Identification of Raspberry Cultivars by Sequence Characterized Amplified Region DNA Analysis

Parent, Jean-Guy; Pagé, Danièle

doi:10.21273/hortsci.33.1.140

Cited by 21 publications

(10 citation statements)

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“…These markers were described as potentially codominant. Amplification of several closely sized bands (Type 3 failure) was described for raspberry (Rubus idaeus L. and R. idaeus x R. occidentalis L.) (Parent and Page, 1998) and strawberry (Fragaria L. sp.)…”

Section: Discussionmentioning

confidence: 99%

“…Thus, two multiplex reactions were developed that included either four or five primer sets that adequately and reliably separated the cultivars examined. Problems associated with multiplexing have been described by several groups (Amicucci et al, 2000;Henegariu et al, 1997;Parent and Page, 1998). Multiplexing, however, was considered to be critical to our purposes since one goal was to reduce the number of reactions required which would adequately discriminate common cranberry cultivars.…”

Section: Discussionmentioning

confidence: 99%

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Development of SCAR Markers for DNA Fingerprinting and Germplasm Analysis of American Cranberry

Polashock¹,

Vorsa²

2002

jashs

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DNA fingerprinting has been useful for genotypic classification of American cranberry (Vaccinium macrocarpon Ait.). Polymerase chain reaction (PCR) based methodologies including randomly amplified polymorphic DNA (RAPD) markers are relatively easy to use, and inexpensive as compared to other methods. However, RAPD markers have some limitations including seamless interlaboratory transferability and susceptibility to certain types of error. An alternative method, sequence characterized amplified regions (SCARs), was developed for cranberry germplasm analysis. Nine primer sets were designed from RAPD-identified polymorphic markers for use in two multiplex PCR reactions. These primer sets generated 38 markers across a cranberry germplasm collection. Estimates of genetic relatedness deduced from employment of the RAPD and SCAR methods were compared among 27 randomly chosen cranberry germplasm accessions. Although both methods produced comparable results above 0.90 coefficient of similarity, branches below this level exhibited variation in clustering. SCAR and RAPD markers can be employed for identifying closely related genotypes. However, the inferences of more distant genetic relationships are less certain. SCAR marker reactions provided more polymorphic markers on a per reaction basis than RAPD marker reactions and as such more readily separated closely related progeny. When SCAR primers were fluorescent dye-labeled for computerized detection and data collection, reduced marker intensity relative to unlabeled reactions was one problem encountered.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Development of SCAR Markers for DNA Fingerprinting and Germplasm Analysis of American Cranberry

Polashock¹,

Vorsa²

2002

jashs

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“…In addition, it is possible to construct very high density DNA marker maps for application in genome research and positional cloning of genes through this method (Monte-Corvo et al, 2000;Russel et al, 1997). Studies on the genetic diversity of Rubus species have been carried out, including species such as R. idaeus (Parent and Fortin 1993, Graham and Mcnicol, 1995, Graham et al 1997 and R. occidentalis (Parent and Page, 1998), as well as Asian species (Amsellem et al 2000). These studies employed AFLP, RAPD (Random Amplified Polymorphic DNA), RFLP (Restriction Fragment Length polymorphism), and SCAR (Sequence Characterized Amplified Region) markers, as well as SSR (Amsellem et al, 2000;Parent and Fortin, 1993, Graham and Mcnicol, 1995, Graham et al 1997Parent and Page, 1998).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Relationship Assessment based on AFLP Analysis in Blackberry (Rubus fructicosus L.) Mutant Lines

Ryu

Kim

et al. 2014

Plant Breed. Biotech.

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This study was carried out to evaluate the genetic diversity and relationships among fifty-six blackberry (Rubus fructicosus) mutants derived from gamma-ray treatment (fifty-two lines) by analysis of Amplified fragment length polymorphism (AFLP) markers. Both cluster analysis and principal coordinate analysis (PCOORDA) were conducted in order to study the genetic diversity, using both morphological traits and AFLP makers. A total of 589 bands were amplified with an average of 58.9 bands per primer. Among them, 560 were identified to be polymorphic, with a rate of 95.08%. A showed a highly significant (P≤0.01) positive correlation with GD and PIC (r 2 =0.999). MI also showed a significant (P≤0.05) positive correlation with GD and PIC. According to the clustering analysis, all mutant lines could be classified into five categories, but the three gamma-ray treatment lines and the cross-bred line were not clustered into any groups. For the morphological traits, cluster analysis divided the blackberry germplasm into six clusters and two independent groups. In addition, the morphological dendrogram indicated an unclear pattern of division among the groups based on AFLP analysis. The findings of this study indicate that mutant lines have high genetic diversity, and can be effectively utilized as materials for the improvement of breeding.

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“…The RAPD is a useful and powerful technique for various polymorphism analyses including genetic diversity, identification of cultivars and phylogenetic analysis of many plant species [Khanuja et al 2000, Besnard et al 2001, Lisek and Rozpara 2010, Okoń et al 2014, Gawroński et al 2017. Some studies using RAPD markers in Rubus have also been reported [Parent et al 1993, Graham et al 1994, Graham and McNicol 1995, Graham et al 1997, Parent and Page 1998, Antonius-Klemola 1999, Badjakov et al 2006, Stafne et al 2003, Patamsyte et al 2010, Umar et al 2010. SSR loci are highly polymorphic co-dominant markers also useful for studying the genetic diversity and genetic fingerprinting of many species.…”

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confidence: 99%

Assessment of Genetic Variability Among Raspberry Accessions Using Molecular Markers

Simlat¹,

Ptak²,

Kula³

et al. 2018

Acta Sci.Pol.Hortorum Cultus

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In this study, random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) loci were used to investigate the genetic relationships in a group of 22 raspberry accessions. Fifteen RAPD primers generated a total of 324 bands, among them 94.1% were polymorphic. From ten used SSR pairs of primers, nine generated only polymorphic bands and the average percentage of polymorphism was 97.8%. Genetic similarity indices calculated on the basis of RAPD and SSR data indicated a wide range of genetic variability of the analyzed raspberry collection. Cluster analysis by UPGMA (Unweighted Pair-Group Method with Arithmetic averaging) and PCA (Principal Component Analysis) clearly delineated the genetic relationships among all the accessions. The highest genetic similarity, determined on the basis of RAPD and SSR markers, was found between two Polish cultivars-'Polesie' and 'Polesie Żółte', whilst 'Jewel' from USA, belonging to Rubus occidentalis, was found to be the cultivar that varied most from all the accessions. The obtained results confirmed the usability of RAPD and SSR markers for discriminating among closely related raspberries and for determining the genetic variability among cultivars. It might be helpful for breeders to plan their breeding strategy.

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Identification of Raspberry Cultivars by Sequence Characterized Amplified Region DNA Analysis

Cited by 21 publications

References 0 publications

Development of SCAR Markers for DNA Fingerprinting and Germplasm Analysis of American Cranberry

Development of SCAR Markers for DNA Fingerprinting and Germplasm Analysis of American Cranberry

Genetic Diversity and Relationship Assessment based on AFLP Analysis in Blackberry (Rubus fructicosus L.) Mutant Lines

Assessment of Genetic Variability Among Raspberry Accessions Using Molecular Markers

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