Genetic differentiation of charcoal rot pathogen,<i>Macrophomina phaseolina</i>, into specific groups using URP-PCR

Jana, Tarakanta; Singh, Nutan; Koundal, K. R.; Sharma, Tilak Raj

doi:10.1139/w04-122

Cited by 55 publications

(45 citation statements)

References 15 publications

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“…A number of molecular studies elsewhere have shown a high level of polymorphism in this fungus when isolates from different host or geographical origins were compared using different molecular tools (Almeida et al, 2003;Jones et al, 1998;Mayek-Perez et al, 2001;Su et al, 2001;Vandemark et al, 2000). Other recent studies have demonstrated the genetic diversity among M. phaseolina isolates (Aboshosha et al, 2007;Aghakhani and Dubey, 2009;Babu et al, 2010;Baird et al, 2010;Beas-Fernandez et al, 2006;Das et al, 2006;Jana et al, 2005a;Jana et al, 2005b;Omar et al, 2007;Purkayastha et al, 2008;Rajkumar and Kuruvinashetti, 2007;Reyes-Franco et al, 2006;Saleh et al, 2010). The high genetic diversity of this pleomorphic fungal species is reflected not only in isolates from distinct hosts and geographical origins but also within isolates collected from a single host or geographical origin.…”

Section: Resultsmentioning

confidence: 99%

“…Different molecular methods have been used for differentiating M. phaseolina populations including Restriction Fragment Length Polymorphism (RFLP) of rDNA-ITS regions (Aghakhani and Dubey, 2009;Almeida et al, 2003;Purkayastha et al, 2006;Su et al, 2001), Random Amplified Polymorphic DNA (RAPD) (Aboshosha et al, 2007;Aghakhani and Dubey, 2009;Almeida et al, 2003;Almeida et al, 2008;Babu et al, 2010;Das et al, 2006;Jana et al, 2003;Omar et al, 2007;Purkayastha et al, Rajkumar and Kuruvinashetti, 2007;Su et al, 2001;Zade et al, 2009), Amplified Fragment Length Polymorphism (AFLP) (Brooker et al, 2008;Mayek-Perez et al, 2001;Reyes-Franco et al, 2006;Saleh et al, 2010;Vandemark et al, 2000), Universal Rice Primer PCR (URP-PCR) (Jana et al, 2005b), Inter simple sequence repeats (ISSR) (Jana et al, 2005a;Purkayastha et al, 2008), Repetitive SequenceBased Polymerase Chain Reaction (Rep-PCR) (Purkayastha et al, 2008) and SSR (Baird et al, 2010). Inter simple sequence repeat (ISSR) markers are powerful tools which can be utilized to access the variation in the flanking regions of microsatellite loci that are dispersed throughout all genomes (Zietkiewicz et al, 1994).…”

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confidence: 99%

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Diversity of Macrophomina phaseolina Based on Morphological and Genotypic Characteristics in Iran

Mahdizadeh¹,

Safaie²,

Goltapeh³

2011

The Plant Pathology Journal

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Fifty two Macrophomina phaseolina isolates were recovered from 24 host plant species through the 14 Iranian provinces. All isolates were confirmed to species using species-specific primers. The colony characteristics of each isolate were recorded, including chlorate phenotype, relative growth rate at 30°C and 37°C, average size of microsclerotia, and time to microsclerotia formation. The feathery colony phenotype was the most common (63.7%) on the chlorate selective medium and represented the chlorate sensitive phenotype of the Iranian Macrophomina phaseolina population. Meantime, inter simple sequence repeats (ISSR) Markers were used to assess the genetic diversity of the fungus. Unweighted pair-group method using arithmetic means (UPGMA) clustering of data showed that isolates did not clearly differentiate to the specific group according to the host or geographical origins, however, usually the isolates from the same host or the same geographic origin tend to group nearly. Our results did not show a correlation between the genetic diversity based on the ISSR and phenotypic characteristics. Similar to the M. phaseolina populations in the other countries, the Iranian isolates were highly diverse based on the phenotypic and the genotypic characteristics investigated and needs more studies using neutral molecular tools to get a deeper insight into this complex species.

