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Cooper, 2014CDCB Meeting Aug. 5(1) T.A. Cooper, G.R. Wiggans and P.M. VanRaden Animal Genomics and Improvement Laboratory, Agricultural Research Service,

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Presentation on theme: "Cooper, 2014CDCB Meeting Aug. 5(1) T.A. Cooper, G.R. Wiggans and P.M. VanRaden Animal Genomics and Improvement Laboratory, Agricultural Research Service,"— Presentation transcript:

1 Cooper, 2014CDCB Meeting Aug. 5(1) T.A. Cooper, G.R. Wiggans and P.M. VanRaden Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350 Tabatha.Cooper@ars.usda.gov Analysis of Genomic Predictor Population

2 Cooper, 2014CDCB Meeting Aug. 5(2) Objectives l Evaluate the accuracy of cow and bull traditional information in the genomic evaluation system for Holstein l How useful are cows? l Would more old bulls increase accuracy? l What is the contribution of additional predictor animals?

3 Cooper, 2014CDCB Meeting Aug. 5(3) Introduction l The number of females genotyped monthly has increased from approximately 1,800 per month in 2010 to 12,650 per month in 2013. l Only a few countries other than the US include cows in the reference population. Ex: Ireland, Australia and Czeck Republic l For bulls, efforts have been made to increase collaborations with many other organizations.

4 Cooper, 2014CDCB Meeting Aug. 5(4) Number of Genotypes Added Monthly

5 Cooper, 2014CDCB Meeting Aug. 5(5) Cut off study (Bulls vs. Cows) l Predictor Bulls – 21,883 l Predictor Cows – 30,852 l Traditional evaluation by August 2012 to predict animals that gained a traditional evaluation between August 2012 and December 2013 l Only females who were genotyped before they were two years old where included in the validation set to avoid selection bias

6 Cooper, 2014CDCB Meeting Aug. 5(6) Bulls and/or Cows Predicting Bulls Gain Gen Rel Trait Validation Bulls (no.) Parent Average Cows Only Bulls OnlyBoth Milk148640.526.234.9 35.8 Fat148640.521.9 33.933.3 Protein148640.516.825.8 26.0 PL148435.321.454.955.2 SCS148437.516.930.3 31.1 DPR128734.9 −5.0 23.322.6 HCR137728.2 −3.2 28.325.1 CCR106328.619.556.9 57.4 Final score93436.317.7 27.026.0 Average* 20.431.732.1 Highest Gen Rel Gain *Excluding $NM

7 Cooper, 2014CDCB Meeting Aug. 5(7) Gain Gen Rel Trait Validation Bulls (no.) Parent Average Cows Only Bulls OnlyBoth Milk2655926.123.930.2 31.8 Fat2656226.120.226.427.5 Protein2655826.114.118.8 20.1 PL35719−6.48.5 14.6 SCS2487924.815.525.1 26.0 DPR906424.6−1.1−0.8−0.6 HCR1261824.5 1.69.313.1 CCR715624.4 25.48.615.2 Final score1075921.919.58.329.8 Average* 20.623.0 25.5 Bulls and/or Cows Predicting Cows Highest Gen Rel Gain *Excluding $NM

8 Cooper, 2014CDCB Meeting Aug. 5(8) Number predictor bulls by birth year

9 Cooper, 2014CDCB Meeting Aug. 5(9) Cut off study (Age) l Predictor Bulls − All – 21,883 − Bulls born before 1996 removed – 17,047 − Bulls born before 2001 removed – 11,507 − Bulls born before 2005 removed – 6,623 l Traditional evaluation by August 2012 to predict animals that gained a traditional evaluation between August 2012 and December 2013

10 Cooper, 2014CDCB Meeting Aug. 5(10) Bulls only excluded by birth year Gain Gen Rel Trait Validation Bulls (no.) Parent AverageAll Birth years included ≥1996≥2001≥2005 Milk148640.534.934.733.530.2 Fat148640.533.934.132.728.7 Protein148640.525.826.325.321.9 PL148635.354.953.048.936.6 SCS148437.530.329.326.623.3 DPR128734.923.321.919.53.7 HCR137728.228.324.023.510.8 CCR106328.656.935.130.05.5 Final score93436.327.025.622.815.9 Average* 31.729.927.4 19.7 Highest Gen Rel Gain *Excluding $NM

11 Cooper, 2014CDCB Meeting Aug. 5(11) Random vs. birth year exclusion (Milk) Gain in genomic rel (Milk)

12 Cooper, 2014CDCB Meeting Aug. 5(12) Conclusions l How useful are cows? − Cows contribute a small amount to genomic accuracy due to low reliabilities in the US. However, if bull genotypes are limited, they become more valuable. l Would more old bulls increase accuracy? − Historic bulls contribute a small amount to genomic accuracy due to linkage decay. Bulls closer in age to the young bulls offer more predictive ability. l What is the contribution of additional predictor animals? − We have not yet reached a plateau of gains in genomic reliability.

13 Cooper, 2014CDCB Meeting Aug. 5(13) Questions? Holstein and Jersey crossbreds graze on American Farm Land Trust’s Cove Mountain Farm in south-central Pennsylvania Source: ARS Image Gallery, image #K8587-14; photo by Bob Nichols

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