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Fine-scale population structure analysis of seven local Swiss sheep breeds using genome-wide SNP data

Published online by Cambridge University Press:  08 December 2014

A. Burren ,
H. Signer-Hasler ,
M. Neuditschko ,
J. Tetens ,
J. Kijas ,
C. Drögemüller  and
C. Flury
A. Burren
Affiliation:
School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052 Zollikofen, Switzerland
H. Signer-Hasler
Affiliation:
School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052 Zollikofen, Switzerland
M. Neuditschko
Affiliation:
Swiss National Stud Farm, Agroscope, Les Long Prés, Case postale 191, CH-1580Avenches, Switzerland
J. Tetens
Affiliation:
Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 6, 24118 Kiel, Germany
J. Kijas
Affiliation:
CSIRO Livestock Industries, St Lucia, Brisbane, Queensland, Australia
C. Drögemüller
Affiliation:
University of Berne, Institute of Genetics, Bremgartenstrasse 109, 3001 Berne, Switzerland
C. Flury*
Affiliation:
School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052 Zollikofen, Switzerland
*
Correspondence to: C. Flury, School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052 Zollikofen, Switzerland. email: christine.flury@bfh.ch
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Summary

As part of the global sheep Hapmap project, 24 individuals from each of seven indigenous Swiss sheep breeds (Bundner Oberländer sheep (BOS), Engadine Red sheep (ERS), Swiss Black-Brown Mountain sheep (SBS), Swiss Mirror sheep (SMS), Swiss White Alpine (SWA) sheep, Valais Blacknose sheep (VBS) and Valais Red sheep (VRS)), were genotyped using Illumina's Ovine SNP50 BeadChip. In total, 167 animals were subjected to a detailed analysis for genetic diversity using 45 193 informative single nucleotide polymorphisms. The results of the phylogenetic analyses supported the known proximity between populations such as VBS and VRS or SMS and SWA. Average genomic relatedness within a breed was found to be 12 percent (BOS), 5 percent (ERS), 9 percent (SBS), 10 percent (SMS), 9 percent (SWA), 12 percent (VBS) and 20 percent (VRS). Furthermore, genomic relationships between breeds were found for single individuals from SWA and SMS, VRS and VBS as well as VRS and BOS. In addition, seven out of 40 indicated parent–offspring pairs could not be confirmed. These results were further supported by results from the genome-wide population cluster analysis. This study provides a better understanding of fine-scale population structures within and between Swiss sheep breeds. This relevant information will help to increase the conservation activities of the local Swiss sheep breeds.

Résumé

En el marco del proyecto internacional Hapmap Ovino, se genotiparon, con el chip Ovine SNP50 BeadChip de Illumina, 24 ejemplares de cada una de las siete razas ovinas autóctonas de Suiza (Oveja del Oberland de los Grisones (OG), Oveja Roja de Engadina (RE), Oveja Negra-marrón de Montaña (NM), Oveja Espejo (OE), Oveja Alpina Blanca (AB), Oveja de Hocico Negro del Valais (HN) y Oveja Pelirroja del Valais (PV)). En total, 167 animales fueron sometidos a un análisis minucioso de diversidad genética, para el cual se usaron 45 193 polimorfismos informativos de nucleótido simple. Los resultados de los análisis filogenéticos confirmaron la ya conocida cercanía entre ciertas poblaciones tales como la HN y la PV o la OE y la AB. El parentesco genómico medio intra-racial fue de 12 por ciento para la OG, de 5 por ciento para la RE, de 9 por ciento para la NM, de 10 por ciento para la OE, de 9 por ciento para la AB, de 12 por ciento para la HN y de 20 por ciento para la PV. Se detectó además parentesco genómico entre razas para ejemplares aislados de la AB y la OE, la PV y la HN y la PV y la OG. Por otro lado, no se pudieron confirmar 7 de las 40 parejas señaladas de progenitores-descendencia. Estos resultados fueron posteriormente respaldados por los resultados de un análisis de conglomerados del genoma completo de la población. Este estudio permite una mejor comprensión de la estructura a pequeña escala de las poblaciones intra- e inter- razas ovinas suizas. Con esta información, será posible llevar a cabo un mayor número de actividades para la conservación de las razas ovinas locales de Suiza.

Resumen

Dans le cadre du projet international Hapmap Ovins, 24 individus de chacune des sept races ovines autochtones de la Suisse (Mouton de l'Oberland Grison (OG), Mouton Roux d'Engadine (RE), Mouton de Montagne Noir-marron (MN), Mouton Miroir (MM), Mouton Alpin Blanc (AB), Mouton Nez-Noir du Valais (NN) et Mouton Roux du Valais (RV)) ont été génotypés en utilisant la puce Ovine SNP50 BeadChip d'Illumina. En tout, 167 animaux ont été soumis à une analyse minutieuse de diversité génétique, pour laquelle 45 193 polymorphismes nucléotidiques informatifs ont été utilisés. Les résultats des analyses phylogénétiques ont corroboré la proximité déjà connue entre certaines populations telles que NN et RV ou MM et AB. La parenté génomique moyenne intra-raciale a été de 12 pour cent pour le OG, de 5 pour cent pour le RE, de 9 pour cent pour le MN, de 10 pour cent pour le MM, de 9 pour cent pour le AB, de 12 pour cent pour le NN et de 20 pour cent pour le RV. En outre, des rapports génomiques interraciaux ont été décelés entre individus isolés des races AB et MM, RV et NN et RV et OG. Par ailleurs, 7 des 40 paires parents-descendants signalées n'ont pas pu être confirmées. Ces résultats ont été ultérieurement corroborés par les résultats d'une analyse de groupement de l'ensemble du génome de la population. Cette étude permet une meilleure compréhension de la structure à petite échelle des populations intra- et inter- races ovines suisses. Cette information servira à mener un plus grand nombre d'activités pour la conservation des races ovines locales de la Suisse.

