scholarly journals Characterising the genetic diversity of Pseudomonas syringae pv. syringae isolated from rice and wheat in Iran

2012 ◽  
Vol 48 (No. 4) ◽  
pp. 162-169 ◽  
Author(s):  
S. Dariush ◽  
A.A. Ebadi ◽  
M. Khoshkdaman ◽  
B. Rabiei ◽  
A. Elahinia
Keyword(s):  
Genetic Diversity ◽  
Pseudomonas Syringae ◽  
Rapd Analysis ◽  
Host Specialization ◽  
Growth Stages ◽  
Randomly Amplified Polymorphic Dna ◽  
Two Populations ◽  
Amova Analysis ◽  
Sheath Rot ◽  
Different Growth Stages

Sheath rot of rice and leaf blight of wheat caused by Pseudomonas syringae pv. syringae are the important bacterial pathogens of rice and wheat in Iran. The randomly amplified polymorphic DNA (RAPD) method was used to investigate the genetic diversity of 60 strains of P. s. pv. syringae obtained from rice and wheat in different growth stages. Cluster analysis by UPGMA method showed that strains were grouped into two clusters. The AMOVA analysis indicated that about 18% of the total genetic variation existed between two populations of rice and wheat, which showed the lack of host specialization in P. s. pv. syringae strains among rice and wheat. We confirmed that high genetic heterogeneity existed in the P. s. pv. syringae strains which are detectable by RAPD analysis, and that molecular and statistical analysis of RAPD fragments can be used both to distinguish between strains and to determine relatedness between them.

scholarly journals Use of Random Amplified Polymorphic DNA Markers for Cultivar Identification in Mint

HortScience ◽  
2001 ◽  
Vol 36 (4) ◽  
pp. 761-764 ◽  
Author(s):  
A.L. Fenwick ◽  
S.M. Ward
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Dna Markers ◽  
Geographical Origin ◽  
Cultivar Identification ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Randomly Amplified Polymorphic Dna ◽  
Commercial Oil

Seventeen mint accessions representing the three species grown for commercial oil production in the United States were characterized using randomly amplified polymorphic DNA (RAPD) analysis. The RAPD profiles readily identified the different Mentha species; calculation of genetic distance, based on the number of shared bands, indicated that M. spicata L. is more closely related to M. × gracilis than to M. × piperita. The RAPD profiles also distinguished among eight peppermint accessions of different geographical origin. However, only limited polymorphism was observed among the most widely grown peppermint and Scotch spearmint cultivars. These results indicate a potential lack of genetic diversity in mint cultivars grown for oil in the United States.

scholarly journals ECOLOGY AND THE RAPD TECHNIQUES USED TO ASSESS THE GENETIC DIVERSITY IN PTEROLOBIUM HEXAPETALUM, A SCRAMBLING MEDICINAL SHRUB IN MARUTHAMALAI AND CHENNIMALAI HILLS, THE WESTERN GHATS

2019 ◽  
pp. 72-77 ◽  
Author(s):  
SHARMILA S. ◽  
AKILANDESWARI D. ◽  
RAMYA E. K. ◽  
MOWNIKA S.
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Tamil Nadu ◽  
Climatic Factors ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Climatic Conditions ◽  
Individual Bands ◽  
Reproductive Characters ◽  
Two Populations

Objective: To investigate the ecological and genetic diversity, climatic factors, edaphic factors morphological and reproductive characters and RAPD analysis of medicinal plant species Pterolobium hexapetalum in two hills viz., Maruthamalai (arid) and Chennimalai (very arid), which is located in Coimbatore and Erode districts, Tamil Nadu. Methods: The present research was carried out by using a random amplified polymorphic DNA (RAPD) analysis was made to determine the genetic variation between the two populations of the medicinal shrub, Pterolobium hexapetalum in an environmental gradient. Among the five primers tested, the OPN7 (80 %) and OPN17 (71.4 %) produced higher polymorphism was used in RAPD analysis. Results: The results of RAPD analysis showed the presence of 51 individual bands were formed, out of which, 29 were polymorphic bands which showed the existence of genetic variation between populations. A dendrogram was constructed based on Jaccard’s coefficient to determine the degree of genetic relationship among the two populations and analysed. The primers OPN7 and OPN17 were clustered together at a genetic distance level 10. Considering the elevation and proximity, the temperature ranges from 18 °C to 37.6 °C in Maruthamalai hill and 20 °C to 39.4 °C in Chennimalai hill. Conclusion: From the morphoecological studies the results indicated that both arid and very arid climatic conditions showed slight differences in their vegetative and reproductive characters.

