Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 362-369 ◽  
Author(s):  
S Archak ◽  
A B Gaikwad ◽  
D Gautam ◽  
E V.V.B Rao ◽  
K R.M Swamy ◽  
...  
Keyword(s):  
Dna Fingerprinting ◽  
Anacardium Occidentale ◽  
Similarity Matrix ◽  
Marker Index ◽  
Polymorphism Detection ◽  
Morphometric Analyses ◽  
Effective Multiplex Ratio ◽  
Rapd And Issr ◽  
Issr Primers ◽  
Similarity Matrices

Nineteen cashew accessions were analysed with 50 random primers, 12 ISSR primers and 6 AFLP primer pairs to compare the efficiency and utility of these techniques for detecting variation in cashew germplasm. Each marker system could discriminate between all of the accessions, albeit with varied efficiency of polymorphism detection. AFLP exhibited maximum discrimination efficiency with a genotype index of 1. The utility of each molecular marker technique, expressed as marker index, was estimated as a function of average band informativeness and effective multiplex ratio. Marker index was calculated to be more than 10 times higher in AFLP than in RAPD and ISSR. Similarity matrices were determined based on the data generated by molecular and morphometric analyses, and compared for congruency. AFLP displayed no correspondence with RAPD and ISSR. Correlation between ISSR and RAPD similarity matrices was low but significant (r = 0.63; p < 0.005). The similarity matrix based on morphometric markers exhibited no correlation with any of the molecular markers. AFLP, with its superior marker utility, was concluded to be the marker of choice for cashew genetic analysis.Key words: Anacardium occidentale, DNA fingerprinting, RAPD, ISSR, AFLP, morphometric.

scholarly journals R-ISSR - Tool for Generation of a New Type of Products, Applied for the Identification of Putative Molecular Marker Linked to QTL Determined Tolerance to Nutrient Deprivation Stress in Rye (Secale cereale L.)

2012 ◽  
Vol 40 (2) ◽  
pp. 238 ◽  
Author(s):  
Milosz SMOLIK
Keyword(s):  
Genetic Similarity ◽  
Plant Material ◽  
Inbred Lines ◽  
Mantel Test ◽  
Nutrient Deprivation ◽  
Secale Cereale L ◽  
New Type ◽  
Similar Range ◽  
Rapd And Issr ◽  
Issr Primers

This study presents results confirming the possibility of the application of various combinations of RAPD and ISSR primers in one multiplex PCR for the rye genome and generating a new type of R-ISSR products. The plant material consisted of two inbred lines (Ot0-6 and Ot1-3), F1 and two bulks (tolerant and susceptible), selected from a population of RILs (F9) with different responses to stress caused by nutrient deprivation at the seedling stage. In one PCR reaction, the DNA of five genotypes was amplified separately, with RAPD, ISSR, and RAPD+ISSR primers. In total, 28 R-ISSR combinations were tested by combining 20 and 8 appropriately selected RAPD and ISSR primers. 567 loci were amplified, including 230 RAPD, 136 ISSR and 207 amplified R-ISSR loci, of which 114 were new. It was shown that only one ISSR product was identified amongst sequenced R-ISSR products with identical electrophoretic mobility as co-migrating RAPDs and ISSRs. The remaining ones had heteroamplicons (R-ISSR) sequences. A similar range of variability was observed both in R-ISSR profiles and in RAPD, as well as in ISSR. The correlation coefficient between the matrices of genetic similarity for five rye genotypes calculated by means of the Mantel test was highly significant rAB.C = 0.964.

scholarly journals Phylogenetic relationships between members of Amaranthaceae and Chenopodiaceae of lower gangetic plains using RAPD and ISSR markers

1970 ◽  
Vol 36 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Tui Ray ◽  
SC Roy
Keyword(s):  
Key Words ◽  
Phylogenetic Relationships ◽  
Issr Markers ◽  
Mantel Test ◽  
Microsatellite Repeat ◽  
Arbitrary Primers ◽  
Gangetic Plains ◽  
First Report ◽  
Rapd And Issr ◽  
Similarity Matrices

