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Highly effective SNP-based association mapping and management of recessive defects in livestock

Abstract

The widespread use of elite sires by means of artificial insemination in livestock breeding leads to the frequent emergence of recessive genetic defects, which cause significant economic and animal welfare concerns. Here we show that the availability of genome-wide, high-density SNP panels, combined with the typical structure of livestock populations, markedly accelerates the positional identification of genes and mutations that cause inherited defects. We report the fine-scale mapping of five recessive disorders in cattle and the molecular basis for three of these: congenital muscular dystony (CMD) types 1 and 2 in Belgian Blue cattle and ichthyosis fetalis in Italian Chianina cattle. Identification of these causative mutations has an immediate translation into breeding practice, allowing marker assisted selection against the defects through avoidance of at-risk matings.

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Figure 1: Congenital muscular dystonia 1 (CMD1).
Figure 2: Congenital muscular dystonia 2 (CMD2).
Figure 3: Ichthyosis fetalis (IF).

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Acknowledgements

The 60K genome-wide SNP panel was constructed with the financial support of Holland Genetics (Arnhem, The Netherlands). This work was funded by grants from the Walloon Ministry of Agriculture, from the Belgian Science Policy organization (SSTC Genefunc PAI), from the Communauté Française de Belgique (Game & Biomod ARC), from the University of Liège and from the Medical Research Council (G0601585 to K.H. and R.J.H.). C.C. is Chercheur Qualifié from the Fonds National de la Recherche Scientifique. This work is dedicated to the memory of Professor Roger Hanset.

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Authors

Contributions

C.C. and M.G. designed the experiments, analyzed data, wrote the manuscript and supervised the project. W.C. designed the Illumina iSelect panel and supervised genotyping. F.R., D.D., J.S.A., M.D., J.-C.F., R.H., C.J., S.V., M.L. and M.F. confirmed diagnosis and provided samples of affected individuals. S.L. and M.K. performed genotyping on the Affymetrix panel. N.C., S.D., C.F., X.H., L.K., P.S., N.T. and H.N. performed genotyping and mutation scanning. X.H. analyzed data and mapped the CMD1 mutation. C.J. and M.F. performed mutation scanning of RL. E.C., K.H., B.R.P. and R.J.H. performed functional test of the CMD2 mutation. R.J.H. participated in writing the manuscript.

Corresponding author

Correspondence to Michel Georges.

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Supplementary Figures 1–5 and Supplementary Tables 1 and 2 (PDF 918 kb)

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Charlier, C., Coppieters, W., Rollin, F. et al. Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat Genet 40, 449–454 (2008). https://doi.org/10.1038/ng.96

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