Redundancies and Genetic Structure among ex situ Apple Collections in Norway Examined with Microsatellite Markers

Gaši, Fuad; Kanlic, K.; Stroil, Belma Kalamujić; Pojskić, Naris; Asdal, Åsmund; Rasmussen, Morten; Kaiser, C.; Meland, Mekjell

doi:10.21273/hortsci11212-16

Cited by 18 publications

(37 citation statements)

References 16 publications

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“…Despite current advances in genome sequencing, microsatellite markers or simple sequence repeats (SSR) that have been converted into a DNA marker are still successfully used worldwide for routine genotyping in many crops, and for protection of ancient autochthonous olive trees in Italy (Rotondi et al 2018), evaluation of genetic redundancy in ex situ apple collections in Norway (Gasi et al 2016), evaluation of genetic structure in subspecies of black cherry from North America (Guzmán et al 2018), estimation of natural outcrossing rate and genetic diversity in Lima bean landraces from Brazil (Penha et al 2017), and in the analysis of the genetic diversity of rice cultivars in India (Dhama et al 2018). This molecular technique is also ideal for designing conservation strategies for genetic resources, and for forming and validating core collections (Porta et al 2018;de Vicente et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Microsatellites to enhance characterization, conservation and breeding value of Capsicum germplasm

Guzmán¹,

Moore

Vicente

et al. 2019

Genet Resour Crop Evol

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Capsicum species are of great economic, medicinal, culinary and cultural value worldwide, however their genetic potential is still underutilized. In this study, a set of 21 microsatellite markers showed utility for distinguishing a diverse group of 42 Capsicum genotypes representing 11 species. The level of polymorphism among these genotypes was evaluated by calculating the polymorphic information content (PIC) and discriminating power (D) for each locus. A total of 208 alleles were detected at the 21 loci evaluated. Markers detecting the highest number of alleles also exhibited the highest number of rare alleles. PIC values and D estimations showed a significant positive correlation (r = 0.98; P \ 0.0000). PIC values ranged between 0.500 (marker NG20) and 0.899 (marker NG17), giving an average of 0.775. Genetic relationships among genotypes were evaluated using UPGMA clustering, Principal Coordinate Analysis (PCoA) and Bayesian model-based clustering, allowing genotypes to be discriminated into groups according to their degree of genetic similarity corresponding to distinct taxa. Based on these analyses, the 21 microsatellite included in this study now define a standard tool for efficient assessment of molecular variability of Capsicum germplasm collections conserved worldwide.

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Section: Introductionmentioning

confidence: 99%

Microsatellites to enhance characterization, conservation and breeding value of Capsicum germplasm

Guzmán¹,

Moore

Vicente

et al. 2019

Genet Resour Crop Evol

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“…The experiences from our laboratory were similar. When commercial kits were ineffective, the original Soltis Lab method was successfully used for DNA extraction in the analysis of European chestnut and apple (Skender et al, 2017;Gaši et al, 2016), while protocol described by Padmalatha et al (2008) enabled isolation of high-quality genomic DNA from five endemic plant species of Lamiaceae family (Lasić et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

The Applicability of Three DNA Isolation Methods in SSR Analysis of Hexaploid Plum (Prunus domestica L.) Cultivars

Hanjalić

Lasić

Gaši

et al. 2018

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The main goal of any DNA extraction procedure is to ensure reliable and reproducible results in a simple, fast and inexpensive manner. When it comes to plant tissues, this goal is challenging to achieve due to the presence of a variety of metabolites that interfere with DNA during isolation and downstream analysis. In this study, we compared the efficiency of three methods for DNA extraction from plum kernels: 1) the standard CTAB Soltis method which is the most common protocol for DNA extraction from various plant tissues (seeds, young leafs, mature leafs, root); 2) CTAB-based method originally described for DNA isolation from medicinal plants with high levels of secondary metabolites; 3) and one of various commercially available kits. The usefulness of the obtained DNA was evaluated by SSR analysis with seven microsatellite markers. Although the latter two extraction protocols retrieved genomic DNA that gave positive PCR results, only DNA isolated by kit produced full SSR profile