The present study is the first report of phylogenetic relationships between some economically important members of Amaranthaceae and Chenopodiaceae of Lower Gangetic Plains of India, using RAPD and ISSR markers. A total of 293 RAPD and 177 ISSR fragments were generated with 15 (out of 50) decamer arbitrary primers and 11 (out of 30) microsatellite repeat anchored primers, respectively. Mean genetic similarities were estimated at 0.47 and 0.45 using RAPDs and ISSRs, respectively. The members of Chenopodiaceae are separated from those of Amaranthaceae in both the cases. The mantel test between the two Jaccard's similarity matrices gave r = 0.83, showing good correlation between RAPD and ISSR based similarities. However, in both the dendrograms Celosia sp. showed distant relationships with other amaranths. Key words: Amaranthaceae, Chenopodiaceae, RAPD, ISSR, Phylogenetic relationships   doi:10.3329/bjb.v36i1.1544 Bangladesh J. Bot. 36(1): 21-28, 2007 (June)

Genetic diversity and relationships among Egyptian Galium (Rubiaceae) and related species using ISSR and RAPD markers

Biologia ◽  
2014 ◽  
Vol 69 (3) ◽  
Author(s):  
Kadry Abdel Khalik ◽  
Magdy Abd El-Twab ◽  
Rasha Galal
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Rapd Markers ◽  
Phylogenetic Analyses ◽  
Randomly Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeats ◽  
Close Relationship ◽  
Rapd And Issr ◽  
Simple Sequence ◽  
Issr Primers

AbstractGenetic diversity and phylogenetic analyses of 24 species, representing nine sections of the genus Galium (Rubiaceae), have been made using the Inter Simple Sequence Repeats (ISSR), Randomly Amplified Polymorphic DNA (RAPD), and combined ISSR and RAPD markers. Four ISSR primers and three RAPD primers generated 250 polymorphic amplified fragments. The results of this study showed that the level of genetic variation in Galium is relatively high. RAPD markers revealed a higher level of polymorphism (158 bands) than ISSR (92 bands). Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrograms were compared. Six clades can be recognized within Galium, which mostly corroborate, but also partly contradict, traditional groupings. UPGMA-based dendrogram showed a close relationship between members of section Leiogalium with G. verum and G. humifusum (sect. Galium), and G. angustifolium (sect. Lophogalium). Principal coordinated analysis, however, showed some minor differences with UPGMA-based dendrograms. The more apomorphic groups of Galium form the section Leiogalium clade including the perennial sections Galium, Lophogalium, Jubogalium, Hylaea and Leptogalium as well as the annual section Kolgyda. The remaining taxa of Galium are monophyletic.

scholarly journals Rapid Plant Regeneration and Molecular Assessment of Genetic Stability Using ISSR and RAPD Markers in Commercial Banana Cv. Grand Naine (G-9)

2014 ◽  
Vol 4 (3) ◽  
pp. 393-403
Author(s):  
J. S. DUHAN ◽  
S. Kajla ◽  
D. Choudhary ◽  
A. K. Poonia
Keyword(s):  
Tissue Culture ◽  
Genetic Stability ◽  
Random Amplified Polymorphic Dna ◽  
Issr Markers ◽  
Ms Medium ◽  
Inter Simple Sequence Repeats ◽  
Rapd Primer ◽  
Molecular Assessment ◽  
Rapd And Issr ◽  
Issr Primers

