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Developing a common bean core collection suitable for association mapping studies Genet. Mol. Biol.
Perseguini,Juliana Morini Küpper Cardoso; Silva,Gliciane Micaele Borges; Rosa,João Ricardo Bachega Feijó; Gazaffi,Rodrigo; Marçal,Jéssica Fernanda; Carbonell,Sérgio Augusto Morais; Chiorato,Alisson Fernando; Zucchi,Maria Imaculada; Garcia,Antonio Augusto Franco; Benchimol-Reis,Luciana Lasry.
Because of the continuous introduction of germplasm from abroad, some collections have a high number of accessions, making it difficult to explore the genetic variability present in a germplasm bank for conservation and breeding purposes. Therefore, the aim of this study was to quantify and analyze the structure of genetic variability among 500 common bean accessions to construct a core collection. A total of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in the 180 common bean accessions selected to compose the core collection ranged from 0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500 accessions were clustered into 15 distinct groups and the 180 accessions into four distinct groups in the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Molecular markers; Genetic diversity; Genetic structure; Microsatellites; Phaseolus vulgaris L.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572015000100067
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Development and characterization of fifteen polymorphic microsatellite loci in Bryconamericus aff. iheringii (Teleostei: Characidae) and cross-amplification in related Characidae species Neotropical Ichthyology
Apolinário-Silva,Caroline; Ferreira,Dhiego G.; Cavenagh,Analiza F.; Aprígio,Nícollas G. O.; Galindo,Bruno A.; Carlsson,Jens; Sofia,Silvia H..
ABSTRACT Data on 15 novel microsatellite loci from the Neotropical fish Bryconamericus aff. iheringii are presented here. Analyses of 32 individuals from four different streams revealed 192 different alleles, ranging from four to 32 alleles per locus (mean of 12.8 per locus). Observed and expected heterozygosities ranged from 0.094 to 0.813 and 0.205 to 0.952, respectively. These loci showed high polymorphic information content and will be a resource for genetic studies of B. aff. iheringii. Furthermore, several loci also amplified other small Neotropical Characidae (Piabarchus stramineus and Piabina argentea) and should be useful for these species.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genetic diversity; Lambarizinho; Molecular markers; Neotropical fish; SSR.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252018000100218
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Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck) Genet. Mol. Biol.
Novelli,Valdenice M.; Cristofani,Mariangela; Souza,Alessandra A.; Machado,Marcos A..
The aims of this study were to develop simple sequence repeat markers (SSRs or microsatellite markers) in citrus and to evaluate the efficiency of these markers for characterization of sweet orange. We developed SSRs from a genomic library of 'Pêra IAC' sweet orange enriched for AG/TC, GT/CA, TCA/AGT and AAC/TTG sequence repeats. We selected 279 sequences from which 171 primer pairs were designed of which 113 with the best banding patterns were selected. Characterization of sweet orange microsatellite loci revealed that AG/TC was the most abundant (69%) microsatellite class isolated, followed by GT/CA (15.9%), TCA/AGT (8%) and AAC/TTG (6.2%). The number of alleles ranged from 1 to 4, with a mean of 2 alleles per locus. Four microsatellite loci developed in...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Citrus species; Germplasm bank; Polymorphism; Molecular markers.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572006000100018
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Differential expression of the KLK2 and KLK3 genes in peripheral blood and tissues of patients with prostate cancer Genet. Mol. Biol.
Meola,Juliana; Goulart,Luiz R.; Oliveira,Jaqueline D.D.; Neves,Adriana F.; Oliveira Jr.,Waldesse P.; Saraiva,Ana C.M.; Capaneli,Andréia C.; Cardoso,Alexandra M.; Prado,Lindolfo D.; Borba,Sebastião A.; Silva,Heyder D..
