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Examination of a region showing linkage map discrepancies across sheep breeds

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Abstract

The availability of accurate linkage maps is an important step for the localization of genetic variants of interest. However, most studies in livestock assume the published map is applicable in their population despite the large differences between the breeds of a species. A region of sheep Chromosome 1 was previously identified as providing evidence for a marker order inconsistent with the published linkage map. In this study the identified region was investigated in more detail. Four microsatellite markers covering the central 5 cM of the inconsistent region and two flanking markers were genotyped in three sheep breeds, a commercial population (Charollais), an experimental population (Scottish Blackface), and a feral population (Soay). With the inclusion of the published linkage map, this provided evidence for three different marker orders across four sheep populations. Evidence for selection in this region was investigated using both a single-point allelic competition model and a multipoint allele-sharing statistic. Only the Charollais population provided evidence for selection, with significant transmission bias observed at marker BM7145. The implications of variation in linkage maps on the design and analysis of fine-mapping studies are discussed.

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Acknowledgments

The Charollais study was funded by the Department for Environment, Food and Rural Affairs (Defra), Scottish Executive Environment and Rural Affairs Department (SEERAD) and the Meat and Livestock Commission (MLC) through the LINK Sustainable Livestock Production Programme. The Scottish Blackface study was funded by Defra. The authors are grateful to S. Bishop, G. Walling, A. Wilson, E. Karamichou, and G. Davies for their role in the collection and extraction of DNA samples and initial data checking. This collection was helped with input from Charollais Sire Referencing Ltd., and Mr. R. Pratt in particular, and from D. Wallace and D. McGavin at Roslin Institute’s Blythbank farm. The authors also acknowledge assistance from MLC’s Signet Breeding Services and Edinburgh Genetics. The collection of the data on the Soay sheep used in this study was funded by the UK Natural Environmental Research Council and the Wellcome Trust. The authors are grateful to the National Trust for Scotland, Scottish Natural Heritage, the Ministry of Defence, Eurest, and QinetiQ for permission and practical support for the St. Kilda Soay Sheep Project. The authors thank all who have contributed to the Soay sheep data set, especially J. Pemberton and J. Pilkington. They thank P. Visscher for many helpful discussions on this topic. Th article was improved by the helpful suggestions of two anonymous referees. A.M. was funded by a Commonwealth Scholarship.

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  1. Allan F. McRae

    Present address: Genetic Epidemiology Group, Queensland Institute of Medical Research, Post Office, Royal Brisbane Hospital, Brisbane, 4006, Australia

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  1. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom

    Allan F. McRae & Dario Beraldi

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  1. Allan F. McRae
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Correspondence to Allan F. McRae.

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McRae, A.F., Beraldi, D. Examination of a region showing linkage map discrepancies across sheep breeds. Mamm Genome 17, 346–353 (2006). https://doi.org/10.1007/s00335-005-0087-y

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