G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2011 National Breeders.

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Presentation transcript:

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2011 National Breeders Roundtable (1) Dairy Cattle Genomic Evaluation Program Update

Wiggans2011 National Breeders Roundtable (2) National Dairy Genetic Evaluation Program l Collaboration between ARS and Dairy industry l Dairy Industry partners w DHI Milk recording w Breed Associations w Artificial Breeding organizations w Other farm service organizations

Wiggans2011 National Breeders Roundtable (3) Expanding Industry Role l Collaboration of: w ARS - Animal Improvement Programs Lab w Council on Dairy Cattle Breeding l Council – Plan to provide staff for data collection, database management, calculation and distribution of evaluations l AIPL – Focus on research and Development

Wiggans2011 National Breeders Roundtable (4) History of genomic evaluations l Dec BovineSNP50 BeadChip available l Apr First unofficial evaluation released l Jan Genomic evaluations official for Holstein and Jersey l Aug Official for Brown Swiss l Sept Unofficial evaluations from 3K chip released l Dec K genomic evaluations official

Wiggans2011 National Breeders Roundtable (5) Genomic Evaluations l Genotype calves l Calculate evaluation l Select intensively l Reduces cost of finding top bulls l Increases rate of genetic progress

Wiggans2011 National Breeders Roundtable (6) Data & evaluation flow Animal Improvement Programs Laboratory, USDA AI organizations, breed associations Dairy producers DNA laboratories samples genotypes nominations evaluations

Wiggans2011 National Breeders Roundtable (7) Changes in last 12 Months l New Chips w Low density 3K, 2900 SNP w High Density − Illumina 777,062 SNP − Affymetrics 648,855 SNP l Collaboration with Italy and Great Britain l Adjustment of cow evaluations to improve compatibility with those of bulls l Improved accuracy of imputation

Wiggans2011 National Breeders Roundtable (8) HD - $20050K - $100 3K - $45 Chip Types HD 50K 3K $200 $100 $45

Wiggans2011 National Breeders Roundtable (9) Cow adjustment – background l Genotyped cows adjusted starting April 2010 l Required to prevent distortions in SNP effect estimates by making genotyped cows and bulls comparable l Made PTA of genotyped cows not comparable (lower) than those of non-genotyped cows l Industry requested adjustment on non- genotyped cows for April 2011 evaluation.

Wiggans2011 National Breeders Roundtable (10) Cow adjustment l Make evaluations of non-genotyped cow more like those of genotyped cows l Reduce variation to that of bulls l Subtract 40% of within year parent average deviation l Additional adjustment for genotyped cows l Discontinue using foreign cow evaluations in predictor population

Wiggans2011 National Breeders Roundtable (11) Imputation l Based on splitting the genotype into individual chromosomes (maternal & paternal contributions) l Missing SNP approximated by tracking inheritance from ancestors and descendents l Imputed Dams increase predictor population l 3K & 50K genotypes merged by imputing SNP not on 3K

Wiggans2011 National Breeders Roundtable (12) Imputation improvements l Use multiple segment lengths to detect common haplotypes l Long segments increase chance that matching haplotype came from a common ancestor l Shorter segments improve fill in l 2 -3 percentage points increase in accuracy achieved

Wiggans2011 National Breeders Roundtable (13) High density (HD) genotypes l Illumina Bovine HD BeadChip available w 777,962 SNP w Collaborations with GBR, ITA, & CAN to provide genotypes w Over 400 genotypes from research projects in database

Wiggans2011 National Breeders Roundtable (14) l Affymetrics HD w 648,855 SNP w Research project to determine usefulness w Optimized for genetic coverage w Over 100,00 SNP in common with Illumina High density (HD) genotypes

Wiggans2011 National Breeders Roundtable (15) Use of HD l Some increase in accuracy from better tracking of QTL l Potential for across breed evaluations l Requires few new HD genotypes once adequate base for imputation developed l Imputation improvements were particularly beneficial in imputing HD

