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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #348215

Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Diversity of copy number variation in the worldwide goat population

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

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.