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
 close



Research
                Research Home
                            National Programs
                            Research Projects
                            Scientific Manuscripts
                            International Engagement
                            Scientific Software/Models
                            Databases and Datasets
                            Office of Scientific Quality Review
            Media
                News & Features
                            Multimedia
                            Briefing Room
                            Down on the Farm
                            Press Room
                            Science in Your Shopping Cart
                            Scientific Discoveries
                            Tellus
                            Under the Microscope
            About ARS
                About ARS Home
                            Staff Directory
                            Labs and Research Centers (Map)
                            Headquarter Offices
                            Organizational Chart
                            Employee Services (REE Employees Only)
                            Office of Outreach, Diversity, and Equal Opportunity
            Work With Us
                Work With Us Home
                            ARS Vacancies at USAJOBS
                            Careers at ARS Information
                            Scientific Collaborations
                            Extramural Agreements
                            1890 Faculty Research Sabbatical ProgramSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home 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

Title:   Author  item
                                            Wiggans, Georgeitem
                                            Vanraden, Paulitem
                                            Bacheller, Lillianitem
                                            Tooker, Melvinitem
                                            Hutchison, Janaitem
                                            Cooper, Tabathaitem
                                            Sonstegard, Tad
  Submitted to: Journal of Dairy Science
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 1/18/2010
                                    Publication  Date: 5/1/2010
                                    Citation: Wiggans, G.R., Van Raden, P.M., Bacheller, L.R., Tooker, M.E., Hutchison, J.L., Cooper, T.A., Sonstegard, T.S. 2010. Selection and management of DNA markers for use in genomic evaluation. Journal of Dairy Science. 93(5):2287-2292.Interpretive Summary: A database was developed to store single-nucleotide polymorphisms (SNP) genotypes from the BovineSNP50 BeadChip. A usability indicator was included so that only sample genotypes consistent with pedigree are used in SNP selection and genomic evaluation. Historical data were reprocessed to obtain genotypes for 50,972 SNP, and a set of 43,385 SNP were selected for the Holstein, Jersey and Brown Swiss breeds. New edits included conflict rate and call rate for each SNP, and all edits except minor allele frequency were applied across breed. Including females, very old bulls, and the larger set of SNP in predictions had only small effects on reliability. Genomic predictions for all 3 breeds became official in 2009. Predictions had higher reliability than parent average by 30% for Holstein, 12% for Jersey, and 8% for Brown Swiss when averaged across traits indicating the benefit of genomic evaluation.
                                Technical Abstract: A database was constructed to store genotypes for 50,972 single-nucleotide polymorphisms (SNP) from the Illumina BovineSNP50 BeadChip for over 30,000 animals. The database allows storage of multiple samples per animal and stores all SNP genotypes for a sample in a single row. An indicator specifies if the genotype for that sample is used in genomic evaluation. Samples with low call rates or pedigree conflicts are marked not usable. Among acceptable samples, the one with the highest call rate is marked as usable. When more than 1 sample is stored for an animal, a composite is formed during extraction by using SNP genotypes from the other samples to fill in ones that are missing. Scanner output for nearly 19,000 samples was reprocessed, and all genotypes were edited using the editing system for the new database. Genomic evaluation in August 2009 used 43,385 SNP as compared to 38,416 for Holstein, 31,658 for Jersey, and 34,593 for Brown Swiss used previously, and SNP were selected if minor allele frequency was above 1% in any of the 3 breeds. A low number of parent-progeny conflicts (< 1%) and high call rate (> 90%) were additional requirements for SNP selection. Because monomorphic SNP did not degrade convergence, a single set of SNP was adopted for all breeds. November 2004 genomic predictions had higher reliability than parent average by 30.4% for Holstein, 11.6% for Jersey, and 8.3% for Brown Swiss when averaged across traits. Including females, very old bulls, and the larger set of SNP in predictions had only small effects on reliability. The use of a database for genotypes, detection of conflicts as genotypes are stored, and use of a single set of SNP for genomic evaluations have simplified genomic evaluation as a routine and official process.


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