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T. A. Cooper and G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD Council.

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Presentation on theme: "T. A. Cooper and G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD Council."— Presentation transcript:

1 T. A. Cooper and G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD Tabatha.cooper@ars.usda.gov Council on Dairy Cattle Breeding meeting April 2010 (1) Cow Adjustment and Genomic Database Update

2 Council on Dairy Cattle Breeding meeting April 2010 (2) Cow Adjustment

3 Council on Dairy Cattle Breeding meeting April 2010 (3) Gains in Reliability as of 2008

4 Council on Dairy Cattle Breeding meeting April 2010 (4) DGV vs Traditional PTA (Bulls) DGV – based on allele effects of all genotyped animals Traditional PTA – no genomics -500 0 500 1000 1500 2000 -15527658879496211041252140315781867 PA Milk (pounds) Milk (pounds) Bull DGVBull Traditional PTA

5 Council on Dairy Cattle Breeding meeting April 2010 (5) DGV vs Traditional PTA (Cows) DGV – based on allele effects of all genotyped animals Traditional PTA – no genomics -1000 -500 0 500 1000 1500 2000 2500 -71528457679396011041253141415921936 PA Milk (pounds) Milk (pounds) Cow DGVCow Traditional PTA -1000 -500 0 500 1000 1500 2000 2500 -71528457679396011041253141415921936 PA Milk (pounds) Milk (pounds) Cow DGVCow Traditional PTAAdjusted Traditional PTA

6 Council on Dairy Cattle Breeding meeting April 2010 (6) l high PTA values were causing the genomic predictions to suffer in accuracy l added information from genotyped cows was not increasing reliability Why reduce cow bias through adjustment?

7 Council on Dairy Cattle Breeding meeting April 2010 (7) Which animals were adjusted? l All genotyped and imputed cows l All genotyped animals including bulls, were affected by the adjustment made to the maternal portion of the parent average l Brown Swiss adjustments were not implemented due to low numbers of genotyped cows

8 Council on Dairy Cattle Breeding meeting April 2010 (8) How was the adjustment made? 0 500 1000 1500 2000 2500 0.40.61.02.5 Daughter Equivalent (progeny) Std. Dev of Dereg M.S. (Milk) Cow Bull -400 -200 0 200 400 600 800 1000 20002001200220032004200520062007 Birth year Milk (lbs.) Cow Bull Cow SD Adj Variance Adjustment Mean Adjustment

9 Council on Dairy Cattle Breeding meeting April 2010 (9) How was the adjustment made? l Deregressed Mendelian Sampling (MS) = (PTA-PA) / f(REL) l Adj. MS =.84*MS - 784 l Adj. PTA = f(REL)*(Adj. MS+ PA n ) + (1- f(REL)*PA n ) f(REL) = weight in PTA from own records and progeny

10 Council on Dairy Cattle Breeding meeting April 2010 (10) Effects of Cow Adjustment (Holstein) BiasRegressionGain REL NoYesDiffNoYesDiffNoYesDiff Milk (lb)-75.3-27.947.4.93.90-.0329.532.53.0 Fat (lb)-5.7-2.92.8.98.97-.0134.037.13.1 Protein (lb)-0.20.81.0.90.97.0725.027.12.1 Fat (%)0.0.97.99.0249.852.42.6 Protein (%)0.0.87.88.0138.841.52.7

11 Council on Dairy Cattle Breeding meeting April 2010 (11) Effects of Cow Adjustment (Jersey) BiasRegressionGain REL NoYesDiffNoYesDiffNoYesDiff Milk (lb)-44.081.5125.5.99.0010.819.68.8 Fat (lb)-7.37.915.2.78.84.069.418.28.8 Protein (lb)1.74.32.6.86.90.044.112.78.6 Fat (%)0.0.90.95.0529.937.67.7 Protein (%)0.0.87.93.0624.834.29.4

12 Council on Dairy Cattle Breeding meeting April 2010 (12) Example (Cow Milk PTA 1934  381) 0 500 1000 1500 2000 2500 Progeny 1Jan PAApril PAProgeny2 Milk (pounds)

13 Council on Dairy Cattle Breeding meeting April 2010 (13) The future l Investigate solutions to the problem of not being able to compare genotyped and non- genotyped cows − Reduce heritability − Add dam-herd interaction − Varying heritability by herd − Other l With 3K chip, adjustments may need to vary by sub-population

