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

Mei Liu, Jennifer Woodward-Greene, Xiaolong Kang, Michael G. Pan, Benjamin Rosen, Curtis P. Van Tassell, Hong Chen, George E. Liu
Genomics 2020 v.112 no.2 pp. 1477-1480
gene dosage, gene ontology, genes, genetic variation, genotype-phenotype correlation, goat breeds, goats, growth traits, indigenous species, meat production, regression analysis, reproductive traits, single nucleotide polymorphism
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. Three significant associations were identified between two CNVs and two body traits after false discovery rate (FDR) correction (P < .05). One of them (CNV27) was significantly associated with both chest width and width of pin bones. It overlaps the SNX29 gene, the Gene Ontology (GO) annotations of which indicate CNV27 could be a potential functional candidate for meat production, health and reproduction traits. To our knowledge, this study is the first CNV-based association test of growth traits using SNP chip data in African meat goats.