RAPD Analysis of DNA Polymorphism in Turkish Sheep Breeds

Abstract RAPD analysis was applied to assess the degree of DNA polymorphism in A. fistulosum calli of high chromosomal instability. Nineteen of 24 randomly selected RAPD primers revealed scorable polymorphism between calli and seeds (reference material). Polymorphic band frequency was 55/237 in seeds and 36/233 in calli; variability on the DNA level was thus lower in calli than in seeds (15.4% vs. 23.2% of band positions). UPGMA analysis of Jaccard's coefficients confirmed the genetic similarity of the analyzed cultures. The most distinctive DNA changes in calli involved coincident loss of original bands or the appearance of novel bands. Seven such changes (4 losses, 3 gains) were observed. Our results suggest that changes on the chromosomal level and on the DNA level occurred independently of each other and that different callus lines underwent similar genetic changes during culture, presumably due to strong selection pressure effected by standard in vitro conditions.

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DNA polymorphism of dogs (Canis familiaris L.). II. RAPD-analysis.

Biomics ◽

10.31301/2221-6197.bmcs.2021-22 ◽

2021 ◽

Vol 13 (3) ◽

pp. 309-320

Author(s):

O.Yu. Kiryanova ◽

R.R. Garafutdinov ◽

D.A. Chemeris ◽

Yu.R. Giniyatov ◽

I.M. Gubaidullin ◽

...

Keyword(s):

Prior Knowledge ◽

In Silico ◽

Dna Polymorphism ◽

Rapd Analysis ◽

Canis Familiaris ◽

Gray Wolf ◽

Wild Relative ◽

Simple Method ◽

Complete Genomes ◽

Similarities And Differences

A rather simple method of detecting DNA polymorphism in dogs in the form of amplification of random fragments of the genome using RAPD analysis with primers with arbitrary nucleotide sequences, which does not require prior knowledge of the sequences of nitrogenous bases of the detected DNA fragments, is considered. However, information about the complete genomes of the investigating species of organisms and, dogs in particular, allows with a preliminary in silico RAPD analysis to predict the expected results for each primer and their multiplex composition, which makes it possible at this stage to reject unsuitable primers before conducting "wet" experiments. In the case of known genomes of a number of related organisms for example in this case dogs, the multiplex RAPD analysis conducted in silico with six decameric primers, the sequences of which exclude the formation of homo- and heterodimers in PCR showed both genomic similarities and differences between different breeds, as well as with their wild relative gray wolf. Multiplex in silico RAPD analysis is a virtual PCR and if amplicons common to all studied organisms are removed from such amplification, leaving only significant ones, then this tool in the form of the ABCDNA_GS program created by us can be used to establish phylogenetic kinship, especially of those organisms whose genomes are highly collinear, which is just typical of the genomes of different dog breeds.

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Genetic biodiversity studies on IGFBP-3 gene in Egyptian sheep breeds

Biotechnology in Animal Husbandry ◽

10.2298/bah0902101a ◽

2009 ◽

Vol 25 (1-2) ◽

pp. 101-109 ◽

Cited By ~ 6

Author(s):

B.A. Ali ◽

A.A. El-Hanafy ◽

H.H. Salem

Keyword(s):

Growth And Development ◽

Genomic Dna ◽

Dna Polymorphism ◽

Restriction Pattern ◽

Exon 2 ◽

Sheep Breeds ◽

Pcr Rflp ◽

Intron 2 ◽

Igfbp 3 ◽

Indian Sheep

The insulin-like growth factor binding protein-3 (IGFBP-3) gene is a structural gene associated with the growth and development of the animals. The present investigation was carried out to study DNA polymorphism by PCR-RFLP of IGFBP-3 gene in four Egyptian local sheep breeds and its comparison with Indian sheep breeds. Genomic DNA was isolated from a total of 20 animals from four Egyptian breeds of sheep namely Rahmani, Ossimi, Awassi, and Barki. A fragment of IGFBP-3 gene, comprising of a part of exon 2, complete intron 2, exon 3, and a part of intron 3, was amplified. The amplified fragment was found to be 654 bp in sheep as compared to earlier reports of 651 bp in cattle and 655 bp in buffalo. On digestion of 654 bp with Hae III restriction enzyme yielded single restriction pattern of five fragments of sizes 201, 201, 87, 67, 57 in all the animals belonging to the four Egyptian breeds studied revealing absence of polymorphism in those four Egyptian sheep breeds. On comparison, this fragment was monomorphic in Indian sheep breeds and buffalo ,while it was reported to be polymorphic in cattle.

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The reproducibility of RAPD profiles: Effects of PCR components on RAPD analysis of four centaurium species

Archives of Biological Sciences ◽

10.2298/abs1201191s ◽

2012 ◽

Vol 64 (1) ◽

pp. 191-199 ◽

Cited By ~ 3

Author(s):

Marijana Skoric ◽

B. Siler ◽

Tijana Banjanac ◽

Jasmina Zivkovic ◽

Slavica Dmitrovic ◽

...

Keyword(s):

Dna Polymerase ◽

Dna Polymorphism ◽

Reliable Method ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Taq Polymerase ◽

Taq Dna Polymerase ◽

Final Volume ◽

Template Dna ◽

Diversity Studies

Random amplified polymorphic DNA (RAPD) analysis is a simple and reliable method used to detect DNA polymorphism. Several factors can affect the amplification profiles, thereby causing false bands and non-reproducibility of the assay. In this study, we analyzed the effects of different concentrations of primer, magnesium chloride, template DNA and Taq DNA polymerase to develop and standardize a RAPD protocol for Centaurium species. The optimized PCR reaction mixture included: 50 ng of DNA extracted using a CTbased protocol, 2.5 mM MgCl2, 7.5 pmol primer and 2 U of Taq polymerase in a final volume of 25 ?l. Each of the five primers used in experiments (OPB11, OPB15, OPB18, OPF05 and OPH02) generated reproducible and distinguishable fingerprinting patterns of four Centaurium species. The obtained optimized RAPD protocol and the selected primers are useful for our further work in the genetic diversity studies of Centaurium species.

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Studies on DNA Polymorphism of Silver Maple (Acer saccharinum L.)

HortScience ◽

10.21273/hortsci.30.4.783a ◽

1995 ◽

Vol 30 (4) ◽

pp. 783A-783

Author(s):

A. Virginia Freire ◽

John E. Preece ◽

David A. Lightfoot

Keyword(s):

Genetic Relationship ◽

Dna Polymorphism ◽

Rapd Analysis ◽

Pcr Amplification ◽

Cesium Chloride ◽

Biomass Feedstock ◽

Red Maple ◽

Silver Maple ◽

Natural Range

Silver maple has great potential as a biomass feedstock. We compared three clones from each of seven provenances located on east to west and north to south transects across the natural range of silver maple and one red maple. DNA extracted by a modification of the CTAB technique (Murray and Thompson, 1980) was not suitable for RAPD analysis. Using this technique, polymorphism was either not reproducible or there was poor amplification for some clones. A new DNA extraction technique using PVPP, chloroform, and cesium chloride was tested (a modification of Yoon et al., 1991). this method yielded DNA that was more suitable for PCR amplification. Both RAPD and DAF (Caetano-Anolles and Gresshoff, 1994) methods were used for amplification. Polymorphism was detected among and within provenances. DAF was more efficient than RAPDs for determination of the genetic relationship among silver maple clones.

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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

Applied and Environmental Microbiology ◽

10.1128/aem.67.8.3379-3384.2001 ◽

2001 ◽

Vol 67 (8) ◽

pp. 3379-3384 ◽

Cited By ~ 16

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.

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