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Diversity of Macrophomina phaseolina Based on Morphological and Genotypic Characteristics in Iran

Mahdizadeh¹,

Safaie²,

Goltapeh³

2011

The Plant Pathology Journal

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“…Based on the degree of polymorphism indicated by the percent of polymorphic loci generated and Shannon's index, URP2R was more suitable for studying genetic diversity in populations of both subgroups. In general, both URP and ISSR marker systems have been useful for evaluating variation in fungal populations (Aggarwal et al 2010;Jana et al 2005;Kiyosi et al 2005;Sharma et al 2005;Stodart et al 2007). The UPGMA dendrogram showed two main clusters separating subgroups.…”

Section: Discussionmentioning

confidence: 99%

“…Most of the studies on population genetics of R. solani or other plant pathogens using dominant markers such as RAPD, URP, AFLP or ISSR have reported that geographic location or host specificity or both had an effect on population structure (Aggarwal et al 2010;Duncan et al 1993;Jana et al 2005;Stodart et al 2007). Because of the limitations of dominant markers, these studies are difficult to compare with other studies where co-dominant markers (microsatellites) were used.…”

Section: Discussionmentioning

confidence: 99%

Assessing genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers

Godoy‐Lutz

Steadman

et al. 2012

J Gen Plant Pathol

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genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers" (2012). Papers in Plant Pathology. 273. http://digitalcommons.unl.edu/plantpathpapers/273 Abstract Web blight, an important foliar disease of dry beans in the Americas, is a challenge to manage. We studied genetic variation of 92 isolates of Rhizoctonia solani subgroups AG-1-IE and AG-1-IF using DNA fingerprinting methods and mycelial compatibility grouping. The isolates were collected over 13 years from bean fields in the Dominican Republic, Honduras and Puerto Rico. Cluster and AMOVA analysis of combined data from two universal rice primers and two internal sequence repeats revealed significant genetic variation among and within populations of both subgroups. Variation was influenced by geographic origin and sampling year for AG-1-IE isolates and geographic origin for AG-1-IF isolates. Mycelial compatibility of paired isolates was mostly scored as incompatible in both subgroups and supported many unique phenotypes. Only two isolates of AG-1-IE displayed mycelial compatibility and DNA fingerprints, suggesting clonal origin. Genetic variation in these AG-1-IE and AG-1-IF isolate populations may explain the lack of durable resistance to web blight reported in dry beans.

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“…URP-PCR protocol employed stringent PCR with high annealing temperature throughout the thermo-cycling reaction, affording high reproducibility. URP-PCR technique is a useful tool for the characterization and grouping of most eukaryotic or prokaryotic genomes, especially at inter-and intraspecies levels (Kang et al, 2000;Jana et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Genetic relationships of Pacific abalone (Haliotidae) species determined using universal rice primer-polymerase chain reaction fingerprinting

Park²,

Myeong³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. Random amplified polymorphic DNA (RAPD) with universal rice primers (URP) was used to identify species and to determine phylogenetic relationships for the 6 economically important Korean Pacific abalone species: Haliotis discus hannai, H. discus discus, H. madaka, H. gigantea, H. diversicolor supertexta, and H. diversicolor diversicolor, whose morphological differentiation is difficult. Of the 12 URPs used in this study, 7 were effective in producing reproducible RAPD markers for these 6 species. Amplifications with the 7 URP primers yielded 129 reproducible amplified fragments ranging between 100 and 6000 bp in length. The dendrogram generated by the unweighted pairgroup method using arithmetic averages showed that the 6 species were divided into 4 groups at 0.44 similarity level, indicating that they were genetically distant from each other and had little internal phylogenetic resolution. One group included H. discus hannai, H. discus discus, H. madaka, and H. gigantea, which were divided into 2 groups at 0.52 similarity level: one group of H. discus hannai, H. discus discus, and H. madaka, and the other of H. gigantea. H. diversicolor supertexta and H. diversicolor diversicolor belonged to the other group. Furthermore, the reproducible pattern of amplified DNA bands by URP primers indicated the possibility of using these as molecular markers for the discrimination of the 6 Pacific abalone species. These results suggest that the URP-PCR approach will be a useful tool for obtaining accurate taxonomic identification and genetic relationship of Korean Pacific abalones, which is one of the first prerequisites in effective conservation programs.

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Genetic differentiation of charcoal rot pathogen,Macrophomina phaseolina, into specific groups using URP-PCR

Cited by 55 publications

References 15 publications

Diversity of Macrophomina phaseolina Based on Morphological and Genotypic Characteristics in Iran

Diversity of Macrophomina phaseolina Based on Morphological and Genotypic Characteristics in Iran

Assessing genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers

Genetic relationships of Pacific abalone (Haliotidae) species determined using universal rice primer-polymerase chain reaction fingerprinting

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