Reproducibility Testing of AFLPs by a Network of European Laboratories

Jones, C. J.; Edwards, Keith J.; Castaglione, S.; Winfield, M. O.; Sala, F.; Wiel, C. Van der; Vosman, B.; Matthes, M.; Daly, A.; Brettschneider, R.; Maestri, Elena; Marmiroli, Nelson; Aert, R.; Volckaert, G.; Karp, A.

doi:10.1007/978-94-009-0019-6_37

Cited by 119 publications

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“…Because one of the main problems of the traditional interspecies taxonomic research of black pine was how to supply sufficient comparative materials from the whole range (Vidakoviae 1991), and because it is not possible to exchange RAPD results among laboratories (Jones et al 1997), at the beginning of this research we tried to join two things which at the first sight seem to be incompatible: the sample from the whole range of black pine (Fig. 1) and the RAPD research restricted to just one laboratory.…”

Section: Discussionmentioning

confidence: 99%

RAPD markers and black pine (Pinus nigra Arnold) intraspecies taxonomy - Evidence from the study of nine populations

et al. 2011

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Although intraspecies researches within the black pine (Pinus nigra Arnold) have a long tradition, the intraspecies taxonomy, classification and chorology are still unclear. Among the numerous reasons that have caused this situation the most important are: the absence of a study that would completely cover the whole range of this species, the impossibility of connection of results of the existing detailed studies of certain areas, and the high variability of traits which have been used so far. Since the characteristics of the molecular systematic techniques could make possible the research free of the mentioned shortages, the intention of this study was to determine the relationships among nine populations of black pine using the random amplified polymorphic DNA (RAPD). The obtained results were compared to the recent results of the morphological and anatomical analysis of the leaves of the same populations. The RAPD results clearly divided the Croatian populations from populations of Austria (subsp. nigra) and Turkey (subsp. pallasiana), while among Croatian populations, as in previous study, the existence of several groups (subsp. illyrica, subsp. dalmatica and transitional population between them) was noticed. It is assumed that the optimisations conducted in this study will finally make possible estimating the relationships on the level of the whole range of the black pine and the classification based on molecular traits that are probably less dependent on environmental influences than it has been the case with the characteristics mostly used so far.

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Section: Discussionmentioning

confidence: 99%

RAPD markers and black pine (Pinus nigra Arnold) intraspecies taxonomy - Evidence from the study of nine populations

et al. 2011

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“…Several studies comparing different molecular techniques have highlighted the key qualities of the AFLP technique, which are a high multiplex ratio (number of polymorphic markers generated in a single PCR experiment) and high reproducibility (Powell et al . 1996; Jones et al . 1998; Pejic et al .…”

Section: Introductionmentioning

confidence: 99%

Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size

et al. 2002

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We investigate the distribution of sizes of fragments obtained from the amplified fragment length polymorphism (AFLP) marker technique. We find that empirical distributions obtained in two plant species, Phaseolus lunatus and Lolium perenne, are consistent with the expected distributions obtained from analytical theory and from numerical simulations. Our results indicate that the size distribution is strongly asymmetrical, with a much higher proportion of small than large fragments, that it is not influenced by the number of selective nucleotides nor by genome size but that it may vary with genome-wide GC-content, with a higher proportion of small fragments in cases of lower GC-content when considering the standard AFLP protocol with the enzyme MseI. Results from population samples of the two plant species show that there is a negative relationship between AFLP fragment size and fragment population frequency. Monte Carlo simulations reveal that size homoplasy, arising from pulling together nonhomologous fragments of the same size, generates patterns similar to those observed in P. lunatus and L. perenne because of the asymmetry of the size distribution. We discuss the implications of these results in the context of estimating genetic diversity with AFLP markers.

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“…The AFLP genotyping technique was chosen because of its high multiplex ratio (number of polymorphic markers generated in a single PCR experiment), high reproducibility (Jones et al 1998, Pejic et al 1998, and because of the lack of publicly available codominant markers (nuclear RFLP, SSR or SNP) in this species. AFLP markers were therefore used to assess: (1) the genetic structure within and among varieties in the industrial chicory type; (2) the population genetic structure of C. intybus in the wild in Belgium; and (3) the genetic variation between cultivated and wild varieties.…”

Section: Introductionmentioning

confidence: 99%

Distinction between cultivated and wild chicory gene pools using AFLP markers

et al. 2003

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The cultivation area of industrial chicory, Cichorium intybus L. cv Sativum, coincides with the natural distribution area of its wild relative, C. intybus L., which could lead to gene flow between wild and cultivated types. The genetic diversity within and between the two types has therefore been studied using AFLP genotyping of samples from 12 wild populations collected in Belgium and ten commercial varieties. The genotyping of 233 individuals allowed the identification of 254 AFLP markers. Similar levels of genetic diversity were observed within wild populations and cultivated varieties, suggesting the absence of any strong bottleneck in the history of the cultivated types. The phylogenetic analysis pointed to a monophyletic origin of cultivated varieties as compared to the local wild populations studied, hence the two types of chicory form two separate gene pools. The genotyping of some individuals sampled in ruderal sites clearly showed that they belong to the cultivated gene pool, which suggests the existence of feral or weedy types. The low differentiation observed among wild populations indicates that gene flow might be important in this species.

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Reproducibility Testing of AFLPs by a Network of European Laboratories

Cited by 119 publications

References 0 publications

RAPD markers and black pine (Pinus nigra Arnold) intraspecies taxonomy - Evidence from the study of nine populations

RAPD markers and black pine (Pinus nigra Arnold) intraspecies taxonomy - Evidence from the study of nine populations

Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size

Distinction between cultivated and wild chicory gene pools using AFLP markers

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