1. 2005 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD wiggans@aipl.arsusda.gov AIPL Projects

2. AIPL Projects (2) G. R. Wiggans 2005 Current Researchers at AIPL Scientists –Duane Norman –George Wiggans –Paul VanRaden –Melvin Kuhn –John Cole Volunteers –Rex Powell –Bob Miller

3. AIPL Projects (3) G. R. Wiggans 2005 Group Photo

4. AIPL Projects (4) G. R. Wiggans 2005 Including crossbred cows in evaluations Interest in cross breeding Expect improved fertility, longevity Want an indication of a bull’s value when used on a dam of different breed Want the crossbred daughters to raise the reliability of the bull’s evaluation

5. AIPL Projects (5) G. R. Wiggans 2005 Plan to incorporate crossbreds Switch to breed of sire from breed of cow to determine breed of evaluation –Carry breed codes of animal, sire and dam into the evaluation system so they can be used to make unknown parent group assignments –Maintain a table of crossbred animals so breed portions are easily determined, and breeds of ancestors displayed Evaluate within breed of sire –Provision to switch to evaluation over all breeds will be included if acceptable to industry Heterosis is considered

6. AIPL Projects (6) G. R. Wiggans 2005 Evaluating male fertility Reproduction data collected since 1993 from several regional centers Hope to get data from all centers Evaluation will replace ERCR currently calculated in Raleigh Expect to include all breedings, not just first as in ERCR Will compare linear and threshold model Consider inbreeding of both bull and embryo in model Implementation expected in 2006

7. AIPL Projects (7) G. R. Wiggans 2005 Developing an evaluation for stillbirth Stillbirth is reported in about half of the calving ease records Studs pay to support data collection and analysis Over 6 million records available since 1985 Expect to apply sire-MGD threshold model similar to calving ease

8. AIPL Projects (8) G. R. Wiggans 2005 Investigating evaluations for persistency Persistency is calculated as part of calculation of lactation records Calculated as slope of deviations from herd lactation curve with intercept in mid lactation Location of intercept selected to eliminate correlation with lactation yield Relation of persistency with health traits being investigated Potential economic value should be investigated

9. AIPL Projects (9) G. R. Wiggans 2005 Investigating development of a parentage verification system based on SNPs Determine if SNPs can make parentage validation cheap enough to make it widespread Develop a database and adapt software to process SNP data and suggest alternatives for invalid parents Cooperate with breed associations and studs to collect DNA from cooperating herds Determine rate of parentage errors in cooperating herds

10. AIPL Projects (10) G. R. Wiggans 2005 Cooperation with BFGL in investigating evaluation of chromosomal segments using SNP Based on panel of 10,000 SNP identify chromosomal segments to infer haplotypes Genotype enough bulls so haplotypes can be evaluated for various traits –Haplotype interactions may need to be evaluated Has potential to provide evaluations with accuracy similar to progeny test Enables tracking the effect of Mendelian sampling

11. AIPL Projects (11) G. R. Wiggans 2005 Revising productive life to credit longer lactations There has been producer interest for crediting cows for production beyond 305 days –Differential weighting by DIM allows giving some advantage to cows that calve more often Also investigating giving credit for more lactations –Intend to craft a revision that maintains present heritability of 8.5% Implementation of female fertility (DPR) evaluations allows productive life to have reduced emphasis on fertility

12. AIPL Projects (12) G. R. Wiggans 2005 Accounting for differences in rate of maturity Cows reach maximum yield at differing ages Bulls with early maturing daughters may have unstable evaluations as the age composition of their progeny test varies Work on individual lactation evaluations shows reasonable heritability for differences between parities Attempts to account for genetic differences in rate of maturity have not yielded expected benefit

13. AIPL Projects (13) G. R. Wiggans 2005 Investigating the possibility of acquiring health data Industry focus on fitness traits Resistance to disease could assist in prediction productive life Analysis of metabolic disorders early in lactation likely to be useful Research data has been converted to common codes for health events Methods to allow owners to retain control over access to health data being investigated

14. AIPL Projects (14) G. R. Wiggans 2005 Detecting abnormal distributions of calving ease scores within herd year Calving ease evaluated with a sire-MGS threshold model –Bulls with large changes or outlier evaluations usually have abnormal distributions of daughter scores Goodness of Fit (GoF) criterion developed to measure the difference between the distribution in a herd-year and the population –Separate distributions for first and later parities –GoF designed to be independent of herd size Threshold set to eliminate 1% of data –Adjoining herd-years eliminated if below a 10% threshold Evaluations with these exclusions included in Sept Interbull test run

15. AIPL Projects (15) G. R. Wiggans 2005 Ways to improve detection of problems in evaluations used by Interbull Interbull evaluations are of increasing importance in the international marketplace for semen The current strategy for determining which data to exclude may result in evaluations that are less useful for everyone Current trend validation tests may not detect serious problems Additional checks and a less draconian response to problems may be necessary

16. AIPL Projects (16) G. R. Wiggans 2005 Extramural work Heat stress –Supporting Ignacy Misztal to investigate differences in response of bulls’ daughters to heat stress AP adjustments –Supporting Mike Schutz in collecting individual milking samples to update AM-PM adjustments

17. AIPL Projects (17) G. R. Wiggans 2005 Other species Dairy goats –Investigate application of a test day model Dairy Sheep –Investigate development of evaluations for milk and component yields