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A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)

Ball, A.D., Stapley, J., Dawson, D.A., Birkhead, T.R., Burke, T. and Slate, J. (2010) A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics, 11. Art no.218. ISSN 1471-2164

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Background: Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four zebra finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled zebra finch genome sequence.

Results: We showed that marker order was less reliable and linkage map lengths were inflated for microsatellite maps relative to SNP maps, apparently due to differing error rates between the two types of marker. Guidelines on how to minimise the effects of error are provided. In particular, we show that when combining both types of marker the conventional process of building linkage maps, whereby the most informative markers are added to the map first, has to be modified in order to improve map accuracy.

Conclusions: When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). This raises questions about the accuracy of marker order and predicted recombination rates in previous microsatellite linkage maps which were created using the conventional building process, however, provided suitable error detection strategies are followed microsatellite-based maps can continue to be regarded as reasonably reliable.

Item Type: Article
Copyright, Publisher and Additional Information: © 2010 Ball et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Single-Nucleotide Polymorphisms; Cross-Species Amplification; Comprehensive Genetic-Map; Genotyping ERRORS; Natural-Populations; Genomewide Linkage; Passerine Birds Chicken Genome; Loci; Chromosome
Institution: The University of Sheffield
Academic Units: The University of Sheffield > Faculty of Science (Sheffield) > School of Biological Sciences (Sheffield) > Department of Animal and Plant Sciences (Sheffield)
Depositing User: Miss Anthea Tucker
Date Deposited: 24 May 2010 08:37
Last Modified: 07 Jun 2014 12:28
Published Version: http://dx.doi.org/10.1186/1471-2164-11-218
Status: Published
Publisher: BioMed Central
Refereed: Yes
Identification Number: 10.1186/1471-2164-11-218
URI: http://eprints.whiterose.ac.uk/id/eprint/10837

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