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Open Access Research article

Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins

Lingyang Xu12, John B Cole1, Derek M Bickhart1, Yali Hou3, Jiuzhou Song2, Paul M VanRaden1, Tad S Sonstegard1, Curtis P Van Tassell1 and George E Liu1*

Author Affiliations

1 Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA

2 Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA

3 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

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BMC Genomics 2014, 15:683  doi:10.1186/1471-2164-15-683

Published: 15 August 2014

Abstract

Background

Milk production is an economically important sector of global agriculture. Much attention has been paid to the identification of quantitative trait loci (QTL) associated with milk, fat, and protein yield and the genetic and molecular mechanisms underlying them. Copy number variation (CNV) is an emerging class of variants which may be associated with complex traits.

Results

In this study, we performed a genome-wide association between CNVs and milk production traits in 26,362 Holstein bulls and cows. A total of 99 candidate CNVs were identified using Illumina BovineSNP50 array data, and association tests for each production trait were performed using a linear regression analysis with PCA correlation. A total of 34 CNVs on 22 chromosomes were significantly associated with at least one milk production trait after false discovery rate (FDR) correction. Some of those CNVs were located within or near known QTL for milk production traits. We further investigated the relationship between associated CNVs with neighboring SNPs. For all 82 combinations of traits and CNVs (less than 400 kb in length), we found 17 cases where CNVs directly overlapped with tag SNPs and 40 cases where CNVs were adjacent to tag SNPs. In 5 cases, CNVs located were in strong linkage disequilibrium with tag SNPs, either within or adjacent to the same haplotype block. There were an additional 20 cases where CNVs did not have a significant association with SNPs, suggesting that the effects of those CNVs were probably not captured by tag SNPs.

Conclusion

We conclude that combining CNV with SNP analyses reveals more genetic variations underlying milk production traits than those revealed by SNPs alone.

Keywords:
Copy number variation (CNV); dPTA; Association; Milk production traits