scholarly journals Genetic Diversity in Muscadine and American Bunch Grapes Based on Randomly Amplified Polymorphic DNA (RAPD) Analysis

1996 ◽  
Vol 121 (6) ◽  
pp. 1020-1023 ◽  
Author(s):  
Xianping Qu ◽  
Jiang Lu ◽  
Olusola Lamikanra
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
The United States ◽  
Average Genetic Distance ◽  
Separate Study ◽  
Randomly Amplified Polymorphic Dna ◽  
And Cluster Analysis ◽  
Grape Cultivars

Two morphologically distinct types of grapes belonging to the subgenera Euvitis and Muscadinia in the genus Vitis are cultivated in the United States. The former is commonly called bunch grapes while the latter is usually called muscadine. Genetic diversity among these grapes was investigated using RAPD markers. Sixteen grape cultivars, with parentage including V. rotundifolia Michx., V. vinifera L., and several American Vitis species, were used for the RAPD analysis. A total of 156 RAPD markers was produced from 19 random primers, over 90% of which was polymorphic among the muscadine and the bunch grapes. Polymorphisms were lower within each subgenus. Relationships between these two subgenera were estimated based on band-sharing and cluster analysis. The average genetic distance between the bunch and the muscadine grape cultivars was 0.45. The results based on DNA analysis agree with isozyme data obtained from a separate study, which demonstrated that muscadine grapes share very few common alleles with American bunch grapes and European grapes.

Effect of habitat fragmentation on the genetic diversity of Stipa krylovii Reshov. in an agro-pastoral ecotone in northern China

2009 ◽  
Vol 89 (5) ◽  
pp. 875-882
Author(s):  
S Zheng ◽  
Z Cao ◽  
K Wang ◽  
M Zhao ◽  
J Mi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Northern China ◽  
Issr Markers ◽  
Inter Simple Sequence Repeats ◽  
Native Grassland ◽  
Stipa Krylovii ◽  
Fragmented Population ◽  
Two Populations ◽  
Amova Analysis

Native grassland in China have been fragmented due to the introduction of agriculture, which has the potential to reduce genetic diversity. In order to understand the potential effects of fragmentation, we conducted a study to examine the genetic diversity between two populations of Stipa krylovii in a typical steppe ecoregion, in northern China. One population was fragmented by farmland (PF) while the second was continuous steppe (PS). The populations were 30 km apart. Genetic diversity was assessed by sampling plants in four geographically similar subpopulations in each population and analyzed for their DNA using the inter-simple sequence repeats (ISSR) markers. Of 50 primers tested, 7 produced 122 amplified bands from 120 individuals, of which 92% (112) were polymorphic. According to the UPGMA dendogram, the four PF subpopulations were grouped separately from the four PS subpopulations. However, AMOVA analysis indicated that habitat fragmentation over the past 50 yr had not changed genetic diversity and variation among S. krylovii populations in an agro-pastoral ecotone in northern China. Therefore, the genetic diversity of this species can be maintained if agriculture disturbance is not increased. Key words: Genetic variation, gene flow, ISSR, fragmented population, non-fragmented population

scholarly journals Inter simple sequence repeat markers to assess genetic diversity of the desert date (Balanites aegyptiaca Del.) for Sahelian ecosystem restoration

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Selouka Mint Abdelaziz ◽  
Leila Medraoui ◽  
Mohammed Alami ◽  
Ouafae Pakhrou ◽  
Meryem Makkaoui ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Inter Simple Sequence Repeat ◽  
Resolving Power ◽  
Balanites Aegyptiaca ◽  
Marker Index ◽  
Information Index ◽  
Genetic Diversity And Structure ◽  
Two Populations ◽  
Amova Analysis

