Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus

BMC Genomics

Research Article

El Hamidi abdel Hay¹  Steven G. Schroeder¹  Derek M. Bickhart¹  Benjamin D. Rosen¹  Curtis P. Van Tassell¹  George E. Liu¹  Yang Zhou²  Lingyang Xu³  Tad S. Sonstegard⁴  Yuri T. Utsunomiya⁵  Jose Fernando Garcia⁶  Roberto Carvalheiro⁷  Haroldo Henrique de Rezende Neves⁷  Pamela Almeida Alexandre⁸  Heidge Fukumasu⁸  José Bento Sterman Ferraz⁸ 

[1] Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, 20705, Beltsville, Maryland, USA;Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, 20705, Beltsville, Maryland, USA;College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, 712100, Yangling, Shaanxi, China;Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, 20705, Beltsville, Maryland, USA;Institute of Animal Science, Chinese Academy of Agricultural Science, 100193, Beijing, China;Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, 20705, Beltsville, Maryland, USA;Present address: Recombinetics, Inc., 55104, St Paul, MN, USA;Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, 14884-900, Jaboticabal, São Paulo, Brazil;Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, 14884-900, Jaboticabal, São Paulo, Brazil;Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP – Univ Estadual Paulista, 16050-680, Araçatuba, São Paulo, Brazil;International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil;Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, 14884-900, Jaboticabal, São Paulo, Brazil;Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, 13635, Pirassununga, SP, Brazil;

关键词: Copy number variation (CNV);    EBV;    Association;    Body size;    Bos indicus;   

DOI  :  10.1186/s12864-016-2461-4

 received in 2015-08-17, accepted in 2016-02-11,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundApart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed).ResultsWe have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits.ConclusionThis study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.

【 授权许可】

CC BY   
© Zhou et al. 2016