytis) grown soils showed black pigmentation in Ashby-Benzoate agar and high similarity (91 percent) with A. nigricans (AB175651) sequence. In this work we demonstrated the utility of molecular techniques and bioinformatics tools as a support to conventional techniques in characterization of the genus Azotobacter from vegetable-grown soils.