updates on the genomic evaluation program
DESCRIPTION
Updates on the genomic evaluation program. 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 - PowerPoint PPT PresentationTRANSCRIPT
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (3)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (4)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (5)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (6)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (7)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (8)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (9)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (10)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (11)
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)
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (12)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (13)
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.
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (14)
Predictor animals
Breed Bulls
Cows
Total
Holstein 7,600
2,711
10,311
Jersey 1,807
337 2,144
Brown Swiss
655 41 696
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (15)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (16)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (17)
Genotype status of active Holsteins Group No.All 713Not genotyped 210 From participating AI organizations
15
Other AI organizations 195
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (18)
Missing sires of genotyped Holsteins
Progeny (no.)
Bulls (no.)
1 2102 573 224 125 76 77 128 39 2
10–111 14
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (19)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (20)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (21)
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)
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (22)
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
G.R. Wiggans 2009Council on Dairy Cattle Breeding meeting prequel (23)
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