Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations

Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, M.; Espinosa, Francisco

doi:10.1371/journal.pone.0152972

Cited by 78 publications

(68 citation statements)

References 34 publications

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“…These discrepancies in the GS revealed by the different marker types could be attributed to the different mechanism of detecting the polymorphism and genome coverage by the different markers .Therefore, the GS based on the combined data could be more representative of the genetic relationships. Such findings were previously reported by Qian et al (2001), McGregor et al (2000), Belaj et al (2003) and Costa et al (2016).…”

Section: Genetic Relationships Among Olive Varietiessupporting

confidence: 88%

“…This may suggest that these markers targeted different genomic areas however other areas were common. Therefore, the analysis of variability may require more than one DNAbased marker (Costa et al, 2016). Given that, our results support that AFLP-based (SASPL and SAMPL) markers had more relative efficiency than other marker systems , similar results were reported in SAMPL (Sarwat et al, 2008) and SSAP (Tam et al, 2005).…”

Section: Comparison Between the In Silico And In Vitro Pcr Analysis Rsupporting

confidence: 86%

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Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

Alsamman¹,

Adawy²,

Ibrahim³

et al. 2017

Plant Omics

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The Selective Amplification of Start Codon Polymorphic Loci (SASPL) has been developed as a new PCR-based molecular marker. SASPL was validated for the analysis of varietal diversity on ten olive varieties. Validation included in vitro comparison against RAPD, SCoT and SAMPL markers. Assessment of these techniques included primer selectivity, genome coverage and the ability to target genic regions through in silico PCR analysis. Candidate PCR fragments were further sequenced to annotate non-identified genes in olive. Eight SASPL primers were compared to 24 RAPD, 39 SCoT and 12 SAMPL primers. The TA produced by the RAPD, SCoT, SAMPL and the eight SASPL primers were 359, 642, 571 and 269 amplicons, respectively. The highest average number of TA was revealed by SAMPL (47.6), average of PA (18.1) and genetic similarity (GS) (96%) among the olive varieties. On the other hand, SASPL analysis provided higher average number of TA (33.6), average of PA (16.2) and GS (93%) than SCoT and RAPD. The highest average of (PIC) (0.2909) was exhibited by SASPL analysis and the lowest average (0.2038) was revealed by SCoT. The highest number of UB (111) was revealed by SCoT and the lowest UB (43) was obtained by SASPL. Across the four marker types, variety Maraki was characterized by the highest number of unique markers (74). Meanwhile, the variety Manzanillo was characterized by the lowest number of unique markers (8). In addition, in the in silico analysis SASPL exhibited the highest chromosomal coverage (0.59%) and targeted genes (1090) using the lowest number of primers. Additionally, the average area covered by the SASPL primers (354kb) was larger than SCoT and SAMPL. RAPD analysis provided the lowest potential, chromosomal coverage (0.04%) and number of targeted genes (17) compared to SASPL, SCoT and SAMPL analysis. The total coverage of the genome, revealed by combined data was higher (1.21%) than that of each technique separately. Meanwhile, the difference between the actual and the total genomic regions covered by the combined data was about 652kb. Our results suggested that the newly developed SASPL marker is the most adequately and each of the studied marker target different genomic areas, while some areas are shared. Two SCoT and one RAPD fragment were sequenced and showed a high similarity to genes of high physiological functions; such as cyclic plant-specific DNA-binding transcription factor, SANT domain and Copia-type retrotransposon.

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Section: Genetic Relationships Among Olive Varietiessupporting

confidence: 88%

Section: Comparison Between the In Silico And In Vitro Pcr Analysis Rsupporting

confidence: 86%

Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

Alsamman¹,

Adawy²,

Ibrahim³

et al. 2017

Plant Omics

View full text Add to dashboard Cite

show abstract

“…Simpler to use than SSR technique [18]. Molecular fingerprints of four different species of Curcuma amada, C.caesia, C.longa and C.zedoa [19].Similar results are also reported in three different DNA based technique such as RAPD, ISSR and AFLP were used for fingerprinting Dactylis glomerata genotype and for detecting genetic variation between the three subspecies [20]. Various species of genus Saccharina are economically important brown algae cultivated in China.…”

