scholarly journals Reliability and comparison of the polymorphism revealed in amaranth by amplified fragment length polymorphisms (AFLPs) and inters simple sequence repeats (ISSRs)

2014 ◽  
Vol 6 (4) ◽  
pp. 48-56 ◽  
Author(s):  
O. A. Oduwaye, ◽  
M. Barnek, ◽  
J. Čechov, ◽  
J. Raddov,
Keyword(s):  
Fragment Length ◽  
Simple Sequence Repeats ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Simple Sequence

scholarly journals Phenetic Characterization of Plum Cultivars by High Multiplex Ratio Markers: Amplified Fragment Length Polymorphisms and Inter-simple Sequence Repeats

2001 ◽  
Vol 126 (1) ◽  
pp. 72-77 ◽  
Author(s):  
Luís Goulão ◽  
Luisa Monte-Corvo ◽  
Cristina M. Oliveira
Keyword(s):  
Fragment Length ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Similarity Coefficients ◽  
Pair Group ◽  
Multiple Loci ◽  
Inter Simple Sequence Repeats ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Simple Sequence

Variability of commercial plum (Prunus L. sp.) cultivars is unknown since breeding often involves intercrossing hybrids with several species but has been based on a low number of parents. Molecular markers like amplified fragment length polymorphisms (AFLP) and inter-simple sequence repeats (ISSR), which sample multiple loci simultaneously, have become increasingly popular, and were used to characterize 24 diploid and four hexaploid cultivars of plum. Seven AFLP and six ISSR primers were used, and resulted in amplification of 379 and 270 products, respectively. Unweighted pair-group method with arithmetic averages (UPGMA) dendrograms, based on similarity coefficients, reflected a clear separation between diploid and hexaploid plums. Among diploid plums, two pairs of cultivars were relatively distinct from the rest, namely `Golden Japan' and `Methley' and `Ozark Premier' and `Songold'. Furthermore, several cultivars were grouped together both with AFLP and ISSR analysis: 1) `Ambra', `Red Beaut', and `Black Beaut', 2) `Black Diamond' and `Royal Diamond', 3) `June Rose', `Santa Rosa', and `Royal Red', and iv) `Freedom', `Larry Ann', and `Queen Rosa'. Although the phenetic classification obtained by the two methods were similar (r = 0.73, for the diploid group), ISSR had a higher reproducibility and percentage of polymorphisms (87.4% vs. 62.8%) than AFLP. Methodological aspects of both markers systems are discussed. Results obtained suggest that the AFLP and ISSR approaches are valuable tools for identification of specific genotypes and analysis of phenetic relationships in plum.

scholarly journals Use of Inter-Simple Sequence Repeats and Amplified Fragment Length Polymorphisms to Analyze Genetic Relationships Among Small Grain-Infecting Species of Ustilago

2003 ◽  
Vol 93 (2) ◽  
pp. 167-175 ◽  
Author(s):  
J. G. Menzies ◽  
G. Bakkeren ◽  
F. Matheson ◽  
J. D. Procunier ◽  
S. Woods
Keyword(s):  
Fragment Length ◽  
Simple Sequence Repeats ◽  
Genetic Relationships ◽  
Molecular Techniques ◽  
Smut Fungi ◽  
Inter Simple Sequence Repeats ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Dna Profiles ◽  
Simple Sequence

In the smut fungi, few features are available for use as taxonomic criteria (spore size, shape, morphology, germination type, and host range). DNA-based molecular techniques are useful in expanding the traits considered in determining relationships among these fungi. We examined the phylogenetic relationships among seven species of Ustilago (U. avenae, U. bullata, U. hordei, U. kolleri, U. nigra, U. nuda, and U. tritici) using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs) to compare their DNA profiles. Fifty-four isolates of different Ustilago spp. were analyzed using ISSR primers, and 16 isolates of Ustilago were studied using AFLP primers. The variability among isolates within species was low for all species except U. bullata. The isolates of U. bullata, U. nuda, and U. tritici were well separated and our data supports their speciation. U. avenae and U. kolleri isolates did not separate from each other and there was little variability between these species. U. hordei and U. nigra isolates also showed little variability between species, but the isolates from each species grouped together. Our data suggest that U. avenae and U. kolleri are monophyletic and should be considered one species, as should U. hordei and U. nigra.

scholarly journals Potato variety identification by molecular markers based on retrotransposon analyses

2009 ◽  
Vol 45 (No. 1) ◽  
pp. 1-10 ◽  
Author(s):  
A. Nováková ◽  
K. Šimáčková ◽  
J. Bárta ◽  
V. Čurn
Keyword(s):  
Molecular Markers ◽  
Solanum Tuberosum ◽  
Potato Variety ◽  
Fragment Length ◽  
Solanum Tuberosum L ◽  
Variety Identification ◽  
Large Sets ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Simple Sequence

We analyzed a set of twenty most grown potato (Solanum tuberosum L.) varieties listed in the Czech Variety List using the PCR-IRAP (Inter-Retrotransposon Amplified Polymorphism) method in order to distinguish fast and unambiguously the varieties. In total, 62 polymorphic alleles were amplified using the three primers P-Tst-1, P-Tst-3 and P-Tst-6. The recorded pattern of markers was stable and reproducible. The analyses were repeated three times and identical results were always obtained. The level of polymorphism varied from 11% to 79% depending on the respective primer. All analysed varieties could be reliably distinguished after multivariate statistics have been applied to the data obtained by the PCO and UPGMA analyses. The best resolution of individual varieties was obtained if all three primers were evaluated as a complex. The use of retrotransposon-based markers appears to be suitable for the differentiation of large sets of potato samples and should be an eligible complement to other molecular markers used in potato variety identification such as Simple Sequence Repeats (SSR) and Amplified Fragment Length Polymorphisms (AFLP).

scholarly journals (5) A Comparative Study of SRAP, AFLP, and SSR Markers for Detecting Genetic Differences among Elite Broccoli Inbreds

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 998E-999
Author(s):  
Anna Hale ◽  
Mark W. Farnham
Keyword(s):  
Fragment Length ◽  
Genomic Dna ◽  
Cost Effective ◽  
Diverse Group ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Private And Public ◽  
Improvement Programs ◽  
Simple Sequence ◽  
Similarity Matrices

Private and public vegetable breeders are interested in using current and emerging PCR-based marker systems in their respective improvement programs. However, before new systems are employed to replace existing ones, the new systems must prove to be efficient and cost-effective alternatives. Sequence related amplified polymorphisms (SRAPs), amplified fragment length polymorphisms (AFLPs), and simple sequence repeats (SSRs) were compared for their ability to differentiate individuals of a diverse group of 24 elite broccoli (Brassica oleracea L. italica) inbreds. Genomic DNA was assayed using 24 AFLP, 24 SRAP, and 44 SSR primer pairs. In this assessment, SSRs produced an average of only two bands per primer, with 25% of these bands being monomorphic, and the remaining bands detecting very few differences among the inbreds. Although the AFLP method resulted in a lower rate (63%) of polymorphism than the SSRs, it produced about 20 bands per primer. SRAPs produced an average of 14 bands per primer, with 82% of these bands being polymorphic. Since AFLP and SRAP markers had a higher multiplex ratio and SSRs were frequently monomorphic, AFLP and SRAPs were more effective in differentiating the elite broccoli inbreds examined in this study. Similarity matrices were generated from the AFLP and SRAP data, and resulting dendographs were compared.

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