Project Number: 1265-31000-096-08
Project Type: Specific Cooperative Agreement

Start Date: Sep 16, 2005
End Date: Sep 15, 2010

Objective:
Develop and validate a robust parentage verification and parentage discovery algorithm and software system using single nucleotides polymorphisms (SNP) that is computationally feasible for large-scale implementation in the dairy cattle industry.

Approach:
Through an existing collaboration involving the US Meat Animal Research Center (MARC) and ANRI scientists, a set of 90 to 100 highly informative SNP markers will soon be commercially available for application in cattle. The genetic sources that were used in identifying these SNP were the US Meat Animal Research Center¿s MARC Beef Diversity Panel and the Beltsville Agriculture Research Center¿s BARC Dairy Diversity Panel. Markers have been selected for application to parentage verification and traceability. Collaborations with Holstein Association USA, Jersey Cattle Association, and (AI) insemination organizations will be developed with the goal of conducting a pilot study to characterize parentage misidentification rates as well as to determine the feasibility of correcting these identification errors using relevant information from a herd. Development of appropriate algorithms and implementation in efficient software will be a key need on this project. The ultimate goal is to have ARS develop a software system that integrates pedigree data from AIPL and breed associations to provide real-time parentage verification and discovery information as well as trace-back capabilities for animals genotyped in the national dairy cattle herd. Providing appropriate weighting for animals based on pedigree validation status is needed to recognize differing accuracies of pedigree information in genetic evaluations. Outstanding bulls tested through AI service may not be recognized as superior if several daughters or their herdmates are recorded having the wrong sire. Bulls graduating into widespread usage after progeny test will have their evaluations regressed toward parent average unless misidentified daughters are detected and corrected. This research project will provide an estimate of the parentage accuracy in a representative sample of US dairy cattle. Furthermore, the results of this project will demonstrate the effectiveness of SNP for parentage verification both in accuracy and cost. A national bank of SNP genotypes will be initiated along with the software for processing the DNA laboratory results. This capability can be transferred to industry, or remain part of the genetic evaluation process. Success of this project could result in a substantial increase in accuracy of genetic evaluations, leading to more rapid genetic improvement. If the project is successful, the breed associations expect to adopt SNP for their parentage verification programs. If the costs are low enough, bull studs may genotype daughters of all progeny test bulls to improve the accuracy of selection. Random testing of herds contributing to genetic evaluations might be used to identify those where the error rate is unacceptably high. Efficient processing could discover each animal¿s actual parents from the genotype database if parents are not reported or incorrectly reported. Nevertheless, improved sire ID has a bigger return on investment than improved dam ID. Availability of new genomics-based tools may dramatically reduce the cost.