We used the multiplex semi-quantitative reverse-transcriptase PCR (RT-PCR) to investigate kallikrein 2 and 3 (KLK2 and KLK3) mRNA levels in prostate tissue from 42 prostate cancer patients, 33 of whom were also assessed for peripheral blood KLK2 expression by qualitative semi-nested RT-PCR. We found that KLK2 was an important tissue biomarker for distinguishing between prostate cancer patients and those with benign prostatic hyperplasia, particularly when KLK2 expression was > 60% of that of the beta2-microglobulin constitutive gene. Patients with an average relative expression value > 0.6 (cutoff value) had an eleven-fold higher chance of having prostate cancer. When one or two tissues samples were evaluated for KLK2 expression using the cutoff...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Kallikrein II; Molecular markers; Prostate cancer; PSA; Semi-quantitative RT-PCR.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572006000200001
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Diversité et différentiation génétique chez l'huître plate européenne : de la population à l'individu (Actes) ArchiMer
Boudry, Pierre; Launey, Sophie; Diaz-almela, A.; Naciri-graven, Yamama; Ledu, Christophe; Mira, S.; Taris, Nicolas; Bonhomme, Francois; Lapegue, Sylvie.
PCR-based DNA markers enable the study of diversity and differentiation of marine organisms at different stages of their life cycle. Our study of European fiat oyster (Ostrea edulis) populations aimed to describe their spatial and temporal dynamics. First, we analyzed adults sampled over the natural range of the species. An Atlantic/Mediterranean differentiation pattern was observed. Similar patterns of variation were found using allozymes, microsatellites and mitochondrial DNA, aIl which support an isolation by distance model. High variability was observed in the range of diversity between populations using a mitochondrial marker, a reflection of small effective population sizes in sorne locations. A 10fold quantitative difference was observed in Fst,...
Tipo: Text Palavras-chave: Recruitment; Diversity; Molecular markers; Population genetics; Ostrea edulis; Flat oyster; Dynamique de recrutement; Diversité génétique; Microsatellites; Marqueurs moléculaires; Génétique des populations; Ostrea edulis; Huître plate.
Ano: 2003 URL: http://archimer.ifremer.fr/doc/2003/acte-2851.pdf
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Diversity and genetic structure of jenipapo (Genipa americana L.) Brazilian accessions Scientia Agricola
Silva,Ana Veruska Cruz da; Freire,Karla Cristina Santos; Lédo,Ana da Silva; Rabbani,Allívia Rouse Carregosa.
Usually known as jenipapo, Genipa americana L. is a Rubiaceae Brazilian native species. It is an important species in the restoration of Brazilian riparian forests and is one of the most promising fruit trees for sustainable harvesting programs. In this study we provide the first data on the genetic diversity and structure of a Jenipapo Germplasm Bank using inter simple sequence repeat (ISSR) markers. We evaluated 160 accessions from wild populations, and the data generated from 12 ISSR primers were used to determine genetic variability via a model-based Bayesian procedure (Structure) and molecular variance analysis. In addition, Shannon index, genetic diversity and Jaccard coefficients were estimated. A total of 12 primers were used, which generated 123...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Tropical fruits; Molecular markers; Germplasm; Conservation.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162014000500007
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Early molecular markers predictive of dengue hemorrhagic fever Anais da ABC (AABC)
Calzavara-Silva,Carlos E.; Gomes,Ana L.V.; Maia,Rita C.C.; Acioli-Santos,Bartolomeu; Gil,Laura H.V.G.; Marques Jr.,Ernesto T.A..
The management of acute dengue patients during outbreaks is a challenging problem. Most of the dengue fever cases are benign, but some cases develop into a severe and possibly lethal vasculopathy, known as dengue hemorrhagic fever. Early symptoms of dengue and hemorrhagic fever are very similar. An early differential diagnosis is needed to predict which of these two clinical presentations is crucial to proper patient care and public health management. This study evaluates the predictive potential of specific mRNA expression markers of dengue hemorrhagic fever using quantitative real-time PCR assays. Six candidate "dengue hemorrhagic fever specific signature genes" were evaluated and all showed good correlation among their transcription levels at early days...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Real-time PCR; Dengue hemorrhagic fever; Molecular markers.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652009000400006
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Efficiency of RAPD, ISSR, AFLP and ISTR markers for the detection of polymorphisms and genetic relationships in camote de cerro (Dioscorea spp.) Electron. J. Biotechnol.
Velasco-Ramírez,Ana Paulina; Torres-Morán,Martha Isabel; Molina-Moret,Sandy; Sánchez-González,José de Jesús; Santacruz-Ruvalcaba,Fernando.
