Updates on the genomic evaluation program

G.R. WiggansAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA Beltsville, MD

[email protected]. WiggansCouncil on Dairy Cattle Breeding meeting prequel (1)

Updates on the genomic evaluation program

G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (2)

Goals

Increase accuracy of genomic evaluations

Provide accurate evaluations on schedule

Provide reliable tracking of use of genotypes


Calling genotypes at AIPL

Labs FTP intensity data from scanner to AIPL

AIPL staff trained to run GenomeStudio using lab-specific cluster files and eliminating poor-quality SNP

Call rate of 90% required for any SNP genotype to be reported


Nomination application

Requester required to record animals to be genotyped

Records bar code or other sample ID

Determines if animal in pedigree table

Allows labs to check ID

Provides ID of recipient of genomic evaluation

Updated with disposition of genotype


Genotype storage

Genotypes stored as 0, 1, 2, or 5 Count of A allele 5 = Missing

Genotypes identified by chip bar code and position to allow multiple genotypes per animal and reassignment

58,336 SNP per genotype stored in long-character object giving 1 row per genotype


Genotype checking

Genotyped marked not usable if Conflict with parents or progeny Heterozygous count on X chromosome wrong for sex

Duplicate of other animal that’s not a twin, split, or clone

Non-pedigree parent-progeny relationship

Problems reported to lab and requester


Preparation for evaluation

Genotypes added or with updated pedigree extracted

Combined with existing master file

Checks for conflicts and duplicates repeated

Evaluations of females requested from Canada

Evaluations and parent averages assembled from domestic, Interbull, and Canadian evaluations


Processing at traditional evaluation For estimation of SNP effects,

previous Interbull evaluation used for bulls if Interbull evaluation was official

Final genomic evaluations calculated using current Interbull evaluation in selection-index combination step

Parent Average reported is from evaluations used in estimation of SNP effects


Plan to redo genotype calls

Reprocess all 20,000+ genotypes to obtain calls on low MAF SNP

Lower minimum MAF from 5% to 2%

Provide SNP for Jerseys and Brown Swiss that are monomorphic for Holsteins

Provide genotypes on full set of 116 parentage SNP


Schedule of genomic evaluations Current frequency = approximately

every 2 months

With successful genotype calling at AIPL and regular submissions from labs, more frequent evaluations possible

Labs need a steady flow of samples to genotype to avoid overload at cutoff


Effect of Interbull on schedule

Interbull proposes providing converted genomic evaluations, test run input due soon

For traditional evaluations, genomic evaluation must be completed by Interbull submission time (data cutoff for labs earlier)

Interbull will provide both traditional and genomic evaluations (output data doubled)


Improved genotype management Hope to enable parentage checking by labs

using 116 publicly available parentage SNP

Would enable labs to detect sample switches

Could lead to earlier correction

Breed associations could provide online checking service to labs

Conflict reports generated at receipt of genotypes at AIPL (before start of evaluation) Chance of correction before start of

evaluation Nomination query updated as genotypes

stored


Genotyped Holsteins in evaluations

0

5,000

10,000

15,000

20,000

25,000

Apr08

Jun08

Aug08

Oct08

Dec08

Jan09

Feb09

Mar09

Apr09

Genomic evaluation date

Anim

als,

no.


Predictor animals

Breed Bulls

Cows

Total

Holstein 7,600

2,711

10,311

Jersey 1,807

337 2,144

Brown Swiss

655 41 696


Brown Swiss

117 genotypes received from Switzerland through exchange

Encouraging results from test using 2004 data to predict current PTA

Official release planned for August 2009


Increase number of predictor animals Automatic increase as genotyped bulls in

waiting receive traditional evaluations

Genotype bull dams

Genotype sires of sons and sires with many genotyped progeny

Exchange genotypes with other countries

Allow other AI organizations to genotype active bulls


Genotype status of active Holsteins Group No.All 713Not genotyped 210 From participating AI organizations

15

Other AI organizations 195


Missing sires of genotyped Holsteins

Progeny (no.)

Bulls (no.)

1 2102 573 224 125 76 77 128 39 2

10–111 14


Ungenotyped bulls, 10+ progeny

Controlling AIGenotyped

Bull ID number organization Bull name progeny (no.)

HODEU000345379222 204 Jardin 111HOFRA002217051448 2139 Roumare 61HOUSA000125349240 555 Zade 30HONLD000255749372 11 Altalucky Mike 29HOUSA000002289236 1 Cash 21HOCAN000000391661 70 Skychief 16HOUSA000002280338 7 Elation 16HOUSA000121883236 14 Mil-Joy Wade Vixen 15HOCAN000000400985 73 Milestone 14HOFRA005994022699 2139 Jesther 13HONLD000343990114 Non-AI Barnkamper Support 12HOCAN000000394485 72 Mystic 10HONLD000160325582 1 Swinger 10HOGBR000000587438 29 Lookout 10


Ways to increase accuracy

Add predictor animals Impute genotypes of missing animals

Use more SNP Impute missing SNP

Improve methods of estimation of SNP effects Haplotyping Improved models


Animal ID with sex-code proposal Sex code helpful in some situations

Interbull and Canada include sex code in ID following country code

In XML files and other genomic-related exchange formats, sex code could be included in ID

In sample ID, trailing sex code has been allowed (could be discontinued)


Proposed Changes

Labs enabled to validate sample ID against nominations Nomination required for genotype to be processed

Brown Swiss evaluations to be official

Various opportunities exist to increase accuracy

Genotype calling to be done at AIPL Control over schedule


Financial support National Research Initiative grants, USDA NAAB (Columbia, MO)

ABS Global (DeForest, WI) Accelerated Genetics (Baraboo, WI) Alta (Balzac, AB) Genex (Shawano, WI) New Generation Genetics (Fort Atkinson, WI) Select Sires (Plain City, OH) Semex Alliance (Guelph, ON) Taurus-Service (Mehoopany, PA)

Holstein, Association USA (Brattleboro, VT) American Jersey Cattle Association

(Reynoldsburg, OH) Brown Swiss Association (Beloit, WI) Agricultural Research Service, USDA

Updates on the genomic evaluation program

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