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“…Multilocus microsatellite analysis has become a standard tool for the assessment of genetic variability and the identification of duplicate accessions in order to contribute to a more efficient management of germplasm collections (e.g. Guarino et al 2006;Pereira-Lorenzo et al 2007;Routson et al 2009;van Treuren et al 2010;Garkava-Gustavsson et al 2013;Ferreira et al 2016;Gasi et al 2016;Urrestarazu et al 2016;Larsen et al 2017;Testolin et al 2019). Furthermore, molecular data can provide a complementary or alternative means for the determination of apple cultivars based on phenotypic traits.…”

Section: Discussionmentioning

confidence: 99%

“…The most commonly applied technique is the analysis of simple sequence repeats (SSRs) or microsatellite markers, which, due to their robustness, reproducibility and high-throughput potential, have been employed to describe the genetic resources of apple in many countries (e.g. Guarino et al 2006;Pereira-Lorenzo et al 2007;Routson et al 2009;van Treuren et al 2010;Garkava-Gustavsson et al 2013;Ferreira et al 2016;Gasi et al 2016;Urrestarazu et al 2016;Larsen et al 2017;Testolin et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Molecular Genetic Identification of Apple Cultivars Based on Microsatellite DNA Analysis. I. The Database of 600 Validated Profiles

et al. 2020

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Apple (Malus × domestica Borkh.) is the most widely grown permanent fruit crop of temperate climates. Although commercial apple growing is based on a small number of globally spread cultivars, its diversity is much larger and there are estimates about the existence of more than 10,000 documented varieties. The varietal diversity can be described and determined based on phenotypic characters of the external and internal traits of fruit, which, however, can be modulated by environmental factors. Consequently, molecular methods have become an important alternative means for the characterisation of apple cultivar diversity. In order to use multilocus microsatellite data for determination of unidentified or misidentified apple varieties, a database with molecular genetic fingerprints of well-determined reference cultivars needs to be available. The objective of the present work was to establish such a database that could be applied for the molecular genetic determination of a large number of historic and modern, diploid and triploid apple cultivars. Based on the analysis of more than 1600 accessions of apple trees sampled in 37 public and private cultivar collections in different European countries at 14 variable microsatellite loci, a database with 600 molecular genetic profiles was finally obtained. The key criterion for considering a molecular genetic profile as confirmed and for including it into the reference database was that at least two accessions of the same cultivar of different provenances generated an identical result, which was achieved for 98% of the apple cultivars present in the database. For the remaining genotypes, the cultivar assignment was supported by a parentage analysis or by comparison to molecular genetic profiles available in published works. The database is composed of 574 scion cultivars, 24 rootstock genotypes and two species of crab apples. Of the 574 scion cultivars, 61% were derived from historic or old cultivars, many of which were grown in Central Europe in the past. The remaining scion cultivars are currently grown or available in testing programmes and may gain importance in the future. In order to validate the genotyping data, parentage analysis was performed involving cultivars and rootstocks that arose after 1900, for which information about at least one parent cultivar was available from pomological and scientific literature and the molecular genetic profiles of the assumed parent(s) were also present in our database. This analysis revealed the presence of null alleles at locus COL, however, when excluding this locus, a mean genotyping error rate of only 0.28% per locus was revealed, which points to a high reliability of the dataset. The datasets with 14 and 13 loci (excluding locus COL) showed a high degree of discrimination power, with a combined non-exclusion probability of identity of 2.6 × 10 -20 and 3.4 × 10 -19 . Five of the microsatellite loci analysed in the present study overlapped with another published dataset and after the application of conversion values, it was p...

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Redundancies and Genetic Structure among ex situ Apple Collections in Norway Examined with Microsatellite Markers

Cited by 18 publications

References 16 publications

Microsatellites to enhance characterization, conservation and breeding value of Capsicum germplasm

Microsatellites to enhance characterization, conservation and breeding value of Capsicum germplasm

The Applicability of Three DNA Isolation Methods in SSR Analysis of Hexaploid Plum (Prunus domestica L.) Cultivars

Molecular Genetic Identification of Apple Cultivars Based on Microsatellite DNA Analysis. I. The Database of 600 Validated Profiles

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