The investigation was carried out to assess the genetic stability in   tissue culture raised plants of banana cv. G-9 using random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers.Aims:  Molecular assessment of genetic stability of tissue culture raised plants of banana cv. G-9 using molecular markers.Material and Results: Apical shoots were established on medium EM4 (MS + BAP 4.0 mg L-1) with maximum of 3.8 buds/explant in 2.6 days. The maximum bud multiplication with 16.5±0.06 shoots was observed on medium Ma3 (MS medium+ 5.0 mg L-1 BAP + 0.25 mg L-1 NAA of + 30 mg L-1 AdSO4). The maximum rooting response (100%) was observed on 1/2 MS medium supplemented with 2.0 mg L-1 NAA in 12.2 days. After acclimatization the hardened plants were examined for genetic stability using RAPD and ISSR primers. Total forty six (twenty six RAPD and twenty ISSR) markers were used. RAPD primers produced 87 distinct and scorable bands, with an average of 3.34 bands per primer and the amplification products range was from 100-1200 bps. The number of scorable bands for RAPD primer varied from 2 to 5 with an average of 3.34 bands per primer. ISSR primers produced 71 distinct and scorable bands in the range of 100-1000 bps and the number of scorable bands for each primer varied from 2 to 6 with an average of 3.55 bands per primer.Conclusion: Similar profile with monomorphic bands was observed for all the tissue culture raised plants when compared to mother plant in both types of markers used. The results corroborate the fact that plant tissue culture technology has immense importance for production of true to type of planting material. 

scholarly journals Cytogenetic and molecular studies on two faba bean cultivars revealed their difference in their aluminum tolerance

2020 ◽  
Vol 116 (2) ◽  
pp. 273
Author(s):  
Ahmed M. HASSANEIN ◽  
Ahmed H. MOHAMED ◽  
Heba Ahmed ABD ALLAH ◽  
Hoida ZAKI
Keyword(s):  
Faba Bean ◽  
Chromosomal Abnormalities ◽  
Aluminum Tolerance ◽  
Issr Markers ◽  
Growth Data ◽  
Al Tolerance ◽  
Al Stress ◽  
Molecular Studies ◽  
Rapd And Issr ◽  
Issr Primers

<p>Two cultivars of faba bean (<em>Vicia faba</em> ‘Giza 843’ and ‘Nobaria 3’) that differ in aluminum (Al) tolerance were used to study cytogenetic and genomic alterations under the influence of Al Cl<sub>3</sub> (5, 15, and 25 mmol AlCl<sub>3</sub>) for different periods (6, 12 and 24 h). Under Al treatments, mitotic index in both cultivars decreased and total chromosomal abnormalities increased. The frequencies of micronuclei and chromosomal abnormalities (C-anaphase, metaphase-star chromosomes, breaks, sticky and disturbed chromosomes during metaphase or anaphase) in ‘Giza 843’ were lower than in ‘Nabaria 3’. Increase of the registered cytogenetic events under the influence of Al stress led to increase the detected polymorphism using RAPD and ISSR markers. Application of RAPD primers gave the same value of polymorphism in both faba bean cultivars under Al stress. Polymorphism average of nine ISSR primers of ’Giza 843’ (65.36 %) was lower than that of ‘Nobaria 3’ (71.59 %). Molecular markers, cytogenetic characteristics and seedling growth data indicate that Al tolerance of ‘Giza 843’ was higher than of ‘Nobaria 3’. This work shows that cytogenetic and ISSR techniques could be used efficiently to distinguish between the ability of two faba bean cultivars to tolerate toxic effects of Al.</p>

scholarly journals Textual Spanning: Finding Discursive Holes in Text Networks

2019 ◽  
Vol 5 ◽  
pp. 237802311982767
Author(s):  
Dustin S. Stoltz ◽  
Marshall A. Taylor
Keyword(s):  
Probability Distribution ◽  
Topic Model ◽  
Structural Features ◽  
Weighted Graphs ◽  
Similarity Matrix ◽  
Document Similarity ◽  
Simulation Based ◽  
Model Probability ◽  
Alternative Measures ◽  
Similarity Matrices

