Signatures of selection and environmental adaptation across the goat genome post-domestication

Authors: BERTOLINI, FRANCESCA - Iowa State University; SERVIN, BERTRAND - Institut National De La Recherche Agronomique (INRA); TALENTI, ANDREA - University Of Milano; ROCHAT, ESTELLE - Ecole Polytechnique Federale De Lausanne (EPFL); KIM, EUI-SOO - Recombinetics, Inc; OGET, CLAIRE - Institut National De La Recherche Agronomique (INRA); PALHIERE, ISABELLE - Institut National De La Recherche Agronomique (INRA); CRISA, ALESSANDRA - Collaborator; CATILLO, GENNARO - Collaborator; STERI, ROBERTO - Collaborator; AMILLS, MARCEL - Autonomous University Of Barcelona; COLLI, LICIA - Università Cattolica Del Sacro Cuore; MARRAS, GABRIELE - Parco Tecnologico Padano; MILANESI, MARCO - Università Cattolica Del Sacro Cuore; NICOLAZZI, EZEQUIEL - Parco Tecnologico Padano; Rosen, Benjamin - Ben; Van Tassell, Curtis - Curt; GULDBRANDTSEN, BERNT - Aarhus University; SONSTEGARD, TAD - Recombinetics, Inc; TOSSER-KLOPP, GWENOLA - Institut National De La Recherche Agronomique (INRA); STELLA, ALESSANDRA - Parco Tecnologico Padano; ROTHSCHILD, MAX - Iowa State University; JOOST, STEPHANE - Ecole Polytechnique Federale De Lausanne (EPFL); CREPALDI, PAOLA - University Of Milano

Submitted to: Genetic Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/15/2019
Publication Date: 11/19/2018
Citation: Bertolini, F., Servin, B., Talenti, A., Rochat, E., Kim, E., Oget, C., Palhiere, I., Crisa, A., Catillo, G., Steri, R., Amills, M., Colli, L., Marras, G., Milanesi, M., Nicolazzi, E., Rosen, B.D., Van Tassell, C.P., Guldbrandtsen, B., Sonstegard, T.S., Tosser-Klopp, G., Stella, A., Rothschild, M.F., Joost, S., Crepaldi, P. 2018. Signatures of selection and environmental adaptation across the goat genome post-domestication. Genetic Selection Evolution. 50:57. https://doi.org/10.1186/s12711-018-0421-y.
DOI: https://doi.org/10.1186/s12711-018-0421-y

Interpretive Summary: There are approximately 600 breeds of goats worldwide with great phenotypic variation and that are adapted to a range of climactic conditions. A selection of goat breeds from diverse geographical areas were analyzed to identify regions in the genome that are involved in important biological processes, such as milk, meat or fiber related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. This analysis provides a comprehensive first look across the global domestication processes and adaptation of goats and underline possible genes that have been contributing to the differentiation of this species worldwide.

Technical Abstract: Background: Many factors have contributed to differentiating goat breeds since the goat was domesticated 10,000 years ago. These factors can be mainly classified into two types: i) adaptation to different breeding systems and/or purposes and ii) adaptation to different environments. All of this has led to the development of approximately 600 breeds worldwide that greatly vary from each other in many phenotypic aspects and are adapted to a wide range of climatic conditions. In this research, the ADAPTmap goat dataset, which is composed of data from more than 3,000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip, was analyzed using several groups of animals based on partitioning by geographical area, production uses, available solid coat color records and environmental variables including the sampling's geographical coordinates to investigate the role of natural and/or artificial selection in shaping the different goat genomes. Results: Several signatures of selection in different chromosomic regions have been detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk, meat or fiber related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences, confirming previous findings in other species about adaptation to extreme environments and human purposes and provide new genes that could explain goat differentiation to geographical distributions and adaptation to different environments. Conclusion: These signatures of selections analyses provide a comprehensive first look across the global domestication processes and adaptation of goats and underline possible genes that have been contributing to the differentiation of this species worldwide.