Background At present, species known as camote de cerro (Dioscorea spp.) are found only in the wilderness in Mexico, but their populations are extremely depleted because they are indiscriminately collected, it is urgent to evaluate the conservation status of these plants in order to design conservation genetics programs. In this study, genetic diversity parameters along with cluster analysis based on Jaccard's coefficient were estimated with the objective to assess the efficiency of Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR), Amplified Fragment Length Polymorphism (AFLP) and Inverse Sequence Tagged Repeat (ISTR) molecular DNA markers in the Dioscorea genus. Results The polymorphic information contents were quite similar...
Tipo: Journal article Palavras-chave: Dioscoreaceae; Genetic diversity; Molecular markers; Tuber.
Ano: 2014 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000200002
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Estrutura genética populacional de Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) utilizando marcadores microssatélites Neotropical Entomology
Valle,GE do; Zucchi,MI; Stabellini,NS; Lourenção,AL; Pinheiro,JB.
We aimed to characterize the population genetic structure within and among five Bemisia tabaci (Gennadius) populations collected from different host plants and geographic regions by using microssatelites as a molecular marker. Each population was represented by 19 specimens. The host plants and geographic origins of these populations were described as follows: Pop 1: Squash Barreiras (BA); Pop 2: Cotton Barreiras (BA); Pop 3: Soybean Campinas (SP); Pop 4: Tomato Cruz das Almas (BA); and Pop 5: Soybean Rondonópolis (MT). Six polymorphic loci were observed, which discriminated 31 different alleles in the studied populations, with a mean number of alleles per population of 3.30 (2.67 - 4.00). Using Fisher's Exact test, it was observed that at least three...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genetic variability; Molecular markers; Whitefly.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1519-566X2011000200008
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Exon-primed intron-crossing (EPIC) markers as a tool for ant phylogeography Rev. Bras. entomol.
Ströher,Patrícia R.; Li,Chenhong; Pie,Marcio R..
Exon-primed intron-crossing (EPIC) markers as a tool for ant phylogeography. Due to their local abundance, diversity of adaptations and worldwide distribution, ants are a classic example of adaptive radiation. Despite this evolutionary and ecological importance, phylogeographical studies on ants have relied largely on mitochondrial markers. In this study we design and test exon-primed intron-crossing (EPIC) markers, which can be widely used to uncover ant intraspecific variation. Candidate markers were obtained through screening the available ant genomes for unlinked conserved exonic regions interspersed with introns. A subset of 15 markers was tested in vitro and showed successful amplification in several phylogenetically distant ant species. These...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Formicidae; Molecular markers; Phylogeny; Population genetics.
Ano: 2013 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0085-56262013000400014
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Extent and structure of genetic diversity in a collection of the tropical multipurpose shrub legume Cratylia argentea (Desv.) O. Kuntze as revealed by RAPD markers Electron. J. Biotechnol.
Andersson,Meike S; Schultze-Kraft,Rainer; Peters,Michael; Duque,Myriam C; Gallego,Gerardo.
The tropical multipurpose shrub legume Cratylia argentea is well adapted to acid soils of low to medium fertility and has excellent drought-tolerance. Due to its high nutritive value it is particularly suited as forage for dry-season supplementation. A collection of 47 C. argentea accessions in a collection, derived from seed replicating of original accessions with differing geographic origin and morphological and agronomic characteristics was investigated using molecular markers (RAPD (random amplified polymorphic DNA)). Genetic diversity (H T = 0.145) in the collection was low, with 30% of differentiation among groups and high genetic similarity among accessions (GS = 0.805). Within-accession variability was high. One taxonomic mismatch and five possible...
Tipo: Journal article Palavras-chave: Agroforestry; Molecular markers; MPT (multipurpose shrubs and trees); Tropics.
Ano: 2007 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582007000300006
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Extração de DNA genômico de Brachiaria e Panicum maximum. Infoteca-e
BONATO, A. L. V.; VALLE, C. B. do; JANK, L.; RESENDE, R. M. S.; LEGUIZAMON, G. O. de C..
bitstream/CNPGC/10572/1/COT79.pdf
Tipo: Comunicado Técnico (INFOTECA-E) Palavras-chave: Molecular markers; Processing.; Brachiaria; DNA; Marcador Molecular; Melhoramento Genético Vegetal; Panicum Maximum; Processamento.; Plant breeding..
Ano: 2002 URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/319897
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Extração de DNA genômico de Stylosanthes spp. Infoteca-e
BONATO, A. L. V.; VERZIGNASSI, J. R.; RESENDE, R. M. S.; FERNANDES, C. D.; LEGUIZAMON, G. O. de C..