We propose a measure of discursive holes well suited for the unique properties of text networks built from document similarity matrices considered as dense weighted graphs. In this measure, which we call textual spanning, documents similar to documents dissimilar from one another receive a high score, and documents similar to documents similar to one another receive a low score. After offering a simulation-based validation, we test the measure on an empirical document similarity matrix based on a preestimated topic-model probability distribution. The results demonstrate that our proposed textual spanning measure captures different structural features of discursive fields than alternative measures.

scholarly journals BOTANICAL AND GENETIC CHARACTERIZATION OF CITRUS MAXIMA (BURM.) MERRILL. F. RUTACEAE

2016 ◽  
Vol 9 (1) ◽  
pp. 260
Author(s):  
Mohammed S. Sedeek ◽  
Farid N. Kirollos ◽  
Camilia G. Michel ◽  
Mostafa A. Abdel Kawy
Keyword(s):  
Genetic Polymorphism ◽  
Dna Fingerprinting ◽  
Citrus Sinensis ◽  
Morphological Characters ◽  
Issr Markers ◽  
Citrus Paradisi ◽  
Citrus Maxima ◽  
Rapd And Issr ◽  
Combined Data

<p><strong>Objective: </strong>Total investigation of the macro-and micromorphological features of <em>Citrus maxima</em> (Burm.) Merrill. In addition, DNA fingerprinting in this study was to estimate genetic polymorphism and relationships with another citrus viz: <em>Citrus paradise</em><strong> </strong>and <em>Citrus sinensis</em> based on RAPD and ISSR markers.</p><p><strong>Methods: </strong>For the establishment of macro-and micromorphological investigation and genetic estimation, this study presents a total investigation of the macro-and micromorphological features of the roots, stems, leaves, flowers, fruits and seeds of the plants through microscopical investigation of the prepared entire, transverse sections and powdered forms of different organs under study. Furthermore, the DNA of the three plants was extracted from leaf samples and two types of DNA markers RAPD and ISSR were assayed.</p><p><strong>Results: </strong>Macro-and micromorphological features of different organs were investigated. On the other hand Genetic polymorphism and relationships among <em>Citrus maxima</em>, <em>Citrus paradisi</em> and <em>Citrus sinensis</em> was revealed. The highest genetic similarity was between <em>Citrus maxima </em>and <em>Citrus paradisi</em> while the lowest similarity was between <em>Citrus paradisi</em> and <em>Citrus sinensis</em> as revealed by RAPD, ISSR and combined data.</p><p><strong>Conclusion: </strong>For the present study, macro and micro-morphological characters, as well as, DNA fingerprinting can be considered as the identifying parameters for authentication of <em>Citrus maxima</em> (Burm.) Merrill.</p>

Efficiency of three PCR-based markers in assessing genetic variation among cowpea (Vigna unguiculata subsp. unguiculata) landraces

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 268-275 ◽  
Author(s):  
Nicola Tosti ◽  
Valeria Negri
Keyword(s):  
Vigna Unguiculata ◽  
Diversity Index ◽  
Local Varieties ◽  
Restricted Area ◽  
Marker Index ◽  
Marker System ◽  
On Farm Conservation ◽  
Genetic Pool ◽  
Effective Multiplex Ratio ◽  
On Farm

The main objective of this study was to investigate the efficiency of RAPD, AFLP, and SAMPL marker systems in detecting genetic polymorphism in cowpea landraces (Vigna unguiculata subsp. unguiculata (L.) Walp.) that probably share a similar genetic pool. A second objective was to determine the level of diversity among landraces from a restricted area, to define the most appropriate strategy of on-farm conservation. Each marker system was able to discriminate among the materials analysed, but a clear distinction between all the local varieties was only obtained with AFLP and SAMPL markers. The average diversity index was quite similar for each marker system, but owing to the differences in the effective multiplex ratio values the marker index was higher for the AFLP and SAMPL systems than for the RAPD system. The AFLP and SAMPL techniques appear to be more useful than the RAPD technique in the analysis of limited genetic diversity among the cowpea landraces tested. The significant correlations of SAMPL similarity and cophenetic matrices with those of the other markers, and the lower number of primer combinations required, indicate that this technique is the most valuable. The low genetic similarity detected among landraces suggests that all the cowpea landraces should be maintained on the respective farms from which they came.Key words: landraces, molecular marker, marker index, Vigna.