Section: Discussionmentioning

confidence: 54%

Intra Specific Analysis of Gloriosa Superba (L) Through Issr Finger Printing and Dna Sequencing of Ecotypes Collected From Different Accessions of Tamil Nadu State, India

Jasmine

Balakrishnan²

2018

RIPB

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Diversity within and among the population of Gloriosa superba collected from five different location of Tamil Nadu State, India, were explored by using Inter Simple Sequence Repeat (ISSR) DNA sequencing method. A total of 86.27% of polymorphic bands were seen in 94 reproducible bands generated from 12 number of ISSR primer ranging between 200bp to1000bp of band width. ISSR primer produces the bands with an average polymorphism of more than ninety nine percent among all the ecotypes. The dendrograms drawn for the analysis of genetic similarity in all the ecotypes. Our studies reveals that, genetic variations among different accessions of Gloriosa superba(L) was very well identified with the help of ISSR finger printings technic. KEYWORDS: Dendrogram, Gloriosa superba, accessions, ecotypes, genetic variationCopyright: © 2018 The authors. This article is open access and licensed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) which permits unrestricted, use, distribution and reproduction in any medium, or format for any purpose, even commercially provided the work is properly cited. Attribution -You must give appropriate credit, provide a link to the license, and indicate if changes were made.

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“…Because this issue, Velascoramirez et al, (2014) recommended that the information that is generated by various markers had a valuable capacity for genetic studies involving both, diversity and relationships. By this criterion, the combining different marker system was critically better for diversity study as recommended through numerous reports such as (Jhang et al, 2010; Wang et al, 2012;Amar and Abd El Wahab, 2013;Velascoramirez et al, 2014;Costa et al, 2016). In view of the performance of the combined tree and the principal components analysis (PCoA) (Fig 4 and 5), formed groups consistent with the cluster analysis.…”

Section: Discussionmentioning

confidence: 59%

Utilization of ISTR, ISSR and SRAP molecular markers to reveal and classify Egyptian pomegranates (Punica granatum L.)

Amar¹,

El-Zayat²

2017

Plant Omics

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This study offers the comprehensive analysis of the genetic diversity among six local varieties (Manfalouti; Nab El-Gamal; Hegazy; Wardi; Assuity; Araby) and three international varieties (Wonderful; Marked Bani Rafie; Red Bani Rafie) of pomegranate in Egypt, based on the behavior of ISTR, ISSR and SRAP markers profiles. A set of 24 ISTR, 16 ISSR and 30 SRAP primers combination were compared, concerning exposed the degree of resolution and efficiency of the discriminating capacity technique alongside with the level of genetic polymorphism, to determine which varieties evolved from the others. Considering the results, SRAP assay had superior, more sensitive, higher discrimination capacity and gives much more evidence about the total number of effective alleles (1411), number of polymorphic amplicons (312), PIC (0.94), assay efficiency index (47.04), effective multiples ratio (10.04) and marker index (9.74). Unexpectedly, the ISTR profile demonstrated a significant moderate level of polymorphism among tested genotypes. To further determine the genetic relationships and the distance among varieties, a graphic demonstration of combined UPGMA tree and the PCA analysis did assemble with clear resolution and accurate along with three categories.Our findings confirm that combining different marker system were greatly better and more effective considered an important priority step toward diversity study and characterization. We can point out that, the two-widespread varieties in Egypt Manfalouti, and Nab El-Gamal, formed a high homogeneity in genetic similarity with the Wonderful, as an essential global species for breeding programs, efforts widening the genetic base of pomegranates and the introduction of new genotypes in Egypt.

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Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations

Cited by 78 publications

References 34 publications

Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

Intra Specific Analysis of Gloriosa Superba (L) Through Issr Finger Printing and Dna Sequencing of Ecotypes Collected From Different Accessions of Tamil Nadu State, India

Utilization of ISTR, ISSR and SRAP molecular markers to reveal and classify Egyptian pomegranates (Punica granatum L.)

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