Journal of Heredity Advance Access originally published online on September 14, 2006
Journal of Heredity 2006 97(5):531-534; doi:10.1093/jhered/esl020
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Brief Communications |
Characterization of 37 Breed-Specific Single-Nucleotide Polymorphisms in Sheep
From the Dipartimento di Produzioni Animali, Università della Tuscia, Viterbo, Italy (Pariset, Cappuccio, and Valentini); the Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy (Ajmone-Marsan); the School of Biosciences, University of Wales, Cardiff, UK (Bruford, Pinto-Juma, and Perez); the Departimento de Producción Animal, Universidad Complutense, Madrid, Spain (Dunner and Cortes); the Institut für Tierzucht und Haustiergenetik, Justus-Liebig-Universität, Giessen, Germany (Erhardt, Prinzenberg, and Gutscher); the Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland (Joost); the Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands (Nijman and Lenstra); and http://www.econogene.eu/ (Econogene Consortium)
Address correspondence to L. Pariset at the address above, or e-mail: pariset{at}unitus.it.
We identified 37 single-nucleotide polymorphisms (SNPs) in sheep and screened 16 individuals from 8 different sheep breeds selected throughout Europe. Population genetic measures based on the genotyping of about 30 sheep from the same 8 breeds are reported. To date, there are no sheep SNPs documented in the National Center for Biotechnology Information dbSNP database. Therefore, the markers presented here contribute significantly to those currently available.
The several complete-genome projects have led to the emergence of single-nucleotide polymorphisms (SNPs) as most modern genetic markers. SNPs occur frequently in the mammalian genome (Brouillette et al. 2000; Shubitowski et al. 2001) and are useful for rapid, large-scale, and cost-effective genotyping (Schlotterer 2004; Syvanen et al. 2001; Vitalis et al. 2001; Vignal et al. 2002) for ecological and conservation studies (Vignal et al. 2002; Morin et al. 2004; Seddon et al. 2005) and for population and evolutionary studies (Kuhner et al. 2000; Sunnucks 2000; Glaubitz et al. 2003). However, SNPs are still scarce in nonmodel organisms, primarily due to the effort needed to find SNPs in species where little DNA sequence data are available, (Aitken et al. 2004) and their full potential is not yet exploited.
The European Union–sponsored Econogene project led to a collection of samples from sheep breeds from different European and Near-Eastern regions. This allowed an SNP discovery by across-breed comparison of 16 unrelated individuals belonging to 8 breeds representing wide phenotypic and geographic variation in Western Eurasia: Akkaraman (Turkey), Bergamasca (Italy), Karagouniko (Greece), Rhönsheep (Germany), Rubia del Molar (Spain), Turcana (Romania), Welsh Mountain (Great Britain), and Zelazna (Poland). DNA was isolated after collection of whole blood using standard techniques. Primers designed using sheep sequences (where available) or the consensus sequences of the closest species in GenBank were used both for polymerase chain reaction amplification and sequencing of the corresponding genomic fragment. Sequences were BLAST aligned to establish homology. Thirty-seven SNPs were identified in 27 genes involved in key metabolic pathways or potentially relevant for production traits (Table 1).
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Most of these were transitions, although we found 5 transversions and 1 deletion. Subsequently, these SNPs were genotyped in usually 30 individuals from each of the same 8 breeds, sampling no more than 3 individuals per farm. Standard population statistics (Weir 1996; Botstein et al. 1980) for each locus and over all populations were computed using the programs POWERMARKER (Liu and Muse 2001) and GENEPOP 3.3 (Raymond and Rousset 1995) and shown in Table 1. Thirty-two SNPs show an overall frequency of the rare allele higher than 5% and are thus generally applicable to population genetic studies. FST values are variable, but several values above 0.2 (MCR1R, TNF_1, ACVR2B, and CSN1S1) suggest that SNPs are indicative for breed-specific selection. The values of 0.82 for both SNPs in the MC1R coat color gene are caused by a high frequency of the minor alleles only in the Welsh Mountain sheep.
Diversity parameters for individual breeds were calculated using the program FSTAT (Goudet 2000) and listed in Table 2. From the 5 SNPs in 3 genes with overall frequencies below 5%, 4 have appreciable frequencies (0.1–0.266) in specific breeds: CAPN_1 in Karagouniko and Rhönsheep, CAPN_2 in Turcana and in Welsh Mountain, LEP_1 in Welsh Mountain, and LEP_2 in Turcana and Welsh Mountain. The minor allele of DES_1 was found only at a low frequency (0.052) in Rhönsheep. Such SNPs may be informative to a reconstruction of the breed history or may be under breed-specific selection.
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Our SNP data contribute to the collection of about 100 SNPs identified so far and to the eventual use of these markers for the genetic analysis of breed history of a variety of phenotypes.
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Acknowledgments |
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This work has been partially supported by the European Union Econogene contract QLK5-CT-2001-02461. Major objectives of the project and a list of participants can be found on the Web site http://lasig.epfl.ch/projets/econogene. We would like to thank all the farmers who kindly provided the material and CBS Technologies for help during sampling. The content of the publication does not represent necessarily the views of the Commission or its services.
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Footnotes |
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Corresponding Editor: Ernest Bailey
Received February 22, 2006
Accepted August 10, 2006
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