Keywords

dense marker datagenetic diversityovis ariesdiversité génétiqueinformation de marqueurs densesovis ariesdiversidad genéticainformación de marcadores densosovis aries
Type
Research Article
Information
Animal Genetic Resources/Resources génétiques animales/Recursos genéticos animales , Volume 55 , December 2014 , pp. 67 - 76
Copyright
Copyright © Food and Agriculture Organization of the United Nations 2014 

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References

Alexander, D., Novembre, J. & Lange, K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res., 19: 1655–1664.Google Scholar
Burren, A., Flury, C., Aeschlimann, C., Hagger, C. & Rieder, S. 2012. Populationsstruktur und genetische Diversität von Schweizer Schafrassen. Agrarforschung Schweiz., 3: 140–147.Google Scholar
Ciani, E., Crepaldi, P., Nicoloso, L., Lasagna, E., Sarti, F.M., Moioli, B., Napolitano, F., Carta, A., Usai, G., D'Andrea, M., Marletta, D., Ciampolini, R., Riggio, V., Occidente, M., Matassino, D., Kompan, D., Modesto, P., Macciotta, N., Ajmone-Marsan, P. & Pilla, F. 2014. Genome-wide analysis of Italian sheep diversity reveals strong pattern and cryptic relationships between breeds. Anim. Genet., 45(2): 256–266.Google Scholar
Corbin, L.J., Liu, A.Y.H., Bishop, S.C. & Woolliams, J.A. 2012. Estimation of historical effective population size using linkage disequilibria with marker data. J. Anim. Breed. Genet., 129: 257–270.Google Scholar
FOAG. 2007. Farm animal genetic resources in Switzerland. Booklet in the Order of the Federal Office of Agriculture for the First Technical Conference on Animal Genetic Resources, Interlaken, 2007 (available at http://www.blw.admin.ch/themen/00013/00082/00087/index.html?lang=en).Google Scholar
Glowatzki-Mullis, M.-L., Muntwyler, J., Bäumle, E. & Gaillard, C. 2009. Genetic diversity of Swiss sheep breeds in the focus of conservation research. J. Anim. Breed. Genet., 126: 164–175.Google Scholar
Groeneveld, E., Westhuizen, B.v.d., Maiwashe, A., Voordewind, F. & Ferraz, J.B.S. 2009. POPREP: a generic report for population management. Genet. Mol. Res., 8(3): 1158–1178.Google Scholar
Hasler, H., Flury, C., Menet, S., Haase, B., Leeb, T., Simianer, H., Poncet, P.A. & Rieder, S. 2011. Genetic diversity in an indigenous horse breed – implications for mating strategies and the control of future inbreeding. J. Anim. Breed. Genet., 128: 394–406.Google Scholar
Hayes, B.J., Visscher, P.M., McPartlan, H.C. & Goddard, M.E. 2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res., 13: 635–643.Google Scholar
Huson, D. & Bryant, D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol., 23: 254–267.Google Scholar
Kijas, J.W., Lenstra, J.A., Hayes, B., Boitard, S., Porto Neto, L.R., Cristobal, M.S., Servin, B., McCulloch, R., Whan, V., Gietzen, K., Paiva, S., Barendse, W., Ciani, E., Raadsma, H., McEwan, J. & Dalrymple, B. 2012. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol., 10: e1001258.Google Scholar
Ligges, U. & Mächler, M. 2003. Scatterplot3d – an R package for visualizing multivariate data. J. Stat. Softw., 8, 1–20.Google Scholar
Neuditschko, M., Kathkar, M.S. & Raadsma, H.W. 2012. NETVIEW: a high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation. PLoS One, 7: e48375.Google Scholar
Pritchard, J.K., Stephens, M. & Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155: 945–959.Google Scholar
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D., Maller, J., Sklar, P., de Bakker, P.I.W., Daly, M.J. & Sham, P.C. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am. J. Hum. Genet., 81: 559–575.Google Scholar
Revell, L.J. 2012. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3: 217–223.Google Scholar
Rosenberg, N.A. 2004. Distruct: a program for the graphical display of population structure. Mol. Ecol. Notes, 4: 137–138.Google Scholar
Rousset, F. 2008. GENEPOP' 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol. Ecol. Resour., 8: 103–106.Google Scholar
Sarkar, D. 2008. Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5.Google Scholar
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. & Ideker, T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13: 2498–2504.Google Scholar
Stahlberger-Saitbekova, N., Schläpfer, J., Dolf, G. & Gaillard, C. 2001. Genetic relationships in Swiss sheep breeds based on microsatellite analysis. J. Anim. Breed. Genet., 118: 379–387.CrossRefGoogle Scholar
Sved, J.A. 1971. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol., 2: 125–141.Google Scholar
Wang, D., Sun, Y., Stand, P., Berlin, J.A., Wilcos, M.A. & Li, Q. 2009. Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: principal-component analysis versus multidimensional scaling. BMC Proc., 3: 109.Google Scholar
Weir, B.S. & Hill, W.G. 1980. Effect of mating structure on variation in linkage disequilibrium. Genetics, 95: 477–488.Google Scholar
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