Applications of random amplified polymorphic DNA (RAPD) in molecular ecology

Hadrys, Heike; Balick, Michael J.; Schierwater, Bernd

doi:10.1111/j.1365-294x.1992.tb00155.x

Cited by 840 publications

(479 citation statements)

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“…because the genotype is not influenced by environmental factors, evolution of closely related taxa can be investigated from an objective point of view with molecular techniques (Hillis, 1987). In addition, some molecular marker assays, e.g., the use of random amplified polymorphic DNA (RAPD), allow the detection of DNA polymorphisms by randomly amplifying multiple regions of the genome by polymerase chain reaction (PCR) using single arbitrary primers designed independently of target DNA sequence (Welsh & McClelland, 1990;Hadry et al, 1992;Williams et al, 1993;Karp et al, 1996). Therefore, it has been extensively used as a genetic marker for estimating genetic, taxonomic, and phylogenetic relationships of plants and animals (Williams et al, 1990;Wachira et al, 1995;Kapteyn & Simon, 2002;belaj et al, 2003;Deshwall et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Taxonomic considerations among and within some Egyptian taxa of <i>Capparis</i> and related genera (Capparaceae) as revealed by RAPD fingerprinting

Moubasher¹,

El-Ghani²,

Kamel³

et al. 2011

Collect. Bot

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Taxonomic considerations among and within some Egyptian taxa of Capparis and related genera (Capparaceae) as revealed by RAPD fingerprinting.-This investigation was carried out to assess the taxonomic relationships among eight taxa of the Egyptian members of Capparaceae based on random amplified polymorphic DNA markers, and to compare the results with those obtained from morphological studies. A total of 46 bands were scored for three RAPD primers corresponding to an average of 15.3 bands per primer. The three primers (A03, A07 and A09) revealed eight polymorphic RAPD markers among the studied taxa ranging in size from 200 bp to 1000 bp. Jaccard's coefficient of similarity varied from 0.28 to 0.84, indicative of high level of genetic variation among the genotypes studied. uPGMA cluster analysis indicated three distinct clusters, one comprised Cleome amblyocarpa and Gynandropsis gynandra, while another included two clusters at 0.74 phenon line; one for Capparis decidua, and the other for Capparis sinaica and all varieties of Capparis spinosa. The four varieties of Capparis spinosa were segregated at 0.84 phenon line. However, one of these varieties was more closely related to Capparis sinaica than to the other three varieties of C. spinosa. The RAPD analysis reported here confirms previous studies based on morphological markers.Key words: Capparis; Cleome; cluster analysis; Egypt; genetic relationships; Gynandropsis; RAPD-PCR; taxonomy; uPGMA. ResumenConsideraciones taxonómicas sobre algunos taxones egipcios de Capparis y géneros relacionados (Capparaceae) a partir de RAPDs.-El objetivo de este trabajo es investigar las relaciones taxonómicas entre ocho taxones pertenecientes a las Capparaceae en base a marcadores de tipo RAPD, y comparar los resultados con los obtenidos previamente en estudios morfológicos. Se han contabilizado un total de 46 bandas para tres pares de cebadores, con una media de 15,3 bandas por cebador. los tres pares de cebadores (A03, A07 y A09) revelan ocho marcadores polimórficos entre los taxones estudiados, de entre 200 y 1000 pares de bases. El coeficiente de similaridad de Jaccard varía entre 0,28 y 0,84, indicativo de un alto nivel de variación genética entre los genotipos estudiados. El análisis uPGMA muestra tres grupos distintos, el primero comprende Cleome amblyocarpa y Gynandropsis gynandra, mientras que el segundo incluye dos grupos a la altura del valor 0,74 del dendrograma: uno se corresponde con Capparis decidua, y el otro comprende Capparis sinaica y todas las variedades de Capparis spinosa. las cuatro variedades de C. spinosa se segregan a la altura del valor 0,84 del dendrograma. Sin embargo, una de estas variedades está más relacionada con C. sinaica que con las otras variedades de C. spinosa. El análisis de RAPD confirma los resultados de estudios anteriores basados en caracteres morfológicos.