14 Council on Dairy Cattle Breeding meeting April 2010 (14) Genomic Database

15 Council on Dairy Cattle Breeding meeting April 2010 (15) Genotyped Holstein by run Run Date Old*Young** Total MaleFemaleMaleFemale 0904760027119690194321944 09067883304911459297425365 09088512372812137367028047 09108568396513288479730618 10018974434814061603133414 10029378508615328762037412 1004 1005 Imputed 9770 9958 7300 7940 (1955) 16002 16594 8732 9772 41804 44264 * Animals with traditional evaluation ** Animals with no traditional evaluation

16 Council on Dairy Cattle Breeding meeting April 2010 (16) Genotyped Jersey by run Run Date Old*Young** Total MaleFemaleMaleFemale 1002197747911721973825 1004 1005 Imputed 2072 2079 637 702 (150) 1250 1368 202 231 4161 4320 * Animals with traditional evaluation ** Animals with no traditional evaluation

17 Council on Dairy Cattle Breeding meeting April 2010 (17) Genotyped Brown Swiss by run Run Date Old*Young** Total MaleFemaleMaleFemale 1002116854179151416 1004 1005 Imputed 1185 1188 98 114 (63) 188 199 31 34 1502 1535 * Animals with traditional evaluation ** Animals with no traditional evaluation

18 Council on Dairy Cattle Breeding meeting April 2010 (18) Genotype Processing l 2,000 New Genotypes a month l Four labs − GeneSeek − Genetic Visions − DNA LandMarks − GIVF

19 Council on Dairy Cattle Breeding meeting April 2010 (19) l All animals should be nominated by the time sample reaches lab l Goal: Parents and Grandparents on every genotyped animal l Minimum: Valid ID Genotype Processing: Nomination

20 Council on Dairy Cattle Breeding meeting April 2010 (20) l Genotypes must pass 62 edits to be added to the database l Most common reasons a genotype fails − Low call rate − Parent / Progeny conflict − Possible split embryo / twin − Wrong gender − Breed Check − Switched samples Genotype Processing: Edits

21 Council on Dairy Cattle Breeding meeting April 2010 (21) Continuous Updates l Pedigree changes update genotype usability daily l Harmonization with breed association important to maintain usability l Blanking a genotyped dam will make the genotype unusable l No automatic receipt of foreign pedigree updates

22 Council on Dairy Cattle Breeding meeting April 2010 (22) Low call rate l 80% on X chromosome l 90% on autosomal chromosomes (43,382) l Labs generally do not send genotypes with low call rates

23 Council on Dairy Cattle Breeding meeting April 2010 (23) Parent Progeny Conflict l Sire / Dam conflict l > 200 SNP conflicts l Sire / dam proposed if genotyped l Sire conflict - young animals from mixed flush l Sire conflicts represent $50,000 genotype cost

24 Council on Dairy Cattle Breeding meeting April 2010 (24) Split embryo / Identical twin / Clone l <1000 SNP differences considered identical l 98% similar, accounts for genotyping errors l Stored in clone table if valid l Animals registered as ETS or ETN (automatic) l Otherwise verification must come from requester

25 Council on Dairy Cattle Breeding meeting April 2010 (25) Wrong Gender l > 50 heterozygous SNP on X (not male) l < 50 heterozygous SNP on X (not female) l Homozygous X female l Common ancestor (source of X)

26 Council on Dairy Cattle Breeding meeting April 2010 (26) Source of X Jeff Erin Elegant BW Marshall Tanya Sam 12144058 Bellwood Mara Patron Mary Mark Sue Patron 14860763

27 Council on Dairy Cattle Breeding meeting April 2010 (27) Breed Check l 622 SNP l Nearly monomorphic in 1 breed and have fewer than 30% of animals homozygous for that allele in another breed l An error when a higher number of conflicts for the reported breed than for another breed l > 10 SNP conflicts reported to requester, but remains usable l Higher conflicts for foreign animals

28 Council on Dairy Cattle Breeding meeting April 2010 (28) Switched Samples l Sample pair with reversed parents l Switched at the lab l Switched at the farm

29 Council on Dairy Cattle Breeding meeting April 2010 (29) Conflicts to Requester l Genotype conflicts reported to the requester immediately l Genotype remains stored in AIPL database as an unusable genotype until conflict is resolved l 2-3 days to fix conflicts before cutoff l Once a month all conflicts remaining in the system are sent to requesters

30 Council on Dairy Cattle Breeding meeting April 2010 (30) Issues Reported to Lab for QC l SNP that have call rate <90% l SNP that have high parent-progeny conflicts l SNP that deviate from HW equilibrium l Labs have the opportunity to re-cluster genotypes

31 Council on Dairy Cattle Breeding meeting April 2010 (31) Closing Thoughts l Currently 477 animals with failed or conflicted genotypes l Big increase in volume when 3K becomes available l Edits will remain with different thresholds for 3K data

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