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Copy Number Deletion Has Little Impact on Gene Expression Levels in Racehorses

  • Park, Kyung-Do (Genomic Informatics Center, Hankyong National University) ;
  • Kim, Hyeongmin (Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University) ;
  • Hwang, Jae Yeon (Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University) ;
  • Lee, Chang-Kyu (Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University) ;
  • Do, Kyoung-Tag (Genomic Informatics Center, Hankyong National University) ;
  • Kim, Heui-Soo (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Yang, Young-Mok (Department of Pathology, School of Medicine, and Institute of Biomedical Science and Technology, Konkuk University) ;
  • Kwon, Young-Jun (Interdisciplinary Program in Bioinformatics, Seoul National University) ;
  • Kim, Jaemin (Interdisciplinary Program in Bioinformatics, Seoul National University) ;
  • Kim, Hyeon Jeong (CHO & KIM genomics) ;
  • Song, Ki-Duk (Genomic Informatics Center, Hankyong National University) ;
  • Oh, Jae-Don (Genomic Informatics Center, Hankyong National University) ;
  • Kim, Heebal (Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University) ;
  • Cho, Byung-Wook (Department of Animal Science, College of Life Sciences, Pusan National University) ;
  • Cho, Seoae (CHO & KIM genomics) ;
  • Lee, Hak-Kyo (Genomic Informatics Center, Hankyong National University)
  • Received : 2013.12.30
  • Accepted : 2014.05.12
  • Published : 2014.09.01

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.

Keywords

Copy Number Variation;Genome-wide Expression;Horse;Thoroughbred

Acknowledgement

Supported by : National Research Foundation of Korea

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