|ZHOU, YANG - Northwest Agricultural & Forestry University|
|WIGGANS, GEORGE - Retired ARS Employee|
|LU, YONGFANG - Michigan State University|
|TEMPELMAN, ROBERT - Michigan State University|
|Schroeder, Steven - Steve|
|CHEN, HONG - Northwest Agricultural & Forestry University|
|Liu, Ge - George|
Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/18/2018
Publication Date: 5/2/2018
Citation: Zhou, Y., Connor, E.E., Wiggans, G.R., Lu, Y., Tempelman, R., Schroeder, S.G., Chen, H., Liu, G. 2018. Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle. BMC Genomics. 19(1):314. https://doi.org/10.1186/s12864-018-4699-5.
Interpretive Summary: Copy number variation (CNV) is an important type of genetic structural variation contributing to phenotypic differences among animals. A total of 191 CNV were indentified in a population of Holstein cows and used in a genome-wide association analysis of 10 economically important traits of cattle. There were 59 CNV found to be associated with at least one of the traits. Of primary interest, 2 feed intake-related traits, residual feed intake and dry matter intake, were found to be associated with CNV within the relaxin/insulin like family peptide receptor 4 (RXFP4) and 2 olfactory receptor gene regions, respectively. Our results identify CNV for genomic evaluation in Holstein cattle, and provide candidate genes contributing to variation in feed efficiency and intake-related traits that may be targeted for genetic selection. This information is useful to animal breeders, dairy scientists, and the dairy industry for understanding genetic factors contributing to variation in important production traits of dairy cattle.
Technical Abstract: Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals and may serve as an alternative molecular marker to single nucleotide polymorphism (SNP) for genome-wide association study (GWAS). Recently, GWAS analysis using CNV has been applied in livestock, although few studies have focused on Holstein cattle. Here, we describe 191 highly confident CNV detected using SNP genotypes generated with the BovineHD Genotyping BeadChip (Illumina, San Diego, CA) among 528 Holstein cows. The CNV were used for GWAS analysis of 10 important production traits of cattle related to feed intake, milk quality, and female fertility, as well as 2 composite traits of net merit and productive life. In total, we detected 59 CNV associated (P < 0.05 after FDR correction) with at least one phenotype. Focusing on feed efficiency and intake-related phenotypes of residual feed intake and dry matter intake, we detected 2 CNV (CNV32 and CNV66) within the RXFP4 and 2 olfactory receptor gene regions, respectively. The RXFP4 gene encodes a receptor for an orexigenic peptide, insulin-like peptide 5 produced by intestinal L cells, which is expressed by enteric neurons. Olfactory receptors are critical for transmitting the effects of odorants, contributing to the sense of smell, and have been implicated in participating in appetite regulation. Our results identify CNV for genomic evaluation in Holstein cattle, and provide candidate genes contributing to variation in feed efficiency and intake-related traits.