Abstract Drought and desertification are the major environmental constraints facing the Sahelian agro-ecosystems for decades. Assessing genetic diversity of native tree species is critical to assist ecosystems restoration efforts. Here we describe genetic diversity and structure of seven Balanites aegyptiaca L. natural populations distributed across the Sahelian-Saharan zone of Mauritania using 16 polymorphic ISSR primers. These generated 505 polymorphic bands. Polymorphism information content (PIC) varied from (0.13–0.29) with an average 0.23, marker index (MI) averaged 7.3 (range 3.3–10.3) and resolving power (RP) ranged from (4.53–14.6) with an average 9.9. The number of observed alleles (Na) ranged from (0.62–1.39), Effective number of alleles (Ne) varied from (1.26–1.37), Shannon’s information index (I) ranged from (0.25–0.36). AMOVA analysis showed that 80% of the genetic variation was fined within populations, which is supported by a low level of genetic differentiation between population (GST = 0.21) and an overall estimate of gene flow among populations (Nm = 1.9). The dendrogram based on Jaccard's similarity coefficient and the structure analysis divided the seven populations into two main clusters in which two populations from the Saharan zone were grouped. Our results provide baseline data for genetic conservation programs of this Sahelian neglected crop and with an important econ-ecological role.

Isozyme and RAPD variation among and within hemp dogbane (Apocynum cannabinum) populations

Weed Science ◽  
1998 ◽  
Vol 46 (4) ◽  
pp. 408-413 ◽  
Author(s):  
Corey V. Ransom ◽  
David S. Douches ◽  
James J. Kells
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Phenotypic Variation ◽  
Population Genetic ◽  
Rapd Analysis ◽  
Analysis Data ◽  
The Other ◽  
Randomly Amplified Polymorphic Dna ◽  
Population Genetic Analysis ◽  
Two Populations

Clonal individuals from 16 hemp dogbane populations with phenotypic variation were analyzed using isozyme and randomly amplified polymorphic DNA (RAPD) analysis. Plants originated from populations in Michigan and Illinois. Three knownApocynumspecies, spreading dogbane, hemp dogbane, and prairie dogbane, were evaluated. Genetic distance among populations was more pronounced with isozyme analysis compared to RAPD analysis. The combined isozyme and RAPD analysis data separated spreading dogbane from all other plants analyzed. Genetic variation was present among the 16 hemp dogbane populations, but was less than expected based on the phenotypic variation present among the collections. The short genetic distance between the 16 hemp dogbane collections and the threeApocynumspecies suggests that variation among populations of hemp dogbane may be from outcrossing with other closely relatedApocynumspecies. Isozyme and RAPD analyses were also conducted on plants from two populations in Michigan to determine the level of genetic variation among plants within the same population. Genetic analysis revealed that one population was entirely clonal, while the other population was a mixture of clonal and segregating plants.

Enterotoxicity and genetic variation among clinical Staphylococcus aureus isolates in Jordan

2006 ◽  
Vol 55 (2) ◽  
pp. 183-187 ◽  
Author(s):  
Randa G. Naffa ◽  
Salwa M. Bdour ◽  
Hussein M. Migdadi ◽  
Asem A. Shehabi
Keyword(s):  
Genetic Diversity ◽  
Staphylococcus Aureus ◽  
Genetic Variation ◽  
Multiplex Pcr ◽  
Dna Fingerprinting ◽  
Rapd Analysis ◽  
Clinical Isolates ◽  
Randomly Amplified Polymorphic Dna ◽  
Toxin Genes ◽  
Enterotoxin Genes

