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The extent and distribution of linkage disequilibrium in a multi-hierarchic outbred canine pedigree

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Abstract

A canine integrated linkage-radiation map has been recently constructed by using microsatellite markers. This map, with a good coverage of the canine genome, allows for a genome-wide search for the extent and distribution of linkage disequilibrium derived from linkage and evolutionary forces. In this study, we genotyped an outbred pedigree between Labrador retriever and Greyhound breeds with a set of microsatellite markers (240) from the canine linkage map. Linkage disequilibrium was measured between all syntenic and nonsyntenic marker pairs. Analysis of syntenic pairs revealed a significant correlation (−0.229, P < 0.001) between linkage disequilibrium and genetic distance (log transformed). Significant linkage disequilibria were observed more frequently between syntenic pairs spaced <40 cM than those paced >40 cM. There is a clear trend for linkage disequilibrium to decline with marker distance. From our results, a genome-wide screen with markers at low to moderate density (1–2 per 10 cM) should take full advantage of linkage disequilibrium for quantitative trait locus mapping in dogs. This study supports the appropriateness of linkage disequilibrium analysis to detect and map quantitative trait loci underlying complex traits in dogs.

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Acknowledgements

We thank two anonymous referees for constructive comments on this manuscript, which led to a better presentation. This work was supported by a grant from the Morris Animal Foundation, NIH grant AR36554, the Consolidated Research Grant Program, the Cornell Advanced Technology, Biotechnology Program, Nestle Purina Inc., NALBI Mammalian Genotyping Service, Marshfield Medical Research Foundation, Marshfield, WI, Cornell University College of Veterinary Medicine Unrestricted Alumni Funds, and an Outstanding Young Investigators Award (No. 30128017) of the National Natural Science Foundation of China to R. Wu. We thank Margaret Vernier-Singer, Alm Jo Williams, and Liz Grisanzio for expert technical assistance.

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Authors and Affiliations

  1. Department of Statistics, 533 McCarty Hall C, University of Florida, Gainesville, Florida 32611, USA

    Xiang-Yang Lou, Min Lin, Qing Lu, Tian Liu, Zuoheng Wang, George Casella & Rongling Wu

  2. Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA

    Rory J. Todhunter & Stuart P. Bliss

  3. James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA

    Gregory M. Acland & George Lust

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  1. Xiang-Yang Lou
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  2. Rory J. Todhunter
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  4. Qing Lu
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  10. George Lust
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  11. Rongling Wu
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Correspondence to Rongling Wu.

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Lou, XY., Todhunter, R.J., Lin, M. et al. The extent and distribution of linkage disequilibrium in a multi-hierarchic outbred canine pedigree . Mamm Genome 14, 555–564 (2003). https://doi.org/10.1007/s00335-003-2272-1

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