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Section: Introductionmentioning

confidence: 99%

Taxonomic considerations among and within some Egyptian taxa of <i>Capparis</i> and related genera (Capparaceae) as revealed by RAPD fingerprinting

Moubasher¹,

El-Ghani²,

Kamel³

et al. 2011

Collect. Bot

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“…Distance methods are most commonly used, although principal coordinate analysis (a multivariate analysis of overall similarity) is also common. The nature of the data set seems suitable for parsimony (Hadrys et a!., 1992), but this is not often used. Stiles et al (1993) found different distance measures gave a similar result, consistent with tradi-…”

Section: Discussionmentioning

confidence: 99%

Variability of the bushcricket Ephippiger ephippiger: RAPDs and song races

et al. 1997

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The tettigoniid bushcricket, Ephippiger, shows extensive variability in morphology and behaviour in Western Europe. Several species and subspecies have been described, but many may only represent local forms of uncertain origin. Within Ephippiger ephippiger, patterns of variation differ between morphology (upon which most taxonomic forms are defined) and behaviour. There is sufficient variation in a sexual signal (calling song) within the species that 'song races' have been described, which show strong premating isolation from each other. Here RAPD markers (138 fragments from 10 primers) have been used to examine the extent and pattern of genetic differentiation within the species and between two congeneric species.Ephippiger ephippiger is clearly distinguished from its relatives. High genetic similarity has been found within E. ephippiger, Nei and Li's S averaging 0.67. Using both distance and parsimony methods resolves the relationships of the song races and morphological forms of E. ephippiger with the exception of one population. The song races represent the deepest division within the species, but the lack of concordance in different traits suggests that a complex pattern of subspecific variation is found within this species.

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“…Molecular identification based on DNA cloning and sequencing has been considered to be a more efficient, faster way compared to the conventional identification methods, such as SSR (simple sequence repeat: Zietkiewicz et al, 1994) method for mono-locus analysis of microsatellites, RAPD (random amplified polymorphic DNA: Hadrys et al, 1992), ISSR (inter simple sequence repeat: Nagaoka et al, 1997) and AFLP (amplified fragment length polymorphism: Vekemans et al, 2002), through which larger portion of the genome can be studied. Among various molecular identification means, the sequence analysis of internal transcribed spacer (ITS: Sang et al, 1995), a region of ribosomal RNA is considered to be an effective method.…”

Section: Introductionmentioning

confidence: 99%

Genetic Variation of Rice Populations Estimated Using nrDNA ITS Region Sequence

Wang¹,

Hong

2014

Korean Journal of Plant Resources

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-The rice belonging to Oryza sativa is not only has significant economic importance, for it is the major source of nutrition for about 3 billion all around the world. But also plays a vital role as a model organism, because it has a number of advantages to be a model plant, such as efficient transformation system and small genome size. Many methods and techniques have been conducted to attempt to distinguish different Oryza sativa species, such as amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and so on. However, studies using sequence analysis of internal transcribed spacer (ITS), a region of ribosomal RNA has not been reported until now. This study was undertaken with an aim to understand the phylogenetic relationships among sixteen isolates of Oryza sativa collected from abroad and fifteen isolates collected from Korea, using ribosomal RNA (rRNA) internal transcribed spacer (ITS) sequences to compare the phylogeny relationships among different Oryza sativa species. The size variation obtained among sequenced nuclear ribosomal DNA (nrDNA) ITS region ranged from 515bp to 1000bp. The highest interspecific genetic distance (GD) was found between Sfejare 45 (FR12) and Anapuruna (FR15). Taebong isolate showed the least dissimilarity of the ITS region sequence with other thirty isolates. This consequence will help us further understanding molecular diversification in intra-species population and their phylogenetic analysis.

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Applications of random amplified polymorphic DNA (RAPD) in molecular ecology

Cited by 840 publications

References 33 publications

Taxonomic considerations among and within some Egyptian taxa of <i>Capparis</i> and related genera (Capparaceae) as revealed by RAPD fingerprinting

Taxonomic considerations among and within some Egyptian taxa of <i>Capparis</i> and related genera (Capparaceae) as revealed by RAPD fingerprinting

Variability of the bushcricket Ephippiger ephippiger: RAPDs and song races

Genetic Variation of Rice Populations Estimated Using nrDNA ITS Region Sequence

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