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Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal

  1. J. I. HOFFMAN1,
  2. R. TUCKER2,
  3. S. J. BRIDGETT3,
  4. M. S. CLARK4,
  5. J. FORCADA4,
  6. J. SLATE2

Article first published online: 23 JUN 2012

DOI: 10.1111/j.1755-0998.2012.03158.x

Issue

Molecular Ecology Resources

Molecular Ecology Resources

Volume 12, Issue 5, pages 861–872, September 2012

Additional Information

How to Cite

HOFFMAN, J. I., TUCKER, R., BRIDGETT, S. J., CLARK, M. S., FORCADA, J. and SLATE, J. (2012), Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Molecular Ecology Resources, 12: 861–872. doi: 10.1111/j.1755-0998.2012.03158.x

Author Information

  1. 1

    Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany

  2. 2

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

  3. 3

    The GenePool, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK

  4. 4

    British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK

*Joseph I. Hoffman, Fax: +49 (0)521 1062998; E-mail: joseph.hoffman@uni-bielefeld.de

Publication History

  1. Issue published online: 16 AUG 2012
  2. Article first published online: 23 JUN 2012
  3. Received 24 February 2012; revision received 30 March 2012; accepted 4 April 2012

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Table S1 Details of 144 GoldenGate SNP assays developed from the Antarctic fur seal transcriptome assembly (see Materials and methods for details). ‘Chromosome in the dog’ refers to the genomic location inferred by mapping each isotig to the dog (Canis familaris) genome. Basic Local Alignment Search Tool (BLAST) results indicate the top match of each isotig to the non-redundant (nr) database. Gene Ontology (GO) codes are given only for isotigs that recovered functional annotations relating to growth or immunity. In silico Minor Allele Frequency (MAF) and depth of coverage refer to the exact site of each SNP and are given only for reads accepted as unambiguous by the program SWAP454 (Brockman et al. 2008). Assay Design Tool (ADT) scores vary between 0 and 1, with values of 0.6 or above indicating a high probability of conversion into a successful genotyping assay.

Table S2 Polymorphism characteristics of 102 polymorphic SNP assays in 440 Antarctic fur seals individuals (see Materials and methods for details). The GenTrain score takes into account the quality, shape and degree of separation of the genotype clusters, with higher values indicating improved clustering (Fan et al. 2003).

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