scholarly journals Informative Inter Simple Sequence Repeat (ISSR) primers for genetic analysis of coconut (Cocos nucifera L.) germplasm

CORD ◽  
2005 ◽  
Vol 21 (02) ◽  
pp. 34 ◽  
Author(s):  
R. Manimekalai
Keyword(s):  
Information Content ◽  
Polymorphism Information Content ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Rapid Screening ◽  
Sequence Repeat ◽  
Marker Index ◽  
Simple Sequence ◽  
Issr Primers

Inter Simple Sequence Repeat (ISSR) markers are versatile and used in a number of applications viz. genetic diversity estimation, phylogenetic relationship and gene tagging in different crops. In coconut, the ISSR markers are being reported here for the first time. In the present paper, thirty-five  primers targeting to amplify the inter microsatellite  regions were screened  using  thirty  different  coconut  germplasm  accessions.  The  ISSR  primers  were evaluated based on polymorphism information content and marker index.  Out of 35 primers screened,  19 primers  produced  clear amplification  pattern.  The polymorphism  information content varied between 0.019 and 0.386, whereas, the marker index ranged from 0.019 to 5.673  among  the  primers.    Based  on  the  high  marker  index,  five  and  ten  primers  were selected.  The similarity  matrices  were constructed  separately  for five, ten and 19 primers using NYSYS software and the correlation was tested using Mantel’s test. There was high correlation  between five and ten primers with 19 primers. Hence, the primers with higher marker index (5 and 10 primers) were regarded as informative  primers. These informative primers can be used to develop more polymorphic markers in coconut for rapid screening of germplasm materials.

Genetic Relationship in Sainfoin (Onobrychis viciifolia) Landraces Cultivated East Anatolia by using RAPD and ISSR Markers

2021 ◽  
Author(s):  
Mehmet Macit Ertuş
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Calcareous Soils ◽  
Similarity Index ◽  
Issr Markers ◽  
High Genetic Diversity ◽  
Onobrychis Viciifolia ◽  
Young Leaves ◽  
Rapd And Issr ◽  
Issr Primers

Background: Sainfoin (Onobrychis viciifolia) is a forage crop that yields high in arid and calcareous soils and is cultivated in large areas. There aren’t many genetic diversity studies on the varieties of cultured sainfoin. This study was conducted to determine the genetic diversity and the degree of relationship between 23 cultivated landraces and one registered variety. Methods: To take samples from the populations, seeds were sown in the field in 2014. Samples were taken from the young leaves of the plants and preserved at -80oC in same year. RAPD and ISSR primers were used in the study. The bands obtained as a result of PCR were recorded and the data of both methods were also evaluated by combining them. Result: In the study, 5 RAPD and 4 ISSR primers were used and a total of 49 bands were obtained. Of 29 bands obtained using RAPD primers, 20 were found to be polymorphic and of 20 bands obtained using ISSR primers, 15 were found to be polymorphic. It was found that there was a very low correlation between the two methods. Using RAPD and ISSR markers and RAPD + ISSR combination, the similarity index among populations was found to be between 0.25-0.95, 0.5-1.00 and 0.45-0.91, respectively. The Nei’s genetic diversity index was found to be between 0.3365, 0.2656 and 0.3018 with RAPD, ISSR primers and RAPD + ISSR combination, respectively. Based on the dendrograms obtained using RAPD, ISSR primers and RAPD + ISSR combination, the populations under analysis were classified into 3, 3 and 5 groups, respectively. With this study, the closest populations were identified and a significantly high genetic diversity was detected.

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