Wiggans2011 National Breeders Roundtable (16) 3K chip l 2900 SNP mostly from SNP50 chip w 14 Y Chr SNP included for sex validation w Evenly spaced across 30 Chr l Developed to reduce cost of genotyping l 2614 SNP used after removing poor performers l Rapid adoption, 4,731 animal genotypes submitted for May genomic evaluation

Wiggans2011 National Breeders Roundtable (17) Genotype processing improvements l Labs submit genotypes for automated checking for: w Nomination issues w Genotype calling issues w Sample ID errors l Reports of conflicts enhanced w Excel compatible format w Additional ID information l Online pedigree correction

Wiggans2011 National Breeders Roundtable (18) Parentage validation and discovery l Parent-progeny conflicts detected w Reported to breeds and requesters w Correct sire usually detected l Maternal Grandsire checking w SNP at a time checking w Haplotype checking more accurate l Breeds moving to accept SNP in place of microsatellites

Wiggans2011 National Breeders Roundtable (19) Genotyped Holsteins Date Young animals** All animals Bulls*Cows* Bulls Heifers ,770 7,415 16,007 8,63041, ,430 9,37218,65211,02149, ,611 9,45319,38913,33352, ,616 9,78720,18415,28855, ,61910,17520,83617,09558, ,29312,82521,16118,33663, ,19413,58222,56722,99970, ,19613,93523,33026,27074, ,71314,38224,50529,92980, ,15211,22425,20236,54585, ,42911,83426,13940,99691,398 *Traditional evaluation **No traditional evaluation

Wiggans2011 National Breeders Roundtable (20) May Genotypes – Holstein and Jersey Birth Year Number of Genotyped Animals HolsteinJersey

Wiggans2011 National Breeders Roundtable (21) May Genotypes − Holstein MalesFemales

Wiggans2011 National Breeders Roundtable (22) May Genotypes − Jersey K50K Chip Type Number of Genotyped Jerseys MalesFemales

Wiggans2011 National Breeders Roundtable (23) Holstein Bulls Birth Year Number of Bulls Total10 HerdsGenotypedBoth

Wiggans2011 National Breeders Roundtable (24) Determination of Reliability l Sum of genomic relationships with the predictor animals weighted by reliability l Call rate l Expected imputation error rate l Reliability of parent average w Larger impact if dam not genotyped

Wiggans2011 National Breeders Roundtable (25) Reliabilities for young Holsteins* *Animals with no traditional PTA in April Reliability for PTA protein (%) Number of animals 3K genotypes 50K genotypes

Wiggans2011 National Breeders Roundtable (26) Use of genomic evaluations l Determine which young bulls to bring into AI service l Use to select mating sires l Pick bull dams l Market semen from 2-year-old bulls

Wiggans2011 National Breeders Roundtable (27) Use of 3K genomic evaluations l Sort heifers for breeding w Flush w Sexed semen w Beef bull l Confirm parentage to avoid inbreeding l Predict inbreeding depression better l Precision mating considering genomics (future)

Wiggans2011 National Breeders Roundtable (28) Future

Wiggans2011 National Breeders Roundtable (29) Increase in accuracy l Genotyped bulls get traditional evaluation when 5 years old l Possible genotyping of 10,000 bulls with semen in CDDR l Collaboration with more countries l Use of more SNP from HD chips l Full sequencing

Wiggans2011 National Breeders Roundtable (30) Application to more traits l Animal’s genotype is good for all traits l Traditional evaluations required for accurate estimates of SNP effects l Traditional evaluations not currently available for heat tolerance or feed efficiency l Research populations could provide data for traits that are expensive to measure l Will resulting evaluations work in target population?

Wiggans2011 National Breeders Roundtable (31) Summary l Extraordinarily rapid implementation of genomic evaluations l Young-bull acquisition and marketing now based on genomic evaluations l Genotyping of many females because of 3K chip l Application of HD chips being developed

Wiggans2011 National Breeders Roundtable (32)