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Short communication
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Allele frequencies and diversity parameters of 27 single nucleotide polymorphisms (SNPs)
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within and across goat breeds
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I. Cappuccio1, L. Pariset1, P. Ajmone-Marsan2, S. Dunner3, O. Cortes3, G. Erhardt4, G.
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Lühken4, C. Peter4, S. Joost5, I.J. Nijman6, J.A. Lenstra6, G. Luikart7, A. Beja-Pereira7, S.
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Zundel7, G. Obexer-Ruff8, A. Valentini1 and the Econogene Consortium9
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Dipartimento di Produzioni Animali, Università della Tuscia, Viterbo, Italy
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Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Departimento de Producción Animal, Universidad Complutense, Madrid, Spain
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Department of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
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Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Laboratoire d’Ecologie Alpine, Université Joseph Fourier, Grenoble, France
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Institute of Genetics, Veterinary Faculty, University of Berne, Switzerland
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http://lasig.epfl.ch/projets/econogene
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Correspondence: L. Pariset, tel. +39 761 357447, fax +39 761 357434, e-mail: pariset@unitus.it
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Author to whom reprint requests should be addressed: corresponding author
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Summary
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Single nucleotide polymorphisms (SNPs) are useful markers for biodiversity Assessment, linkage
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analysis, traceability and paternity testing. To date, there are in the NCBI dbSNP database no SNPs
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available for goat and only 26 are reported in the literature. Within the European Union Econogene
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project, we characterized 27 SNPs in goats using a targeted-gene approach. Polymorphisms were
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identified in a panel of 16 unrelated individuals belonging to 8 different goat breeds selected
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throughout Europe. Genotypes of 30 goats from each of the 8 breeds were determined for all the
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SNPs characterized and diversity measures were estimated. As there are no caprine SNPs in the
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NCBI dbSNP database, the SNPs described will be a useful complement to the available genome
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markers.
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Keywords
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Goat, single nucleotide polymorphisms, gene diversity.
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Ideal genetic markers for population and evolutionary studies should be abundant and distributed
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widely across the genome, while genotyping data must be comparable across laboratories with
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different scoring methods (Sunnucks 2000). These requirements are fulfilled by the single
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nucleotide polymorphisms (SNPs) (Brouillette et al. 2000; Sachidanandam et al. 2001; Shubitowski
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et al. 2001), which have been shown to be informative suitable for ecological and conservation
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studies (Morin et al., 2004; Seddon et al., 2005; Vignal et al. 2002; Brumfield et al. 2003), for
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estimation of parameters such as population history and for inference of relationships (Kuhner et
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al., 2000; Glaubitz et al., 2003). Furthermore, SNPs are cost-effective for high-throughput and
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accurate linkage or association studies (Schlotterer, 2004; Syvanen, 2001; Vitalis, 2001; Vignal,
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2002). However, in spite of these obvious advantages and their increasing use in human and model
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organism studies, SNPs have not been employed frequently in studies of non-model organisms,
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which is primarily due to a lack of availability.
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Within the Econogene project, we have selected 23 genes involved in key metabolic pathways or
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potentially relevant for production traits Primers were designed on the basis of goat sequences, , or
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on the basis of the consensus of genomic sequences of related species and used both for PCR
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amplification and sequencing For SNP discovery, PCR reactions were carried out with DNA from
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16 unrelated individuals belonging to 8 goat breeds from different European regions, thus
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representing a large part of the genetic variation across a wide geographic area: German Alpine
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(Germany), Corsican (France), Verata (Spain), Greek goat (Greece), Grigia Molisana (Italy),
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Baladie (Egypt), Polish fawn improved goat (Polony), Brava (Portugal). The authenticity of the
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amplification was checked by BLAST searches. A requirement to accept a SNP as authentic (not a
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sequencing error) and sufficiently polymorphic was that at least two copies of the rarer allele be
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observed (out of the 32 chromosomes observed).
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SNPs were identified in exons, introns and 5’- or 3’- flanking regions (Table 1). In four genes, two
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SNPs were identified. Of the 27 SNPs, 18 were transitions, eight were transversions and one was a
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deletion.
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The SNPs were subsequently typed by PCR-RFLP, SSCP, DHPLC, SnaPshot, direct sequencing or
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custom service (K-Bioscience, UK). We genotyped 30 individuals from each of the 8 breeds with at
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most three individuals per farm. The program Powermarker (Liu & Muse, 2001) was used to
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compute the frequencies of the rare allele, the expected heterozygosity (He), the observed
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heterozygosity (Ho) (Weir, 1996), PIC value (Botstein et al., 1980) and F statistics of genetic
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differentiation (Weir & Cockerham, 1984) (Table 1).
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Expected heterozygosity values ranged from 0.549 (MEG3) to 0.051 (IL2_1) with a mean of 0.358;
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observed heterozygosity values from 0.475 (DES) to 0.040 (IL2_1) with a mean of 0.290. Except
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one of the two SNPs in the interleukin-2 gene, all SNPs have a frequency of the rare allele higher
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than 5% over all breeds and are suitable for genetic analysis. FST values are variable within the
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range of 0.004 to 0.224, but suggest that breed differentiation by a panel of well selected SNPs is
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feasible. If these markers are used to analyse non-European breeds a potential limitation of
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ascertainment bias should be accounted for.
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So far, only 26 SNPs in goats have been reported in the literature. This study may be a further step
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towards the exploitation of the vast potential of SNP-based typing within and across goat breeds for
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a variety of purposes.
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Acknowledgements:
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This work was partially supported by the EU Econogene contract QLK5-CT-2001-02461. Major
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objectives of the project and a list of participants can be found on the website
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http://lasig.epfl.ch/projets/Econogene. We would like to thank all the farmers who kindly provided
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the material.
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The content of the publication does not represent necessarily the views of the Commission or its
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services.
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