Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean

Lorraine Pariset, Stephane Joost, Paolo Ajmone Marsan, Alessio Valentini, Mahamoud Abo-Shehada, Al Tarrayrah Jamil, Antonella Angiolillo, Philip Baret, Roswitha Baumung, Albano Beja-Pereira, Marco Bertaglia, Salvatore Bordonaro, Mike Bruford, Régis Caloz, Gabriele Canali, Javier Canon, Irene Cappuccio, Antonello Carta, Mario Cicogna, Paola CrepaldiStella Dalamitra, Daniela Krugmann, Dobi Petrit, Dominik Popielarczyk, Dunner Susana, Giuseppe D'Urso, M. A.A. El-Barody, Phillip England, Georg Erhardt, Okan Ertugrul, Prinzenberg Eva-Maria, Ibeagha Awemu Eveline, Strzelec Ewa, Aziz Fadlaoui, Francesca Fornarelli, David Garcia, Andreas Georgoudis, Lühken Gesine, Stefano Giovenzana, Katja Gutscher, Godfrey Hewitt, Anila Hoda, Brandt Horst, Anton Istvan, Gabriela Juma, Stéphane Joost, Sam Jones, Katerina Karetsou, Georgios Kliambas, Evren Koban, Olga Kutita, Fesus Lazlo, Johannes A. Lenstra, Christina Ligda, Shirin Lipsky, Gordon Luikart, Glowatzki Marie-Louise, Marta Marilli, Donata Marletta, Elisabetta Milanesi, Riccardo Negrini, Isaäc J. Nijman, Gabriela Obexer-Ruff, Christos Papachristoforou, Lorraine Pariset, Marco Pellecchia, Christina Peter, Trinidad Perez, Emilio Pietrolà, Fabio Pilla, Niznikowski Roman, Jutta Roosen, Riccardo Scarpa, Tiziana Sechi, Pierre Taberlet, Martin Taylor, Inci Togan, Michel Trommetter, Cann Van, M. Lisette, Augustin Vlaic, Louise Wiskin, Stéphanie Zundel

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Background: In this study we compare outlier loci detected using a FST based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of goat breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring. Results: The combined use of the two outlier detection approaches, never tested before using SNP polymorphisms, resulted in the identification of the same three loci involved in milk and meat quality data by using the two methods, while the FST based method identified 3 more loci as under selection sweep in the breeds examined. Conclusion: Data appear congruent by using the two methods for FST values exceeding the 99% confidence limits. The methods of FST and SAM can independently detect signatures of selection and therefore can reduce the probability of finding false positives if employed together. The outlier loci identified in this study could indicate adaptive variation in the analysed species, characterized by a large range of climatic conditions in the rearing areas and by a history of intense trade, that implies plasticity in adapting to new environments.

Original languageEnglish
Article number7
JournalBMC Genetics
StatePublished - Feb 19 2009


This work has been partially supported by the ECONOGENE project, funded by the European Union (project QLK5-CT2001-02461). The content of the publication does not necessarily represent the views of the Commission or its services. The authors wish to thank Flora Jane Dause for help with the language.

FundersFunder number
European CommissionQLK5-CT2001-02461


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