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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 #361257

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

Location: Animal Genomics and Improvement Laboratory

Title: Genome-wide CNV analysis revealed variants associated with growth traits in African indigenous goats

Author
item LIU, MEI - NORTHWEST AGRICULTURAL & FORESTRY UNIVERSITY
item Woodward-Greene, Jennifer
item KANG, XIAOLONG - NINGXIA UNIVERSITY
item PAN, MICHAEL - VOLUNTEER
item Rosen, Benjamin
item Van Tassell, Curtis - Curt
item CHEN, HONG - NORTHWEST AGRICULTURAL & FORESTRY UNIVERSITY
item Liu, Ge - George

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2019
Publication Date: 3/1/2020
Citation: Liu, M., Woodward Greene, M.J., Kang, X., Pan, M.G., Rosen, B.D., Van Tassell, C.P., Chen, H., Liu, G. 2020. Genome-wide CNV analysis revealed variants associated with growth traits in African indigenous goats. Genomics. 112(2):1477-1480. https://doi.org/10.1016/j.ygeno.2019.08.018.
DOI: https://doi.org/10.1016/j.ygeno.2019.08.018

Interpretive Summary: Copy number variation (CNV) represents a major source of genomic variation. By performing the first goat genome-wide association studies based on CNVs called from SNP chips, we explored their relationships with meat growth traits. These results fill our knowledge gaps and provide the foundation for incorporating CNV into the future goat breeding program. 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: Using the CaprineSNP50 data generated by the AGIN consortium, we detected common CNVs in 126 samples from four African indigenous goat breeds. A total of 30 CNVs ranging from 30,237 bp to 4,910,757 bp were identified. These CNVs were then associated with six growth traits by a linear regression analysis with principal components correction. Three significant associations were identified between two CNVs and two body traits after false discovery rate (FDR) correction (P < 0.05). One of them (CNV27) was significantly associated with both chest width and width of pin bones. It overlaps the SNX29 gene, whose Gene Ontology (GO) annotations are related to microtubule motor activity and phosphatidylinositol binding, indicating it could be a potential functional candidate for meat production traits. To our knowledge, this study is the first CNV-based association test of growth traits using SNP chip data in African meat goats.