Diversity of copy number variation in the worldwide goat population

Authors: LIU, MEI - Northwest Agricultural & Forestry University; ZHOU, YANG - Huazhong Agricultural University; Rosen, Benjamin - Ben; Van Tassell, Curtis - Curt; STELLA, ALESSANDRA - Parco Tecnologico Padano; TOSSER, GWENOLA - Institut National De La Recherche Agronomique (INRA); RUPP, RACHEL - Institut National De La Recherche Agronomique Du Niger (INRAN); PALHIERE, ISABELLE - Institut National De La Recherche Agronomique (INRA); COLLI, LICIA - Catholic University Of The Sacred Heart Italy; SAYRE, BRIAN - Virginia State University; CREPALDI, PAOLA - Universit Di Milano; FANG, LINGZHAO - Collaborator; MESZAROS, GABOR - University Of Natural Resources & Applied Life Sciences - Austria; CHEN, HONG - Northwest Agriculture And Forestry University; Liu, Ge - George; ADAPTMAP CONSORTIUM - Collaborator

Submitted to: Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/18/2018
Publication Date: 11/6/2018
Citation: Liu, M., Zhou, Y., Rosen, B.D., Van Tassell, C.P., Stella, A., Tosser, G., Rupp, R., Palhiere, I., Colli, L., Sayre, B., Crepaldi, P., Fang, L., Meszaros, G., Chen, H., Liu, G., Adaptmap Consortium. 2018. Diversity of copy number variation in the worldwide goat population. Heredity. 122:636–646. https://doi.org/10.1038/s41437-018-0150-6.
DOI: https://doi.org/10.1038/s41437-018-0150-6

Interpretive Summary: Copy number variation (CNV) represents a major source of genomic variation. Using SNP array data collected from a large collection of goat, we systematically stuided CNV distribution across goat breeeds. These results fill our knowledge gaps and provide the foundation for future studies of CNV role in genome evolution and selection. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: Goat (Capra hircus) represents one of the most important farm animal species. Copy number variation (CNV) is a major source of genomic variation. The object of this research is to investigate the diversity of CNV distribution using Illumina SNP50 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 according to the geography distribution and constructed a comparative CNV map. Our results reveal a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa and Southeastern Africa groups. Based on the CNV count per individual across different groups, we performed a cluster heatmap analysis and obtained a result, which was 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 (EDNRA, ADAMTS2, CHRNB1, CLCN7, EXOSC4, and DGAT1), which are involved in local adaptations such as coat color, osteopetrosis, embryonic development and metabolic processes. In summary, our study generated a comprehensive CNV map in a worldwide population of goat, which offer novel insights into the goat genome and its functional annotation.