U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 Animal Genomics and Improvement Laboratory: Beltsville, MD
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                                    Software
                People

                    Staff Listing
                                    Careers


        


                    AIP
                        Home
                                    About
                                    Publications
                                    Software
                                    People
                                    Collaborations
                                    Careers
                                    Centennial
                                    Contact
                                    Dairy industry links
                    DirectionsSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Animal Genomics and Improvement Laboratory Research Publications at this Location





- ARS National Programs
- Search for a scientific manuscript
- Search for a research project
- ARS Software
- Programs and Projects
- Collaborations
- Subjects of Investigation
- Publications
- IACUC
- Home
- About
- Publications
- Software
- People
- Collaborations
- Careers
- Centennial
- Contact
- Dairy industry links
- Home
- Queries login
- News
- Animal Evaluation lists
- Genotype counts

Title:   Author  item
                                            Bickhart, Derekitem
                                            XU, LINGYANG - University Of Marylanditem
                                            Hutchison, Janaitem
                                            Cole, Johnitem
                                            Schroeder, Steven

                                                         - *Steve*item
                                            SONG, JUIZHOU - University Of Marylanditem
                                            GARCIA, JOSE FERNANDO - Faculdade De Ciências Agrárias E Veterinárias De Jaboticabal-Unespitem
                                            Van Tassell, Curtis

                                                         - *Curt*item
                                            Sonstegard, Taditem
                                            SCHNABEL, ROBERT - University Of Missouriitem
                                            TAYLOR, JEREMY - University Of Missouriitem
                                            LEWIN, HARRIS - University Of Californiaitem
                                            Liu, Ge

                                                         - *George*
  Submitted to: DNA Research
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 2/29/2016
                                    Publication  Date: 4/15/2016
                                    Citation: Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes. DNA Research. 23(3):253-62.Interpretive Summary: Structural and functional impacts of copy number variations (CNVs) on livestock genomes are not yet well understood. We identified 1853 CNV regions (CNVRs) using population-scale sequencing data generated from 75 cattle of 8 breeds. We porformed the first detailed population-genetic analyses of cattle CNVs and multicopy genes in modern domesticated cattle. These CNV results provide a new glimpse of diverse selections during cattle speciation, domestication, breed formation, and recent genetic improvement. Farmers, scientist, and policy planners who need to improve animal health and production based on genome-enable animal selection will benefit from this manuscript.
                                Technical Abstract: Structural and functional impacts of copy number variations (CNVs) on livestock genomes are not yet well understood. We identified 1853 CNV regions using population-scale sequencing data generated from 75 cattle representing 8 breeds (Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, Romagnola). Individual genome sequence coverage ranged from 4 to 30 fold, with a mean of 11.8 fold. A total of 3.1% (87.5 Mb) of the cattle genome is predicted to be copy number variable, representing a substantial increase over previous estimates (~2%). CNV calls made with sequence data showed good correlation with array comparative genomic hybridization (CGH) data (r2 = 0.761) and had an estimated 12% false positive rate and a 19% false negative rate based upon qPCR and array CGH, respectively. Hundreds of CNVs were found to be either breed specific or differentially variable across breeds, including the RICTOR gene in dairy breeds and the PNPLA3 gene in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization or overdominance play roles in diversifying those fertility related genes. Further population-genetic analyses based on CNVs revealed the population structures of these taurine and indicine breeds and uncovered potential positively selected CNV candidates near important functional genes, such as AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds during speciation, domestication, breed formation, and more recently, genetic improvement.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov