Reproducibility Testing of SSRs by a Network of European Laboratories

Jones, C. J.; Edwards, K. J.; Wiel, C. Van der; Vosman, B. L.; Matthes, M.; Daly, A.; Bettini, P.; Buiatti, M.; Maestri, E.; Marmiroli, N.; Rueda, J.; Vazquez, A.; Karp, A.

doi:10.1007/978-94-009-0019-6_42

Cited by 107 publications

(114 citation statements)

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“…The lower similarities obtained by the RAPD compared to ISSR markers were also observed by Korbin et al (2002), who reached the conclusion that six times more RAPD marker primers were necessary to reach values similar to those obtained by the ISSR markers. This fact was related to the low repeatability of the RAPD markers caused by its elevated sensitivity to experimental conditions (Jones et al, 1997), which can be considered the main limiting factor of the technique.…”

Section: Resultsmentioning

confidence: 99%

Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers

Morales

Resende

Faria

et al. 2011

Sci. agric. (Piracicaba, Braz.)

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Most strawberry (Fragaria × ananassa Duchesne) cultivars used in Brazil are developed in other countries, it became clear the need to start the strawberry breeding program in the country. To start a breeding program is necessary the genetic characterization of the germplasm available. Molecular markers are important tools that can be used for this purpose. The objectives of the present study were to assess the genetic similarity among 11 strawberry cultivars using RAPD and ISSR molecular markers and to indicate the possible promising crosses. The DNA of the eleven strawberry cultivars was extracted and amplified by PCR with RAPD and ISSR primers. The DNA fragments were separated in agarose gel for the RAPD markers and in polyacrylamide gel for the ISSR markers. The genetic similarity matrix was estimated by the Jaccard coefficient. Based on this matrix, the cultivars were grouped using the UPGMA method. The dendogram generated by the RAPD markers distributed the cultivars in three groups while the ISSR markers generated two groups. There was no direct relationship between the marker groups when the two types of markers were compared. The grouping proposed by the ISSR markers was more coherent with the origin and the genealogy of the cultivars than that proposed by the RAPD markers, and it can be considered the most efficient method for the study of genetic divergence in strawberry. The most promising crosses, based on the genetic divergence estimated from the RAPD and ISSR molecular data were between the Tudla and Ventana and the Oso Grande and Ventana cultivars, respectively.

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Section: Resultsmentioning

confidence: 99%

Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers

Morales

Resende

Faria

et al. 2011

Sci. agric. (Piracicaba, Braz.)

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“…The main limitation of the sequence markers is their limited variation. We applied AFLP as an alternative, because AFLP generates polymorphic markers at a high frequency, has a high reproducibility, and has genome wide sampling and its markers are not under direct selection pressure (Jones et al 1997;McGregor et al 2000;Russell et al 1997).…”

Section: Aflp Markers For Phylogenymentioning

confidence: 99%

“…AFLP is a DNAfingerprinting technique that generates large numbers of highly reproducible fragment markers with a genome-wide distribution. The technique is relatively fast and cost efficient and requires no prior knowledge of the genome (Jones et al 1997;McGregor et al 2000;Russell et al 1997;Vos et al 1995). Relative to morphological markers, AFLPs have the advantage that they are not under direct selection pressure, since most of the fragments represent noncoding parts of the genome (Vos et al 1995).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers

Schenk¹,

Thienpont

Koopman³

et al. 2008

Tree Genetics & Genomes

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The genus Betula comprises various species in boreal and temperate climate zones of the Northern Hemisphere. The taxonomy of Betula is controversial and complicated by parallel evolution of morphological traits, polyploidization events, and extensive hybridization and introgression among species. Multilocus molecular data from AFLPs were used to provide phylogenetic information. A large number of polymorphic markers (321 variable bands) were produced in 107 Betula accessions from 23 species and 11 hybrids. The AFLP results were largely congruent with the results from previously examined nuclear DNA markers. Four distinct subgenera were identified within the genus Betula. These subgenera were partly in disagreement with the traditional (but disputed) division of the genus. In addition, the results indicated several groups of conspecific taxa. The majority of the species fell within subgenus Betula and shared a high degree of similarity with B. pendula. All hybrids were associated with this group, and the AFLP data contained signals on putative parents for some of the interspecific hybrids. Subgenus Chamaebetula and part of the Neurobetula species should be merged with Betula. The subgenera Betulenta, Betulaster, and the remaining part of Neurobetula are distinct and well supported. Although our results indicate that four major taxonomic groups can be recognized within the genus Betula, the relationship between them remains unclear. This may be due to the occurrence of hybridization and introgression, which would have a homogenizing effect on the relationships between species. Naturally occurring Betula species of hybrid origin may explain the low bootstrap values within the Betula clade.

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“…For the present study, microsatellite markers were chosen due to their applicability in earlier studies of hybridization (Muir et al, 2000;Beaumont et al, 2001;Coart et al, 2003), codominance, and ease of interpretation in studies of population differentiation (Balloux and Lugon-Moulin, 2002), high level of diversity, and reproducibility allowing for future comparisons of European data (Jones et al, 1997). Potentially, homoplasy can pose a problem in delineating the relationship between taxonomic units (Goldstein & Pollock, 1997).…”

Section: Introductionmentioning

confidence: 99%

Hybridization and genetic variation in Danish populations of European crab apple (Malus sylvestris)

Larsen

Asmussen²,

Coart³

et al. 2006

Tree Genetics & Genomes

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The aim of the present study was to investigate the genetic variation in Danish populations of the endangered European crab apple (Malus sylvestris). Special emphasis was given to hybridization between the wild species and its cultivated relative Malus ×domestica. A total of 178 wild individuals from four Danish populations were studied along with a reference sample of 29 old cultivars. The genetic variation within and among samples was studied at ten microsatellite marker loci. Additionally, a morphological analysis was carried out to identify hybrids and test for correspondence between phenotypic and genotypic indices of hybridization.From application of ordination and a model based cluster analysis to the molecular data, two clusters were identified consisting of wild and cultivated individuals respectively. This indicates that pronounced admixture between the two species is not present. At the population level, a high correspondence was found between geographic isolation from M. ×domestica and genotypic and morphological indices of hybridization. As expected, isolated populations appeared less affected by hybridization than poorly isolated populations. Isolated 'pure' M. sylvestris populations could thus be identified. However, morphological and molecular evidence of hybridization was found to be divergent at the individual level. This is suggestive of some historical introgression into the M. sylvestris gene pool, and indicates that relying exclusively on either morphological or molecular characters as diagnostic markers in studies of hybridization between M. ×domestica and M. sylvestris might lead to fallible results. Combined application of genetic and morphological markers is therefore recommended.3

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Reproducibility Testing of SSRs by a Network of European Laboratories

Cited by 107 publications

References 0 publications

Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers

Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers

Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers

Hybridization and genetic variation in Danish populations of European crab apple (Malus sylvestris)

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