Protocolo. Considerações sobre os procedimentos.
Tipo: Comunicado Técnico (INFOTECA-E) Palavras-chave: Molecular markers; Processing.; DNA; Marcador Molecular; Melhoramento Genético Vegetal; Processamento.; Stylosanthes; Plant breeding..
Ano: 2002 URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/318167
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Generalized composite interval mapping offers improved efficiency in the analysis of loci influencing non-normal continuous traits Ciencia e Investigación Agraria
Mora,Freddy; Scapim,Carlos Alberto; Baharum,Adam; Teixeira do Amaral Júnior,Antonio.
In genetic studies, most Quantitative Trait Loci (QTL) mapping methods presuppose that the continuous trait of interest follows a normal (Gaussian) distribution. However, many economically important traits of agricultural crops have a non-normal distribution. Composite interval mapping (CIM) has been successfully applied to the detection of QTL in animal and plant breeding. In this study we report a generalized CIM (GCIM) method that permits QTL analysis of non-normally distributed variables. GCIM was based on the classic Generalized Linear Model method. We applied the GCIM method to a F2 population with co-dominant molecular markers and the existence of a QTL controlling a trait with Gamma distribution. Computer simulations indicated that the GCIM method...
Tipo: Journal article Palavras-chave: Bioinformatics; Generalized Linear Model; Molecular markers; Quantitative Trait Loci (QTL).
Ano: 2010 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-16202010000300007
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Genetic and phenotypic characterization of isolates of Pyricularia grisea from the rice cultivars epagri 108 and 109 in the State of Tocantins Trop. Plant Pathol.
PRABHU,ANNE S.; FILIPPI,MARTA C.; ARAUJO,LEILA G.; FARIA,JOSIAS C..
An epidemic of rice (Oryza sativa) blast occurred on cultivars Epagri 108 and 109 in the municipalities of Lagoa da Confusão and Duerê in the State of Tocantins, during the rice-growing season 1998-99. DNA fingerprinting and virulence phenotype analysis were utilized to determine the diversity of Pyricularia grisea isolates collected from these cultivars in one epidemic year. Rep-PCR analysis of isolates was done by using two primer sequences from Pot2. Two distinct fingerprint groups or lineages were identified among 53 isolates collected from nine different commercial fields. The virulence pattern of isolates retrieved from these two cultivars was analyzed in artificial inoculation tests utilizing 32 genotypes in the greenhouse. A dendrogram constructed...
Tipo: Info:eu-repo/semantics/other Palavras-chave: Magnaporthe grisea; Molecular markers; Oryza sativa; Rep-PCR analysis; Rice blast.
Ano: 2002 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-41582002000600002
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Genetic distance estimated by RAPD markers and its relationship with hybrid performance in maize PAB
Bruel,Daniela Cristina; Carpentieri-Pípolo,Valéria; Gerage,Antonio Carlos; Fonseca Júnior,Nelson da Silva; Prete,Cássio Egídio Cavenaghi; Ruas,Claudete de Fátima; Ruas,Paulo Maurício; Souza,Silvia Graciele Hülse de; Garbuglio,Deoclécio Domingos.
The objective of this work was to evaluate the genetic diversity of 16 maize inbred lines, and to determine the correlation between genetic distance and hybrid performance, using random amplified polymorphic DNA (RAPD) molecular markers. Twenty-two different random primers were used, which resulted in the amplification of 265 fragments, 237 (84.44%) of them being polymorphic. A genetic similarity matrix was created from the RAPD data, using Jaccard coefficient, and a dendrogram was constructed. Hybrid analyses were carried out using random block design and Griffing method VI for diallel crossings. The genetic associations showed five distinct heterotic groups. Correlations between genetic divergences detected by RAPD, as well as the means observed in the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Zea mays; Diallel; Heterotic patterns; Molecular markers.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2006001000006
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Genetic divergence between populations of the stingless bee uruçu amarela (Melipona rufiventris group, Hymenoptera, Meliponini): is there a new Melipona species in the Brazilian state of Minas Gerais? Genet. Mol. Biol.
