Selection signatures in worldwide sheep populations

Maria Ines Fariello; Bertrand Servin; Gwenola Tosser-Klopp; Rachel Rupp; Carole Moreno; Magali San Cristobal; Simon Boitard; Juan Jose Arranz; Georgios Banos; William Barendse; Ahmedn El Beltagy; Jorn Benenwitz; Steven Bishop; Lutz Bunger; Jorge Calvo; Antonello Carta; Ibrahim Cemal; Elena Ciani; Noelle Cockett; Dave Coltman; Brian Dalrymple; Mariasilvia D'Andrea; Ottmar Distl; Cord Drogemuller; Georg Erhardt; Emma Eythorsdottir; Kimberly Gietzen; Clare Gill; Elisha Gootwine; Vidya Gupta; Olivier Hanotte; Ben Hayes; Michael Heaton; Stefan Hiendleder; Han Jialin; Juha Kantanen; Matthew Kent; James Kijas; Denis Larkin; Johannes A. Lenstra; Kui Li; Terry Longhurst; Runlin Ma; Russell McCulloch; David MacHugh; Sean McWilliam; John McEwan; Jillian Maddox; Massoud Malek; Faruque Mdomar; Despoina Miltiadou; Luis V. Monteagudo Ibez; Frank Nicholas; Kristen Nowak; V. Hutton Oddy; Samuel Paiva; Varsha Pardeshi; Josephine Pemberton; Fabio Pilla; Laercio R. Porto Neto; Herman Raadsma; Cyril Roberts; Magali San Cristobal; Tiziana Sechi; Paul Scheet; Mohammad Shariflou; Pradeepa Silva; Henner Simianer; Jon Slate; Mikka Tapio; Selina Vattathil; Vicki Whan

doi:10.1371/journal.pone.0103813

Selection signatures in worldwide sheep populations

Maria Ines Fariello, Bertrand Servin, Gwenola Tosser-Klopp, Rachel Rupp, Carole Moreno, Magali San Cristobal, Simon Boitard, Juan Jose Arranz, Georgios Banos, William Barendse, Ahmedn El Beltagy, Jorn Benenwitz, Steven Bishop, Lutz Bunger, Jorge Calvo, Antonello Carta, Ibrahim Cemal, Elena Ciani, Noelle Cockett, Dave ColtmanBrian Dalrymple, Mariasilvia D'Andrea, Ottmar Distl, Cord Drogemuller, Georg Erhardt, Emma Eythorsdottir, Kimberly Gietzen, Clare Gill, Elisha Gootwine, Vidya Gupta, Olivier Hanotte, Ben Hayes, Michael Heaton, Stefan Hiendleder, Han Jialin, Juha Kantanen, Matthew Kent, James Kijas, Denis Larkin, Johannes A. Lenstra, Kui Li, Terry Longhurst, Runlin Ma, Russell McCulloch, David MacHugh, Sean McWilliam, John McEwan, Jillian Maddox, Massoud Malek, Faruque Mdomar, Despoina Miltiadou, Luis V. Monteagudo Ibez, Frank Nicholas, Kristen Nowak, V. Hutton Oddy, Samuel Paiva, Varsha Pardeshi, Josephine Pemberton, Fabio Pilla, Laercio R. Porto Neto, Herman Raadsma, Cyril Roberts, Magali San Cristobal, Tiziana Sechi, Paul Scheet, Mohammad Shariflou, Pradeepa Silva, Henner Simianer, Jon Slate, Mikka Tapio, Selina Vattathil, Vicki Whan

Epidemiology

Research output: Contribution to journal › Article › peer-review

119 Scopus citations

Abstract

The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.

Original language	English (US)
Article number	e103813
Journal	PloS one
Volume	9
Issue number	8
DOIs	https://doi.org/10.1371/journal.pone.0103813
State	Published - Aug 15 2014

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Fariello, M. I., Servin, B., Tosser-Klopp, G., Rupp, R., Moreno, C., Cristobal, M. S., Boitard, S., Arranz, J. J., Banos, G., Barendse, W., El Beltagy, A., Benenwitz, J., Bishop, S., Bunger, L., Calvo, J., Carta, A., Cemal, I., Ciani, E., Cockett, N., ... Whan, V. (2014). Selection signatures in worldwide sheep populations. PloS one, 9(8), Article e103813. https://doi.org/10.1371/journal.pone.0103813

Fariello, MI, Servin, B, Tosser-Klopp, G, Rupp, R, Moreno, C, Cristobal, MS, Boitard, S, Arranz, JJ, Banos, G, Barendse, W, El Beltagy, A, Benenwitz, J, Bishop, S, Bunger, L, Calvo, J, Carta, A, Cemal, I, Ciani, E, Cockett, N, Coltman, D, Dalrymple, B, D'Andrea, M, Distl, O, Drogemuller, C, Erhardt, G, Eythorsdottir, E, Gietzen, K, Gill, C, Gootwine, E, Gupta, V, Hanotte, O, Hayes, B, Heaton, M, Hiendleder, S, Jialin, H, Kantanen, J, Kent, M, Kijas, J, Larkin, D, Lenstra, JA, Li, K, Longhurst, T, Ma, R, McCulloch, R, MacHugh, D, McWilliam, S, McEwan, J, Maddox, J, Malek, M, Mdomar, F, Miltiadou, D, Monteagudo Ibez, LV, Nicholas, F, Nowak, K, Oddy, VH, Paiva, S, Pardeshi, V, Pemberton, J, Pilla, F, Porto Neto, LR, Raadsma, H, Roberts, C, San Cristobal, M, Sechi, T, Scheet, P, Shariflou, M, Silva, P, Simianer, H, Slate, J, Tapio, M, Vattathil, S & Whan, V 2014, 'Selection signatures in worldwide sheep populations', PloS one, vol. 9, no. 8, e103813. https://doi.org/10.1371/journal.pone.0103813

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abstract = "The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.",

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AU - Cristobal, Magali San

AU - Boitard, Simon

AU - Arranz, Juan Jose

AU - Banos, Georgios

AU - Barendse, William

AU - El Beltagy, Ahmedn

AU - Benenwitz, Jorn

AU - Bishop, Steven

AU - Bunger, Lutz

AU - Calvo, Jorge

AU - Carta, Antonello

AU - Cemal, Ibrahim

AU - Ciani, Elena

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AU - Coltman, Dave

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AU - Eythorsdottir, Emma

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AU - Gill, Clare

AU - Gootwine, Elisha

AU - Gupta, Vidya

AU - Hanotte, Olivier

AU - Hayes, Ben

AU - Heaton, Michael

AU - Hiendleder, Stefan

AU - Jialin, Han

AU - Kantanen, Juha

AU - Kent, Matthew

AU - Kijas, James

AU - Larkin, Denis

AU - Lenstra, Johannes A.

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AU - Longhurst, Terry

AU - Ma, Runlin

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AU - MacHugh, David

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Selection signatures in worldwide sheep populations

Abstract

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