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Open Access Highly Accessed Research article

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

Alexander D Ball*, Jessica Stapley, Deborah A Dawson, Tim R Birkhead, Terry Burke and Jon Slate

Author Affiliations

Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK

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BMC Genomics 2010, 11:218  doi:10.1186/1471-2164-11-218

Published: 1 April 2010

Additional files

Additional file 1:

Table S1. Characterisation of microsatellite markers. Characterisation of 26 zebra finch (Taeniopygia guttata) microsatellite markers used to create the linkage maps for the zebra finch chromosomes 1, 1A, 2, and 9.

Tm, melting temperature (calculated using PRIMER3)

EST, expressed sequence tag

†, all primer sequences were identical to zebra finch sequence (obtained either via trace files or assembled genomic sequences)

a, Excluded after CHROMPIC revealed an excess of double recombination events with adjacent markers, indicative of high error rate.

b, Excluded from linkage maps as parent-offspring mismatches estimated the error rate > 0.02

c, Could not be accurately scored after multiplexing

Format: XLS Size: 30KB Download file

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Additional file 2:

Table S2. Results of linkage mapping. Summary of the linkage map results for four zebra finch (Taeniopygia guttata) chromosomes (Tgu1, Tgu1A, Tgu2 and Tgu9). The predicted positions of all markers on the zebra finch genome sequence after a BLAST analysis are included. Linkage map positions highlighted in bold are the framework loci that are supported at a LOD score ≥ 3 for that linkage map.

Format: XLS Size: 54KB Download file

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