Open Access Research article

Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs

Eyal Seroussi1*, Giora Glick1, Andrey Shirak1, Emanuel Yakobson1, Joel I Weller1, Ephraim Ezra2 and Yoel Zeron3

Author Affiliations

1 Institute of Animal Sciences, ARO, The Volcani Center, Bet Dagan 50250, Israel

2 Israel Cattle Breeders Association, Caesaria Industrial Park 38900, Israel

3 Sion, AI Institute, Shikmim 79800, Israel

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BMC Genomics 2010, 11:673  doi:10.1186/1471-2164-11-673

Published: 29 November 2010

Additional files

Additional file 1:

Detailed mathematical solution for the trinomial expansion of the Hardy-Weinberg principle. Text in PDF format.

Format: PDF Size: 12KB Download file

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Additional file 2:

Allele distribution, χ2 test, rl and rg values for SNPs of the Illumina BovineSNP50 BeadChip. Spread sheet in Excel format summarizing the genotypes obtained from the 912 sire samples for all 54,001 genetic markers on BovineSNP50.

Format: XLS Size: 19.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

Common CNVs. Spread sheet in Excel format summarizing the positions and gene content of copy losses (red background) and copy gains (blue background) that displayed significantly high frequency by both the HWE-based and SI-based methods. Previously reported common (frequency > 2.5%) cattle CNVs are also reported using yellow and no colour backgrounds for CNVs confirmed and not confirmed, respectively, by this study. For each CNVR, positions of SNP markers that displayed the same loss or gain status and fell within 0.5 Kb distance from each other are presented in the cell of the position column, and the corresponding estimated frequency is the average frequency of these markers.

Format: XLS Size: 927KB Download file

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Additional file 4:

Gene ontology categories in Holstein CNV. Spread sheet in Excel format.

Format: XLS Size: 96KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data