Increased reliability of genetic evaluations for dairy cattle in the United States from use of genomic information Abstr.

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Presentation transcript:

Increased reliability of genetic evaluations for dairy cattle in the United States from use of genomic information Abstr.

Genomic evaluation system Became official for Holstein and Jersey in January 2009 and in August 2009 for Brown Swiss 466 bulls marketed based on genomic evaluation only (out of 8,131 genotyped young bulls) Holstein predictor population included 10,430 bulls and 9,372 cows for August

Characteristics of system Full sharing of genotypes with Canada 542 Brown Swiss genotypes from exchange with Switzerland Interbull evaluations used for foreign predictor bulls, converted evaluations for cows 10% polygenetic effect 10 countries contribute > 100 genotypes

Genotyped Holsteins Date Young animals** All animals Bulls* Cows* Heifers 04-09 7,600 2,711 9,690 1,943 21,944 01-10 8,974 4,348 14,061 6,031 33,414 02-10 9,378 5,086 15,328 7,620 37,412 04-10 9,770 7,415 16,007 8,630 41,822 05-10 9,958 7,940 16,594 9,772 44,264 06-10 8,122 17,507 10,713 46,300 07-10 9,963 8,186 18,187 11,309 47,645 08-10 10,430 9,372 18,652 11,021 49,475 *Traditional evaluation **No traditional evaluation

Adjustment of Cow Evaluations Traditional cow evaluations inflated compared to bull evaluations US industry wanted cow’s own performance to influence genomic evaluations. Most countries use only bull evaluations for SNP effect estimation Information from genotyped cows did not increasing reliability of yield traits Cow contributions adjusted to be comparable to those from bulls Beltsville Agricultural Research Center Centennial • 1910-2010

Validation Populations Predictor population - Animals with August 2006 evaluations No Females No adjustment of cows Cow evaluations adjusted Predicted population – Bulls with no evaluation in August 2006 but did have an evaluation in June 2010 Beltsville Agricultural Research Center Centennial • 1910-2010

Adjustment Method Mean and variance of deregressed values reduced to be comparable with bull evaluations of similar accuracy

Adjustment Parameters Breed Milk Fat Protein SD Mean (kg) Holstein 0.84 -356 0.72 -12.5 0.77 -10.4 Jersey -292 0.67 -14.2 -11.0 Deregressed Mendelian Sampling (MS) = (PTA-PA) / f(REL) Adj. MS = .84*MS - 356 Adj. PTA = f(REL)*(Adj. MS+ PAn) + (1- f(REL)*PAn) f(REL) = weight in PTA from own records and progeny Beltsville Agricultural Research Center Centennial • 1910-2010

Effects on Regression (ß) Deregressed value = α + ß·PTA Trait No Females Unadjusted Adjusted Milk 0.91 0.87 Fat 0.95 0.96 Protein 0.89 0.83 0.88 % Fat 0.99 1.00 1.02 % Protein 0.90 Beltsville Agricultural Research Center Centennial • 1910-2010

Beltsville Agricultural Research Center Effects on Bias Bias = actual - predicted Trait No Females Unadjusted Adjusted Milk -127.5 -117.0 -8.7 Fat -6.9 -5.8 -1.9 Protein -2.5 -1.8 1.3 % Fat -0.005 -0.002 % Protein 0.007 0.008 Beltsville Agricultural Research Center Centennial • 1910-2010

Effects on Genomic Reliability Trait No Females Unadjusted Adjusted Milk 66.5 64.6 67.5 Fat 72.4 69.8 73.1 Protein 63.0 60.6 63.7 % Fat 85.3 85.8 % Protein 76.0 76.4 78.0 Beltsville Agricultural Research Center Centennial • 1910-2010

Genotyped Populations animalsa Predictor populationb Predicted populationc Bulls Cows Total Breed Holstein 46,300 5,822 2,461 8,283 2,654 Jersey 4,478 1,623 390 2,013 394 Brown Swiss 1,584 994 111 1,105 132 a As of June 2010. b Bulls and cows with official evaluations for yield traits as of August 2006. c Bulls with a June 2010 domestic traditional evaluation.

Holstein prediction accuracy Traita Biasb b REL (%) REL gain (%) Milk (kg) −4.0 0.91 67.5 29.4 Fat (kg) −0.9 0.96 73.1 35.0 Protein (kg) 0.6 0.88 63.7 25.6 Fat (%) 0.0 1.02 85.7 47.6 Protein (%) 0.90 77.9 39.8 PL (months) −1.5 1.04 64.2 33.2 SCS 60.4 26.5 DPR (%) −0.2 1.08 46.8 17.0 Sire CE 1.0 0.79 40.9 13.8 Daughter CE −1.0 0.93 44.3 18.1 Sire SB 2.1 0.87 29.8 7.2 Daughter SB 0.3 0.89 29.3 2.7 a CE = calving ease and SB = stillbirth. b 2010 deregressed value – 2006 genomic evaluation.

Jersey and Swiss Gains Breed Trait (Avg) REL (%) REL gain (%) Jersey Yield 55.8 16.3 Health 53.2 20.7 Brown Swiss 56.2 18.2 31.8 4.7

Selective Genotyping Superiority of test population which biases estimated regressions and reliability Trait PTA diff SD of PTA PTA diff / SD Milk (kg) 16.9 304.0 0.06 Fat (kg) 1.4 11.2 0.12 Protein (kg) 0.9 8.0 0.11 PL (months) 0.5 2.3 0.21 SCS −0.04 0.2 −0.11 DPR (%) 0.13 0.10

Adding predictor animals Collaboration Willing to collaborate at various levels Sharing genotypes Discussions with DEU (BS) & DNK (JE)

Conclusions Number of predictor animals determines accuracy Increase in reliability over parent average 25% points across traits for Holstein Investigating increasing predictor population through exchange and collaboration

New Chips 3K chip HD Chip 2,882 SNP for imputation 14 Y-Chromosome SNP for sex determination Impute 43,382 and use like SNP50 genotype More labs HD Chip 777,962 SNP on chip ~600K useful for Dairy >1,000 HD genotypes needed for imputation Cost/Benefit being considered