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Diversity of copy number variation in the worldwide goat population

Abstract

Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map. Our results revealed a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa, and Southeastern Africa groups. The results of a cluster heatmap analysis based on the CNV count per individual across different groups was generally consistent with the one generated from the SNP data, likely reflecting the population history of different goat breeds. We sought to determine the gene content of these CNV events and found several important CNV-overlapping genes (e.g. EDNRA, ADAMTS20, ASIP, KDM5B, ADAM8, DGAT1, CHRNB1, CLCN7, and EXOSC4), which are involved in local adaptations such as coat color, muscle development, metabolic processes, osteopetrosis, and embryonic development. Therefore, this research generated an extensive CNV map in the worldwide population of goat, which offers novel insight into the goat genome and its functional annotation.

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Acknowledgements

This work was supported in part by AFRI grant no. 2013-67015-20951 from USDA NIFA and grant no. US-4997-17 from the US-Israel Binational Agricultural Research and Development Fund. We thank members of the ADAPTmap Consortium and Italian Goat consortium for sharing their data. We thank Daniel Allain, Michel Naves, Nathalie Mandonnet (INRA, France), Coralie Danchin (IDELE, France), Pierre Martin (Capgenes, France), George C. Fthenakis (University of Thessaly, Greece), Wen Wang and Wenguang Zhang (KIZ, China) for the sample collection and data provided in this research. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. The USDA is an equal opportunity provider and employer.

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Correspondence to George E. Liu.

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