A total of 100 Jordanian clinical Staphylococcus aureus isolates was analysed for the presence of the enterotoxin genes sea, seb, sec, sed and see using multiplex PCR. Twenty-three isolates (23 %) were potentially enterotoxigenic. The prevalence of sea, sec and sea plus sec among the total clinical isolates was 15, 4 and 4 %, respectively. None of the isolates harboured sed, seb or see genes. S. aureus isolates were subjected to DNA fingerprinting by randomly amplified polymorphic DNA (RAPD) analysis to test whether isolates harbouring the toxin genes were genetically clustered. A total of 13 genotypes was identified at a 47 % similarity level. Genotypes I and V accounted for the largest number of enterotoxigenic isolates (19 %). This study has demonstrated the genetic diversity of Jordanian clinical S. aureus isolates and shown that the presence of the toxin genes is not genotype specific.

scholarly journals Assessment of the Genetic Diversity among Strains of Xanthomonas cynarae by Randomly Amplified Polymorphic DNA Analysis and Development of Specific Characterized Amplified Regions for the Rapid Identification of X. cynarae

2001 ◽  
Vol 67 (8) ◽  
pp. 3379-3384 ◽  
Author(s):  
Gaëlle Trébaol ◽  
Charles Manceau ◽  
Yves Tirilly ◽  
Stéphane Boury
Keyword(s):  
Genetic Diversity ◽  
Genetic Background ◽  
Genomic Dna ◽  
Dna Polymorphism ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Rapid Identification ◽  
Randomly Amplified Polymorphic Dna ◽  
Pcr Markers

ABSTRACT The randomly amplified polymorphic DNA (RAPD) method was used to investigate the genetic diversity in Xanthomonas cynarae, which causes bacterial bract spot disease of artichoke. This RAPD analysis was also intended to identify molecular markers characteristic of this species, in order to develop PCR-based markers which can be used to detect this pathogenic bacterium in artichoke fields. Among the 340 RAPD primers tested, 40 were selected on their ability to produce reproducible and reliable fingerprints in our genetic background. These 40 primers produced almost similar patterns for the 37 X. cynarae strains studied, different from the fingerprints obtained for other Xanthomonas species and other xanthomonad-like bacteria isolated from artichoke leaves. Therefore, X. cynarae strains form a homogeneous genetic group. However, a little DNA polymorphism within this species was observed and the collection of X. cynarae isolates was divided into two groups (one containing three strains, the second one including all other strains). Out of seven RAPD markers characteristic of X. cynarae that were cloned, four did not hybridize to the genomic DNA of strains belonging to other Xanthomonas species. These four RAPD markers were converted into PCR markers (specific characterized amplified regions [SCARs]); they were sequenced, and a PCR primer pair was designed for each of them. Three derived SCARs are good candidates to develop PCR-based tests to detectX. cynarae in artichoke fields.

scholarly journals Genetic Diversity of Basil (Ocimum spp.) Based on RAPD Markers

2003 ◽  
Vol 128 (1) ◽  
pp. 94-99 ◽  
Author(s):  
Roberto F. Vieira ◽  
Peter Goldsbrough ◽  
James E. Simon
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Distinct Species ◽  
Major Constituent ◽  
Randomly Amplified Polymorphic Dna ◽  
Base Pairs ◽  
Bootstrap Analysis ◽  
Similarity Indices ◽  
Polymorphic Bands

Molecular markers were used to assess genetic diversity in basil (Ocimum L. spp., Lamiaceae). Using randomly amplified polymorphic DNA (RAPD) analysis, 11 primers generated 98 polymorphic bands, ranging from 300 to 2,000 base pairs, that discriminated among 37 accessions across nine Ocimum spp. Means of genetic similarities within Ocimum spp. showed that the domesticated species, O. minimum L. (0.887), O. basilicum L. (0.769), and O. ×citriodorum Vis. (0.711) had highest similarity indices within species, while the nondomesticated, O. americanum L. (0.580), O. gratissimum L. (0.408), and O. kilimandscharicum Guerke (0.559) showed the lowest similarity. RAPD results indicated that O. minimum should not be considered a distinct species but rather a variety of O. basilicum. Consistent clusters among all but one of the O. ×citriodorum spp., all containing citral as the major constituent, were identified using bootstrap analysis. RAPD analysis was useful in discriminating among Ocimum spp., although within species resolution will require a higher number of polymorphic bands.

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