Codominant scoring of AFLP in association panels

Gort, Gerrit; Eeuwijk, F.A. van

doi:10.1007/s00122-010-1313-x

Cited by 15 publications

(16 citation statements)

References 37 publications

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“…However, we do not attempt to estimate the genotype of each individual like previous approaches (e.g. Piepho & Koch 2000; Gort & van Eeuwijk 2010). Instead, we focus on population data for which the distribution of the band intensity of polymorphic markers is expected to be overall bimodal (band intensities for recessive homozygotes are assumed to be zero; see Fig.…”

Section: Methodsmentioning

confidence: 99%

Enhanced AFLP genome scans detect local adaptation in high‐altitude populations of a small rodent (Microtus arvalis)

et al. 2011

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Adaptation to adverse environmental conditions such as high altitude requires physiological and/or morphological changes. Genome scans provide a means to identify the genetic basis of such adaptations without previous knowledge about the particular genetic variants or traits under selection. In this study, we scanned 3027 amplified fragment length polymorphisms (AFLP) in four populations of the common vole Microtus arvalis for loci associated with local adaptation and high altitude. We investigated voles from two populations at high elevation (~2000 m a.s.l.) representing the upper limit of the altitudinal distribution of the species and two geographically close low-altitude populations (<600 m a.s.l.). Statistical analysis incorporated a new Bayesian F(ST) outlier approach specifically developed for AFLP markers, which considers the intensity of AFLP bands instead of mere presence/absence and allows to derive population-based estimates of allele frequencies and F(IS) values. Computer simulations showed that this approach increases the statistical power of the detection of AFLP markers under selection almost to the power of single nucleotide polymorphism (SNP) data without compromising specificity. Our enhanced genome scan resulted in 20 prime candidate markers for positive selection, which show mostly extremely high allele frequency differences between the low- and high-altitude populations. The comparison of global- and pairwise-enhanced genome scans demonstrated further that very strong selective signatures may also be associated with single populations suggesting the importance of local adaptation in alpine populations of common voles.

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Section: Methodsmentioning

confidence: 99%

Enhanced AFLP genome scans detect local adaptation in high‐altitude populations of a small rodent (Microtus arvalis)

et al. 2011

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“…This has resulted in improved techniques such as FluoMEP [44]. Automated fragment analysis [37] is also increasingly used together with other technological or methodological advances such as different scoring protocols [45,46] or statistical corrections [29,47,48]. Software specifically designed for band scoring [49] has also been developed.…”

Section: Arbitrarily Amplified Dna Markers (Aads)mentioning

confidence: 99%

Advances in plant gene-targeted and functional markers: a review

et al. 2013

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Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.

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“…The copy number of a fragment may be inferred by fitting normal mixture models (see e.g. Piepho and Koch 2000;Gort and van Eeuwijk 2010). However, collisions yield more amplified DNA as well, and hence produce darker bands.…”

Section: Conclusion and Discussionmentioning

confidence: 99%

Review and simulation of homoplasy and collision in AFLP

Gort

Eeuwijk

2011

Euphytica

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In this paper we give a short review of the problems of homoplasy and collision in AFLP, and describe a software tool that we developed to illustrate these problems. AFLP is a DNA fingerprinting technique, producing profiles of bands, the result of the separation of DNA fragments by length on a gel or microcapillary system. The profiles are usually interpreted as binary band absence/presence patterns. We focus on two major problems: (1) Within a profile two or more fragments of the same length but of different genomic origin may have been selected, colliding into a single band. This collision problem, akin to the birthday problem, may be surprisingly large. (2) In a pair of profiles two equally long fragments of different genomic origin may have been selected, appearing as identical bands in the two profiles. This is called homoplasy. Both problems are quantified by modeling AFLP as a random sampling technique of fragment lengths. AFLP may be used in phylogenetic studies to estimate the pairwise genetic similarity of individuals. Similarity coefficients like Dice and Jaccard coefficients overestimate the true genetic similarity because of homoplasy, with increasing bias for higher numbers of bands per profile. Corrected estimators are described, which do not suffer from bias. The ideas are illustrated using a new software tool. Data from studies on Arabidopsis and tomato serve as examples. Finally, we make some recommendations with respect to the use of AFLP.

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Codominant scoring of AFLP in association panels

Cited by 15 publications

References 37 publications

Enhanced AFLP genome scans detect local adaptation in high‐altitude populations of a small rodent (Microtus arvalis)

Enhanced AFLP genome scans detect local adaptation in high‐altitude populations of a small rodent (Microtus arvalis)

Advances in plant gene-targeted and functional markers: a review

Review and simulation of homoplasy and collision in AFLP

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