ArticleAnnals of botany2005
The effects of nuclear DNA content (C-value) on the quality and utility of AFLP fingerprints.
Article in Annals of botany, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed.
- Genomic C-Value Variation Analysis in Jujube (Plants (Basel, Switzerland) · 2023Article
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- Progress in the study of genome size evolution in Asteraceae: analysis of the last update.Database : the journal of biological databases and curation · 2019Article
- Do genome size differences withinHydrobiologia · 2017Article
- LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species.Genetica · 2015Article
- Recent updates and developments to plant genome size databases.Nucleic acids research · 2014Article
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- Ecology and genetic diversity of the dense-flowered orchid, Neotinea maculata, at the centre and edge of its range.Annals of botany · 2009Article
- Genetic diversity in Cypripedium calceolus (Orchidaceae) with a focus on north-western Europe, as revealed by plastid DNA length polymorphisms.Annals of botany · 2009Article
- Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic.Annals of botany · 2009Article
- Genome size diversity in orchids: consequences and evolution.Annals of botany · 2009Review
- Use of AFLP and RAPD molecular genetic markers and cytogenetic analysis to explore relationships among taxa of the Patagonian Bromus setifolius complex.Genetics and molecular biology · 2009Article
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- Plant genome horizons: Michael Bennett's contribution to genome research.Annals of botany · 2008Article
- Friends or relatives? Phylogenetics and species delimitation in the controversial European orchid genus Ophrys.Annals of botany · 2008Article
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3 authors.
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Abstract
BACKGROUND AND
aimsNuclear DNA content (C-value) varies approximately 1000-fold across the angiosperms, and this variation has been reported to have an effect on the quality of AFLP fingerprints. Various methods have been proposed for circumventing the problems associated with small and large genomes. Here we investigate the range of nuclear DNA contents across which the standard AFLP protocol can be used.
methodsAFLP fingerprinting was conducted on an automated platform using the standard protocol (with 3 + 3 selective bases) in which DNA fragments are visualized as bands. Species with nuclear DNA contents ranging from 1C = 0.2 to 32.35 pg were included, and the total number of bands and the number of polymorphic bands were counted. For the species with the smallest C-value (Bixa orellana) and for one of the species with a large C-value (Damasonium alisma), alternative protocols using 2 + 3 and 3 + 4 selective bases, respectively, were also used. KEY
resultsAcceptable AFLP traces were obtained using the standard protocol with 1C-values of 0.30-8.43 pg. Below this range, the quality was improved by using 2 + 3 selective bases. Above this range, the traces were generally characterized by a few strongly amplifying bands and noisy baselines. Damasonium alisma, however, gave more even traces, probably due to it being a tetraploid.
conclusionsWe propose that for known polyploids, genome size is a more useful indicator than the 1C-value in deciding which AFLP protocol to use. Thus, knowledge of ploidy (allowing estimation of genome size) and C-value are both important. For small genomes, the number of interpretable bands can be increased by decreasing the number of selective bases. For larger genomes, increasing the number of bases does not necessarily decrease the number of bands as predicted. The presence of a small number of strongly amplifying bands is likely to be linked to the presence of repetitive DNA sequences in high copy number in taxa with large genomes.
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