Genetic diversity of Opuntia spp. varieties assessed by classical marker tools (RAPD and ISSR)

Valadez-Moctezuma, Ernestina; Samah, Samir; Luna-Paez, Arturo

doi:10.1007/s00606-014-1112-y

Cited by 27 publications

(22 citation statements)

References 38 publications

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“…For these reasons, many studies have suggested revising the classification of the Opuntia genus (Helsen et al, 2009;Caruso et al, 2010;Valadez-Moctezuma et al, 2015). It should be noted that many of the genotypes considered in this study have not yet been taxonomically assigned; however, several hypotheses can be proposed for the non-divergent accessions identified here.…”

Section: Discussionmentioning

confidence: 92%

“…Some Opuntia accessions were classified in delimited species but others had no specific assignation (S1 Table). Total genomic DNA was extracted using the CTAB protocol according to Valadez-Moctezuma et al (2015). DNA quantification was estimated by spectrophotometry (Thermo Scientific NanoDrop TM 1000, Wilmington, DE, USA), and DNA quality was determined on 1% agarose gel.…”

Section: Plant Materials and Dna Extractionmentioning

confidence: 99%

“…The continuous morphological variations in the genus, the synonyms, and the insufficient and inadequate morphological descriptors have all led to misclassifications (Labra et al, 2003;Caruso et al, 2010;Valadez-Moctezuma et al, 2015). Moreover, species limits are still poorly understood because of the high frequency of polyploid taxa.…”

Section: Introductionmentioning

confidence: 99%

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Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis

Samah

Valadez-Moctezuma

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc. We obtained 5850 bp from the seven regions, and 136 fragments were detected with eight enzymes, 37 of which (27.2%) were polymorphic. We found that 40% of the fragments from the chloroplast regions were polymorphic, 9.8% of the bands detected in the nuclear genes were polymorphic, and 20% of the bands in the mitochondrial locus were polymorphic. trnL-trnF and psbA-trnH were the most variable regions. The Nei and Li/Dice distance was very short, and ranged from 0 to 0.12; indeed, 77 of the 103 genotypes had the same genetic profile. All the xoconostle accessions (acidic fruits) were grouped together without being separated from three genotypes of prickly pear (sweet fruits). We assume that the genetic divergence between prickly pears and xoconostles is very low, and question the number of Opuntia species currently considered in Mexico.

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Section: Discussionmentioning

confidence: 92%

Section: Plant Materials and Dna Extractionmentioning

confidence: 99%

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Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis

Samah

Valadez-Moctezuma

et al. 2016

Genet. Mol. Res.

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“…Genomic DNA was extracted from young leaves (200 mg) using a slightly modified cetyltrimethylammonium bromide method (Saghai-Maroof et al, 1984). Genetic markers were developed using random-amplified polymorphic DNA (RAPD) and the inter simple sequence repeat (ISSR) (with anchor) techniques, both of which scan the whole genomes (Fontaine et al, 2004;Valadez-Moctezuma et al, 2014;Valadez-Moctezuma et al, 2015). Polymerase chain reaction (PCR) for RAPD comprised of 100 ng genomic DNA, 1.5 U Taq DNA polymerase (Fermentas, USA), 200 mM dNTPs, 1X Taq buffer, 2.0 mM MgCl 2 , and pM primer in a 25-µL total volume.…”

Section: Development Of Molecular Markersmentioning

confidence: 99%

“…DNA markers have been used successfully to discern genealogies, design breeding strategies, and support systematization and conservation in germplasm banks (Zietkiewicz et al, 1994;Gilbert et al, 1999;Valadez-Moctezuma et al, 2014;Valadez-Moctezuma et al, 2015). Using these tools, races of P. americana and some hybrids have been distinguished (Davis et al, 1998;Clegg et al, 1999;Ashworth and Clegg, 2003).…”

Section: Introductionmentioning

confidence: 99%

Assessment of genetic relationship in Persea spp by traditional molecular markers

Valadez-Moctezuma

Barrientos-Priego

2016

Genet. Mol. Res.

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Currently, the reclassification of the genus Persea is under discussion with molecular techniques for DNA analysis representing an alternative for inter- and intra-specific differentiation. In the present study, the traditional random-amplified polymorphic DNA (RAPD) and the inter simple sequence repeat (ISSR) markers were used to determine the genomic relationship of different species and hybrids representative of the subgenera Eriodaphne and Persea in a population conserved in a germplasm bank. The data were analyzed statistically using multivariate methods. In the RAPD analysis, a total of 190 polymorphic bands were produced, with an average of 23.7 bands per primer, the percentage contribution of each primer was from 7.66 to 19.63; the polymorphic information content (PIC) ranged from 0.23 to 0.45, with an average of 0.35. In the ISSR analysis, a total of 111 polymorphic bands were considered, with an average of 18.5 bands per primer, the percentage contribution of each was from 11.83 to 19.57; the PIC ranged from 0.35 to 0.48, with an average of 0.42. The phenograms obtained in each technique showed the relationship among the accessions through the clusters formed. In general, both the techniques grouped representatives of the Persea americana races (P. americana var. drymifolia, P. americana var. guatemalensis, and P. americana var. americana). However, it was not possible to separate the species of Persea used as reference into independent clades. In addition, they tended to separate the representatives of subgenera Eriodaphne and Persea.

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Cactus Pear (Opuntia spp.) Species and Cultivars

Mazri

2021

Opuntia Spp.: Chemistry, Bioactivity and Industrial Applications

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Genetic diversity of Opuntia spp. varieties assessed by classical marker tools (RAPD and ISSR)

Cited by 27 publications

References 38 publications

Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis

Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis

Assessment of genetic relationship in Persea spp by traditional molecular markers

Cactus Pear (Opuntia spp.) Species and Cultivars

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