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

dc.contributor.authorXu, Lingyang
dc.contributor.authorCole, John B
dc.contributor.authorBickhart, Derek M
dc.contributor.authorHou, Yali
dc.contributor.authorSong, Jiuzhou
dc.contributor.authorVanRaden, Paul M
dc.contributor.authorSonstegard, Tad S
dc.contributor.authorVan Tassell, Curtis P
dc.contributor.authorLiu, George E
dc.date.accessioned2021-09-20T19:20:52Z
dc.date.available2021-09-20T19:20:52Z
dc.date.issued2014-08-15
dc.description.abstractMilk 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. 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. We conclude that combining CNV with SNP analyses reveals more genetic variations underlying milk production traits than those revealed by SNPs alone.en_US
dc.description.urihttps://doi.org/10.1186/1471-2164-15-683
dc.identifierhttps://doi.org/10.13016/qlin-kfov
dc.identifier.citationXu, L., Cole, J.B., Bickhart, D.M. et al. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BMC Genomics 15, 683 (2014).en_US
dc.identifier.urihttp://hdl.handle.net/1903/27884
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Agriculture & Natural Resourcesen_us
dc.relation.isAvailableAtAnimal & Avian Sciencesen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectCopy number variation (CNV)en_US
dc.subjectdPTAen_US
dc.subjectAssociationen_US
dc.subjectMilk production traitsen_US
dc.titleGenome wide CNV analysis reveals additional variants associated with milk production traits in Holsteinsen_US
dc.typeArticleen_US
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