Open Access Methodology article

Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.)

Mikhail Ozerov1, Anti Vasemägi27, Vidar Wennevik3, Eero Niemelä4, Sergey Prusov5, Matthew Kent6 and Juha-Pekka Vähä2*

Author Affiliations

1 Kevo Subarctic Research Institute, University of Turku, Turku, 20014, Finland

2 Department of Biology, Division of Genetics and Physiology, University of Turku, Turku, 20014, Finland

3 Institute of Marine Research, PO Box 1870, Nordnes, N-5817, Bergen, Norway

4 Finnish Game and Fisheries Research Institute, Rakentajantie 3,PL 413, 90014, Oulun yliopisto, Finland

5 Freshwater Resources Laboratory, Knipovitch Polar Research Institute of Marine Fisheries and Oceanography, 6. Knipovitch Street, 183767, Murmansk, Russia

6 Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Norwegian University of Life Sciences, PO Box 5003, Ås, Norway

7 Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014, Tartu, Estonia

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BMC Genomics 2013, 14:12  doi:10.1186/1471-2164-14-12

Published: 16 January 2013

Additional files

Additional file 1: Figure S1:

Example of SNP loci failed to pass QC: a) call rate < 95%; b) cluster separation < 0.40; and SNP loci met QC requirements: c) cluster separation = 0.41 and d) call rate 100%, cluster separation = 1.00. Figure S2. Box-plot showing estimated variation of theta in two sets of SNPs with cluster separation score < 0.4 and > 0.4 for (a) array and (b) pool construction replicates (both tests, Mann–Whitney U test, P < 0.0001). Horizontal line, grey square, whiskers, open circles, and stars indicate median, 25th and 75th quartiles, non-outlier range, outliers and extreme outliers, respectively. Figure S3. A significant negative correlation between (a) array-(Pearson’s r = − 0.346, P < 0.0001) and (b) pool-construction (Pearson’s r = − 0.246, P < 0.0001) variation and cluster separation scores. Figure S4. Proportion of loci remained in each allele frequency class after application of (a) uniform and (b) spherical filter.

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