Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): 1) Use the BovineSNP50 assay to provide high-accuracy predictions of genetic merit to U.S. dairy and beef breeds. 2) Enable the adoption of WGEAS by developing low-density and low-cost SNP assays for: a) intermediate-accuracy genetic prediction, b) mate selection, and c) parentage verification and traceability. 3) Develop, adapt and optimize statistical metodologies to: a) fully integrate SNP genotype or haplotype effects into existing genetic evaluation technologies, and b) supplement or replace pedigree data. 4)Collaborate and coordinate U.S. and European Union WGEAS activities. Approach (from AD-416): 1) Collect genotypic data using the bovineSNP50 in both dairy and beef cattle breeding programs. 2) Develop statistical algorithms needed to implement whole genome enabled animal selection specific to dairy and beef cattle populations as needed. 3) Determine subset of markers needed for low density SNP assay for application to parentage verification and reduced accuracy genetic prediction. 4) Collaborate with many organizations to utilize data generated by this project as well as other projects to obtain maximum utilization of resources generated. Activities during this project period included: 1) continued genomic re- sequencing of animals for the purposes of single nucleotide polymorphism (SNP) discovery, diversity characterization, and fine mapping of causative mutations, 2) analysis of beadchip genotypic data for the continued refinement of genetic prediction equations within breed, 3) collaborative development of the beadchips as enhanced-value genotyping platforms optimized for value and imputation, and 4) identification of haplotypes affecting fertility in Holstein, Jersey, and Brown Swiss breeds of cattle. Through industry partnerships, over 500,000 animals to date were genotyped using a variety of platforms. These data are being used for the estimation of genomic breeding values in the dairy and beef industries. The rate of growth of data collection for genotypes continues to accelerate in both industries. The BovineLD assay and products derived from this platform were rapidly adopted in dairy cattle genetic evaluations. The vast majority of animals recently genotyped were done using a BovineLD or derived assay. This research supports two objectives of its related in-house project: 1) to use genotypic data and the resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches (Objective 2), and 2) to characterize conserved genome elements and identify functional genetic variation (Objective 3).
Impacts
(N/A)
Publications
|
Progress 09/01/09 to 08/31/12
Outputs
Progress Report Objectives (from AD-416): 1) Use the BovineSNP50 assay to provide high-accuracy predictions of genetic merit to U.S. dairy and beef breeds. 2) Enable the adoption of WGEAS by developing low-density and low-cost SNP assays for: a) intermediate-accuracy genetic prediction, b) mate selection, and c) parentage verification and traceability. 3) Develop, adapt and optimize statistical metodologies to: a) fully integrate SNP genotype or haplotype effects into existing genetic evaluation technologies, and b) supplement or replace pedigree data. 4)Collaborate and coordinate U.S. and European Union WGEAS activities. Approach (from AD-416): 1) Collect genotypic data using the bovineSNP50 in both dairy and beef cattle breeding programs. 2) Develop statistical algorithms needed to implement whole genome enabled animal selection specific to dairy and beef cattle populations as needed. 3) Determine subset of markers needed for low density SNP assay for application to parentage verification and reduced accuracy genetic prediction. 4) Collaborate with many organizations to utilize data generated by this project as well as other projects to obtain maximum utilization of resources generated. Activities in this project period focused on 1) continued genomic resequencing of animals for the purposes of single nucleotide polymorphism (SNP) discovery and diversity characterization, 2) analysis of Illumina BovineSNP50 data for the continued refinement of genetic prediction equations both within and across breeds, 3) collaborative development of the Illumina BovineLD beadchip as a replacement and improvement for the Illumina Bovine 3K assay, 4) development and genotyping of industry validation herds for the characterization of the accuracies of molecular estimates of breeding value in beef cattle, 5) identification of haplotypes affecting fertility in Holstein, Jersey, Brown Swiss, and Angus cattle, and 6) collaborative development of bovine exome capture assays with commercial vendors. Through industry partnerships, over 230,000 animals have now been genotyped on a variety of platforms, and these data are being used for the estimation of genomic breeding values in the dairy and beef industries. The rate of growth of genotype data collection continues to accelerate in both industries. The BovineLD assay was adopted rapidly in dairy cattle genetic evaluations. A total of five different haplotypes were identified that impact fertility through early embryonic loss in dairy cattle, and through the sequencing of 11 Angus bulls, loss-of-function alleles were found in 176 genes known to be embryonic or early development lethal in knockout mice. At least two commercial vendors are introducing products designed to capture bovine exonic regions for targeted re-sequencing using coordinates derived by ARS scientists. This research supports two objectives of its related in-house project: 1) to use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole-genome selection and enhanced parentage verification approaches (obj. #2), and 2) to characterize conserved genome elements and identify functional genetic variation (obj. #3).
Impacts
(N/A)
Publications
|
Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) 1) Use the BovineSNP50 assay to provide high-accuracy predictions of genetic merit to U.S. dairy and beef breeds. 2) Enable the adoption of WGEAS by developing low-density and low-cost SNP assays for: a) intermediate-accuracy genetic prediction, b) mate selection, and c) parentage verification and traceability. 3) Develop, adapt and optimize statistical metodologies to: a) fully integrate SNP genotype or haplotype effects into existing genetic evaluation technologies, and b) supplement or replace pedigree data. 4)Collaborate and coordinate U.S. and European Union WGEAS activities. Approach (from AD-416) 1. Collect genotypic data using the bovineSNP50 in both dairy and beef cattle breeding programs. 2. Develop statistical algorithms needed to implement whole genome enabled animal selection specific to dairy and beef cattle populations as needed. 3. Determine subset of markers needed for low density SNP assay for application to parentage verification and reduced accuracy genetic prediction. 4. Collaborate with many organizations to utilize data generated by this project as well as other projects to obtain maximum utilization of resources generated. The first objective to provide high-accuracy predictions of genetic merit enhanced by DNA marker data (BovineSNP50) in U.S. cattle has been met in dairy cattle and progress has been achieved in beef cattle. Genetic evaluations using genomic data have been considered �official� evaluations for Holstein and Jersey since January 2009. Brown Swiss genomic evaluations became available in August 2009. For Angus cattle, a targeted 384-SNP panel was developed and commercialized. This product includes the most predictive SNP for Heifer Pregnancy Rate, Ribeye Muscle Area, Marbling, and Yearling Weight. The next objective was to enable the adoption of whole genome enabled animal selection (WGEAS) by developing low-density and low-cost SNP assays for: a) intermediate-accuracy genetic prediction, b) mate selection, and c) parentage verification and traceability. Development of a 96-SNP set for parentage has been completed. This set of SNP has been identified as a candidate list to replace the current list of microsatellites by the International Society of Animal Genetics. Additionally, this list has been deployed in at least 6 commercial assays and is under consideration by several other vendors. The third objective, to develop, adapt and optimize statistical methodologies to: a) fully integrate SNP genotype or haplotype effects into existing genetic evaluation technologies, and b) supplement or replace pedigree data, is progressing. The final objective, to collaborate and coordinate U.S. and European Union WGEAS activities began in 2009. A second meeting of researchers contributing to this project as well as several European projects met at the International Plant and Animal Genome conference. The objectives to foster collaboration and reduce duplication were met. Monitoring activities associated with this project included regular email correspondence and conference calls. This research supports two objectives of its related in-house project: 1) to use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches (obj. #2) and 2) to characterize conserved genome elements and identify functional genetic variation (obj. #3).
Impacts
(N/A)
Publications
|
|