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 Crepaldi; Stella 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

doi:10.1186/1471-2156-10-7

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

Flathead Lake Biological Station

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Abstract

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 language	English
Article number	7
Journal	BMC Genetics
Volume	10
DOIs	https://doi.org/10.1186/1471-2156-10-7
State	Published - Feb 19 2009

Funding

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.

Funders	Funder number
European Commission	QLK5-CT2001-02461

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10.1186/1471-2156-10-7

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Pariset, L., Joost, S., Marsan, P. A., Valentini, A., Abo-Shehada, M., Jamil, A. T., Angiolillo, A., Baret, P., Baumung, R., Beja-Pereira, A., Bertaglia, M., Bordonaro, S., Bruford, M., Caloz, R., Canali, G., Canon, J., Cappuccio, I., Carta, A., Cicogna, M., ... Zundel, S. (2009). Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean. BMC Genetics, 10, Article 7. https://doi.org/10.1186/1471-2156-10-7

@article{54f0adfadfc04b119cff43a2bc6592a8,

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

abstract = "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.",

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

note = "Funding Information: 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.",

year = "2009",

month = feb,

day = "19",

doi = "10.1186/1471-2156-10-7",

language = "English",

volume = "10",

journal = "BMC Genetics",

issn = "1471-2156",

publisher = "BioMed Central Ltd",

}

Pariset, L, Joost, S, Marsan, PA, Valentini, A, Abo-Shehada, M, Jamil, AT, Angiolillo, A, Baret, P, Baumung, R, Beja-Pereira, A, Bertaglia, M, Bordonaro, S, Bruford, M, Caloz, R, Canali, G, Canon, J, Cappuccio, I, Carta, A, Cicogna, M, Crepaldi, P, Dalamitra, S, Krugmann, D, Petrit, D, Popielarczyk, D, Susana, D, D'Urso, G, El-Barody, MAA, England, P, Erhardt, G, Ertugrul, O, Eva-Maria, P, Eveline, IA, Ewa, S, Fadlaoui, A, Fornarelli, F, Garcia, D, Georgoudis, A, Gesine, L, Giovenzana, S, Gutscher, K, Hewitt, G, Hoda, A, Horst, B, Istvan, A, Juma, G, Joost, S, Jones, S, Karetsou, K, Kliambas, G, Koban, E, Kutita, O, Lazlo, F, Lenstra, JA, Ligda, C, Lipsky, S, Luikart, G, Marie-Louise, G, Marilli, M, Marletta, D, Milanesi, E, Negrini, R, Nijman, IJ, Obexer-Ruff, G, Papachristoforou, C, Pariset, L, Pellecchia, M, Peter, C, Perez, T, Pietrolà, E, Pilla, F, Roman, N, Roosen, J, Scarpa, R, Sechi, T, Taberlet, P, Taylor, M, Togan, I, Trommetter, M, Van, C, Lisette, M, Vlaic, A, Wiskin, L & Zundel, S 2009, 'Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean', BMC Genetics, vol. 10, 7. https://doi.org/10.1186/1471-2156-10-7

TY - JOUR

T1 - Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean

AU - Pariset, Lorraine

AU - Joost, Stephane

AU - Marsan, Paolo Ajmone

AU - Valentini, Alessio

AU - Abo-Shehada, Mahamoud

AU - Jamil, Al Tarrayrah

AU - Angiolillo, Antonella

AU - Baret, Philip

AU - Baumung, Roswitha

AU - Beja-Pereira, Albano

AU - Bertaglia, Marco

AU - Bordonaro, Salvatore

AU - Bruford, Mike

AU - Caloz, Régis

AU - Canali, Gabriele

AU - Canon, Javier

AU - Cappuccio, Irene

AU - Carta, Antonello

AU - Cicogna, Mario

AU - Crepaldi, Paola

AU - Dalamitra, Stella

AU - Krugmann, Daniela

AU - Petrit, Dobi

AU - Popielarczyk, Dominik

AU - Susana, Dunner

AU - D'Urso, Giuseppe

AU - El-Barody, M. A.A.

AU - England, Phillip

AU - Erhardt, Georg

AU - Ertugrul, Okan

AU - Eva-Maria, Prinzenberg

AU - Eveline, Ibeagha Awemu

AU - Ewa, Strzelec

AU - Fadlaoui, Aziz

AU - Fornarelli, Francesca

AU - Garcia, David

AU - Georgoudis, Andreas

AU - Gesine, Lühken

AU - Giovenzana, Stefano

AU - Gutscher, Katja

AU - Hewitt, Godfrey

AU - Hoda, Anila

AU - Horst, Brandt

AU - Istvan, Anton

AU - Juma, Gabriela

AU - Joost, Stéphane

AU - Jones, Sam

AU - Karetsou, Katerina

AU - Kliambas, Georgios

AU - Koban, Evren

AU - Kutita, Olga

AU - Lazlo, Fesus

AU - Lenstra, Johannes A.

AU - Ligda, Christina

AU - Lipsky, Shirin

AU - Luikart, Gordon

AU - Marie-Louise, Glowatzki

AU - Marilli, Marta

AU - Marletta, Donata

AU - Milanesi, Elisabetta

AU - Negrini, Riccardo

AU - Nijman, Isaäc J.

AU - Obexer-Ruff, Gabriela

AU - Papachristoforou, Christos

AU - Pariset, Lorraine

AU - Pellecchia, Marco

AU - Peter, Christina

AU - Perez, Trinidad

AU - Pietrolà, Emilio

AU - Pilla, Fabio

AU - Roman, Niznikowski

AU - Roosen, Jutta

AU - Scarpa, Riccardo

AU - Sechi, Tiziana

AU - Taberlet, Pierre

AU - Taylor, Martin

AU - Togan, Inci

AU - Trommetter, Michel

AU - Van, Cann

AU - Lisette, M.

AU - Vlaic, Augustin

AU - Wiskin, Louise

AU - Zundel, Stéphanie

N1 - Funding Information: 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.

PY - 2009/2/19

Y1 - 2009/2/19

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=64049114149&partnerID=8YFLogxK

U2 - 10.1186/1471-2156-10-7

DO - 10.1186/1471-2156-10-7

M3 - Article

C2 - 19228375

AN - SCOPUS:64049114149

SN - 1471-2156

VL - 10

JO - BMC Genetics

JF - BMC Genetics

M1 - 7

ER -

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

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