Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers

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

Research output: Contribution to journalArticlepeer-review

Abstract

Background: During the past decades, neutral DNA markers have been extensively employed to study demography, population genetics and structure in livestock, but less interest has been devoted to the evaluation of livestock adaptive potential through the identification of genomic regions likely to be under natural selection. Methodology/Principal findings: Landscape genomics can greatly benefit the entire livestock system through the identification of genotypes better adapted to specific or extreme environmental conditions. Therefore we analyzed 101 AFLP markers in 43 European and Western Asian goat breeds both with MATSAM software, based on a correlative approach (SAM), and with MCHEZA and BAYESCAN, two FST based software able to detect markers carrying signatures of natural selection. MATSAM identified four loci possibly under natural selection - also confirmed by FST-outlier methods - and significantly associated with environmental variables such as diurnal temperature range, frequency of precipitation, relative humidity and solar radiation. Conclusions/Significance: These results show that landscape genomics can provide useful information on the environmental factors affecting the adaptive potential of livestock living in specific climatic conditions. Besides adding conservation value to livestock genetic resources, this knowledge may lead to the development of novel molecular tools useful to preserve the adaptive potential of local breeds during genetic improvement programs, and to increase the adaptability of industrial breeds to changing environments.

Original languageEnglish
Article numbere86668
JournalPLoS ONE
Volume9
Issue number1
DOIs
StatePublished - Jan 30 2014

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