title: Copy number deletion has little impact on gene expression levels in racehorses.
abstract: Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.
authors.affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.
authors.forename: Kyung-Do
authors.initials: KD
authors.lastname: Park
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea .
authors.forename: Hyeongmin
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea .
authors.forename: Jae Yeon
authors.initials: JY
authors.lastname: Hwang
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea .
authors.forename: Chang-Kyu
authors.initials: CK
authors.lastname: Lee
authors.affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.
authors.forename: Kyoung-Tag
authors.initials: KT
authors.lastname: Do
authors.affiliation: Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea .
authors.forename: Heui-Soo
authors.initials: HS
authors.lastname: Kim
authors.affiliation: Department of Pathology, School of Medicine, and Institute of Biomedical Science and Technology, Konkuk University, Seoul 143-701, Korea .
authors.forename: Young-Mok
authors.initials: YM
authors.lastname: Yang
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea .
authors.forename: Young-Jun
authors.initials: YJ
authors.lastname: Kwon
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea .
authors.forename: Jaemin
authors.initials: J
authors.lastname: Kim
authors.affiliation: CHO & KIM genomics, Seoul 151-919, Korea .
authors.forename: Hyeon Jeong
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.
authors.forename: Ki-Duk
authors.initials: KD
authors.lastname: Song
authors.affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.
authors.forename: Jae-Don
authors.initials: JD
authors.lastname: Oh
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea . ; CHO & KIM genomics, Seoul 151-919, Korea .
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Animal Science, College of Life Sciences, Pusan National University, Miryang 627-702, Korea .
authors.forename: Byung-Wook
authors.initials: BW
authors.lastname: Cho
authors.affiliation: CHO & KIM genomics, Seoul 151-919, Korea .
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.
authors.forename: Hak-Kyo
authors.initials: HK
authors.lastname: Lee
keywords: Copy Number Variation; Genome-wide Expression; Horse; Thoroughbred