Tavares,Mara Garcia; Dias,Luiz Antonio dos Santos; Borges,Andréia Arantes; Lopes,Denilce Meneses; Busse,Angélica Helene Pereira; Costa,Ronaldo Guimarães; Salomão,Tânia Maria Fernandes; Campos,Lucio Antonio de Oliveira.
Allozyme, microsatellite and random amplified polymorphic DNA (RAPD) molecular markers were used to investigate the within and between population genetic variability and between population genetic differentiation of the Brazilian stingless bee uruçu amarela (nominally Melipona rufiventris Lepeletier, 1836) present in savanna and Atlantic forest habitats of the Brazilian state of Minas Gerais (MG). We found low levels of within population variability, although there were a large number of private alleles that specifically characterized these populations. The F ST values indicated a high level of genetic diversity between populations. Analysis of molecular variance (AMOVA) showed a high degree of population differentiation between the savanna and Atlantic...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Endangered species; Genetic divergence; Molecular markers; Stingless bees; Uruçu amarela.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000400027
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Genetic divergence in Tetragonisca angustula Latreille, 1811 (Hymenoptera, Meliponinae, Trigonini) based on rapd markers Genet. Mol. Biol.
Oliveira,Rosana de Cássia; Nunes,Francis de Morais Franco; Campos,Ana Paula Soraggi; Vasconcelos,Soraya Matos de; Roubik,David; Goulart,Luiz Ricardo; Kerr,Warwick Estevam.
One of the commonest neotropical stingless bees is Tetragonisca angustula (Latreille, 1811), popularly known in Portuguese as jataí, which occurs in variable nesting sites from Mexico to Argentina. We used 18 primers to generate 218 RAPD markers which we used to determined the genetic distance between T. angustula populations from 25 localities in three different Latin America countries, using Tetragonisca weyrauchi from the Brazilian state of Acre and the common honey bee (Apis mellifera) as outgroups. Genetic distance, calculated as the Percentage of Dissimilarity (14%), based on all markers divided the T. angustula population into eastern (group 1) and western (group 2) groups. However, we were able to separate the two groups by using only two primers...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Tetragonisca angustula; Genetic divergence; Molecular markers; UPGMA.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000200009
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Genetic diversity among Brazilian okra landraces detected by morphoagronomic and molecular descriptors Agronomy
Massucato, Luana Rainieri; Nakamura, Karina Kazue; Ruas, Paulo Mauricio; Zefa, Douglas Mariani; Silva, Derly José Henrique da; Gonçalves, Leandro Simões Azeredo.
The conservation of okra landraces [Abelmoschus esculentus (L.) Moench] in gene banks is essential for the success of their use in breeding programmes. This study evaluated the genetic diversity among okra landraces in Brazil based on morphoagronomic descriptors and AFLP markers. We studied 30 accessions of the vegetable gene bank of the Universidade Federal de Viçosa. To this end, 17 morphoagronomic descriptors and five combinations of AFLP primers were used. Genetic parameters were estimated for the quantitative traits and the accessions were grouped by Ward’s method, using the Gower’s and Jaccard’s distance measures, respectively, for the morphoagronomic and molecular data. Polymorphisms were observed for all qualitative traits, while the quantitative...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genetic variability; Molecular markers; Phenotype; Bayesian analysis.; Recursos Genéticos.
Ano: 2019 URL: http://periodicos.uem.br/ojs/index.php/ActaSciAgron/article/view/43426
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Genetic diversity among natural populations of Mandevilla velutina Horticultura Brasileira
Bertoni,Bianca Waléria; Souza,Ana Valéria de; Biondo,Ronaldo; França,Suzelei de C; Telles,Mariana PC; Pereira,Ana Maria S.
Mandevilla velutina (Mart. Ex Stadelm) Woodson (Apocynaceae) is an endemic species in the Cerrado (Brazilian Savannah), whose alcoholic extracts and root infusions are extensively used in the popular medicine to treat inflammatory diseases and against snake bites. Currently, this species has been pointed out as crucial in conservation programs. Therefore, studies on its genetic diversity, as well as the development of methodology for in vitro conservation in germplasm banks are imperative to avoid its extinction. The objective of this work was to investigate the intra- and inter-populational genetic variability of M. velutina to enhance the representativeness of germplasm banks. To this aim, we used RAPD molecular markers. The analysis of molecular...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Mandevilla velutina; Medicinal plant; Extinction risk; Molecular markers.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-05362010000200012
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