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USDA genetic evaluation update

USDA genetic evaluation update. Changes for April. Adjustment of yield evaluations for all cows Improved imputation Chip type and genomic inbreeding added to output Multitrait heifer and cow conception rates. Cow adjustment – background. Genotyped cows adjusted starting April 2010

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USDA genetic evaluation update

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  1. USDA genetic evaluation update

  2. Changes for April Adjustment of yield evaluations for all cows Improved imputation Chip type and genomic inbreeding added to output Multitrait heifer and cow conception rates

  3. Cow adjustment – background Genotyped cows adjusted starting April 2010 Required to prevent distortions in SNP effect estimates by making genotyped cows and bulls comparable Made PTA of genotyped cows not comparable (lower) than those of non-genotyped cows Industry requested adjustment on non-genotyped cows for April.

  4. Cow adjustment Make evaluations of non-genotyped cow more like those of genotyped cows Make similar to bull evaluations Reduce variation to that of bulls Subtract 40% of within year parent average deviation Additional adjustment for genotyped cows

  5. Cow adjustment for genomics Cow PTA compared to bull only direct genomic values Cows with reliability from records and progeny > 55 further adjusted Canadian and other foreign cow evaluations excluded from estimation of SNP effects Not adjusted by all cow adjustment Receive larger adjustment for own evaluation and for use in Parent Average

  6. Cow adjustment

  7. Comparison of top 100 Cows

  8. Imputation Based on splitting the genotype into individual chromosomes (maternal & paternal contributions) Missing SNP approximated by tracking inheritance from ancestors and descendents Imputed Dams increase predictor population 3K & 50K genotypes merged by imputing SNP not on 3K

  9. Imputation improvements Use multiple segment lengths to detect common haplotypes Long segments increase chance that matching haplotype came from a common ancestor Shorter segments improve fill in 2 -3 percentage points increase in accuracy achieved

  10. High density (HD) genotypes Illumina Bovine HD BeadChip available 777,962 SNP Collaborations with GBR, ITA, & CAN to provide genotypes Over 400 genotypes from research projects in database Affymetrics HD 648,855 SNP Optimized for genetic coverage NAAB negotiating plan for use

  11. Use of HD • Some increase in accuracy from better tracking of QTL • Potential for across breed evaluations • Requires few new HD genotypes once adequate base for imputation developed • Imputation improvements were particularly beneficial in imputing HD

  12. 3K chip 2900 SNP mostly from SNP50 chip 14 Y Chr SNP included for sex validation Evenly spaced across 30 Chr Developed to reduce cost of genotyping 2614 SNP used after removing poor performers Rapid adoption, 4,288 animal genotypes submitted for April genomic evaluation

  13. Genotype processing improvements Labs submit genotypes for automated checking for: Nomination issues Genotype calling issues Sample ID errors Reports of conflicts enhanced Excel compatible format Additional ID information Online pedigree correction

  14. Genotyped Holsteins *Traditional evaluation **No traditional evaluation

  15. April Genotypes – Holstein 2000 1500 1000 Number of Genotypes 500 0 1998-2006 2007 2008 2009 2010 2011 Birth year 3K Females 3K Males 50K Females 50K Males

  16. April Genotypes - Jersey 250 200 150 Number of Genotypes 100 50 0 2001-2006 2007 2008 2009 2010 2011 Birth year 3K Females 3K Males 50K Females 50K Males

  17. Holstein Bulls 10000 9000 8000 7000 6000 Number of Bulls 5000 4000 3000 2000 1000 0 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 Birth Year Total 10 Herds Genotyped Both

  18. Reliabilities for young animals* *Animals with no traditional PTA in March 2011

  19. Determination of Reliability • Sum of genomic relationships with the predictor animals weighted by reliability • Call rate • Expected imputation error rate • Reliability of parent average • Larger impact if dam not genotyped

  20. Use of genomic evaluations • Determine which young bulls to bring into AI service • Use to select mating sires • Pick bull dams • Market semen from 2-year-old bulls

  21. Use of 3K genomic evaluations • Sort heifers for breeding • Flush • Sexed semen • Beef bull • Confirm parentage to avoid inbreeding • Predict inbreeding depression better • Precision mating considering genomics (future)

  22. Future

  23. Increase in accuracy • Genotyped bulls get traditional evaluation when 5 years old • Possible genotyping of 10,000 bulls with semen in CDDR • Collaboration with more countries • Use of more SNP from HD chips • Full sequencing

  24. Application to more traits Animal’s genotype is good for all traits Traditional evaluations required for accurate estimates of SNP effects Traditional evaluations not currently available for heat tolerance or feed efficiency Research populations could provide data for traits that are expensive to measure Will resulting evaluations work in target population?

  25. Summary • Extraordinarily rapid implementation of genomic evaluations • Young-bull acquisition and marketing now based on genomic evaluations • Genotyping of many females because of 3K chip

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