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

doi:10.1016/j.ygeno.2019.08.018

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

Genomics. 2020 Mar;112(2):1477-1480. doi: 10.1016/j.ygeno.2019.08.018. Epub 2019 Aug 23.

Authors

Mei Liu¹, Jennifer Woodward-Greene², Xiaolong Kang³, Michael G Pan⁴, Benjamin Rosen⁵, Curtis P Van Tassell⁶, Hong Chen⁷, George E Liu⁸

Affiliations

¹ Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA; College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China. Electronic address: chmeier158@gmail.com.
² Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA. Electronic address: Jennifer.Woodward@ARS.USDA.GOV.
³ Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA; College of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China. Electronic address: garykang513@gmail.com.
⁴ Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA. Electronic address: mpan9999@gmail.com.
⁵ Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA. Electronic address: Ben.Rosen@ARS.USDA.GOV.
⁶ Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA. Electronic address: Curt.VanTassell@ARS.USDA.GOV.
⁷ College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China. Electronic address: chenhong1212@263.net.
⁸ Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA. Electronic address: George.Liu@ars.usda.gov.

PMID: 31450006
DOI: 10.1016/j.ygeno.2019.08.018

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. 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.

Keywords: African goats; Association; Body size; Copy number variation.

Published by Elsevier Inc.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Body Size / genetics*
DNA Copy Number Variations*
Goats / genetics*
Goats / growth & development
Quantitative Trait Loci*
Quantitative Trait, Heritable
Selective Breeding