Whats Coming in Genomic Evaluations and How It Affects You

G.R. Wiggans

Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george.wiggans@ars.usda.gov
DHI-Provo Herd Management Conference (1) G.R. Wiggans
2008

What are genomic evaluations?

DNA extracted from blood, hair, or semen ~40,000 genetic markers (SNPs) evaluated For each SNP, difference in PTA between animals with one allele compared to the other is estimated Genomic evaluation combines SNP effect estimates with existing PA or PTA Genomic data contribute ~11 daughter equivalents to reliability
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (2)

What is a SNP?

Single-nucleotide polymorphism Place on the chromosome where animals differ in the nucleotides (A, C, T, or G) they have Usually not part of the gene that controls a trait quantitative trait locus (QTL) With enough SNPs, association between SNP alleles and QTL alleles gives useful evaluations SNPs chosen to be distributed evenly and have both alleles well represented in population
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (3)

Genomic vs. traditional PTA

Genotype can be thought of as source of information like parents, progeny, and records Official PTA will have a indicator if they include a genomic contribution One genotype is used to calculate genomic evaluations for all 29 traits Genomic evaluations used the same way as traditional PTA Expected to increase rate of genetic improvement because of a large decrease in generation interval
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (4)

Whats happened so far

Illumina BovineSNP50 BeadChip developed Accuracy of genomic information assessed by using 2003 evaluations of bulls born before 2000 to predict 2008 evaluations of young bulls Test evaluations began to provide genomic evaluations of bull calves in April Jersey results released in October

New results released every 2 months

Nearly 15,000 animals genotyped through October
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (5)

Genotyped animals (October 2008)

Breed Holstein Jersey Brown Swiss Bulls 12,275 1,205 365 Cows 2,445 369 3 Predictors 7,821 1,428 359

DHI-Provo Herd Management Conference (6)

G.R. Wiggans

2008

How to get animals genotyped

Participating AI organizations have 5-year exclusive right to evaluate bulls genomically

Each AI organization genotypes first-choice flushes, thereby usually avoiding duplicate genotypes
Web-based system being developed to collect nominations Avoid duplication Confirm validity of ID and pedigree Breed associations developing cow genotyping service
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (7)

What can go wrong

Sample doesnt provide adequate DNA quality or quantity Genotype has many SNPs that cant be determined (90% call rate required) Genotype conflicts with parent(s)

Pedigree error Sample ID error Laboratory error Genotype checked against all others to find true parent
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (8)

Collaboration with Canada

Semex

Supported since beginning of genomics research Contributed valuable genotypes to first accuracy test

Genotypes will be shared between AIPL and Canadian Dairy Network AIPL and University of Guelph collaboration
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (9)

Collaboration with Canada (cont.)

Canadian and U.S. evaluations of genotyped animals expected to have same accuracy because same set of predictor animals used Canada expects official release of genomic evaluations in April 2009 Young animals expected to be evaluated only by one country

Common procedures between 2 countries assist in industry acceptance

G.R. Wiggans
2008

DHI-Provo Herd Management Conference (10)

DNA laboratories

Research Bovine Functional Genomics Laboratory (BFGL), USDA (Beltsville, MD) University of Alberta (Edmonton, AB, Canada) University of Missouri (Columbia, MO) Illumina (San Diego, CA)

Commercial GeneSeek (Lincoln, NE) Genetics & IVF Institute (Fairfax, VA) Genetic Visions (Middleton, WI) DNA LandMarks (Saint-Jean-sur-Richelieu, QC, Canada) Maxxam Analytics (Mississauga, ON, Canada) ABS (DeForest, WI, through SyGen/PIC, Franklin, KY )
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (11)

Use of genomic evaluations

AI organizations determine which young bulls to buy Considered in selection of mating sires

Impact on bull dam selection will increase

May be used to market semen from 2year-old bulls

DHI-Provo Herd Management Conference (12)

G.R. Wiggans

2008

January 2009

Genomic evaluations become official Genotyped ancestors contribute their evaluations to descendents Evaluations of all genotyped females are public Evaluations of males enrolled with NAAB or 24 months old are public

Young-bull genomic evaluations may be shared among AI organizations or disclosed by owner

G.R. Wiggans
2008

DHI-Provo Herd Management Conference (13)

Impact on producers

Young-bull evaluations will have accuracy of early first-crop evaluations AI organizations may market genomically evaluated 2-year-olds

Genotypes for bull dams likely to be required

Rate of genetic improvement likely to increase by up to 50% Progeny-test programs will change
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (14)

Schedule

Calculate SNP effects with each of 3 annual traditional evaluations Calculate genomic evaluations once or more between traditional evaluations, monthly?

Recalculate SNP effects if significant number of predictor animals added

Use existing SNP effects if only young animals added

G.R. Wiggans
2008

DHI-Provo Herd Management Conference (15)

Improvements

Require bar codes on sample containers to reduce errors and improve lab efficiency Establish routine system to detect, report, and resolve parent-progeny genotype conflicts

Enroll animals that might be genotyped at birth to minimize ID issues when genotyped
Reduce processing time by enabling labs to report genotypes directly to AIPL

DHI-Provo Herd Management Conference (16)

G.R. Wiggans

2008

Plans to increase accuracy

Genotype more predictor bulls (most active bulls expected to be genotyped soon) Reach 1,500 Brown Swiss through foreign collaboration?

Increase genotyped Jerseys from both domestic animals and possible foreign collaboration
Investigate across-breed analysis to allow data from Holsteins to improve accuracy for Jerseys and Brown Swiss
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (17)

International implications

All major dairy countries investigating genomic selection Interbull meeting in January to discuss how genomic evaluations should be integrated

AI organizations need to find balance between competitive benefits from treating genotypes as proprietary versus sharing Importing countries must change rules to allow for genomically evaluated young bulls
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (18)

Low-cost genotyping research

Develop a genetic test thats cheap enough to enable use for most animals Provide parentage verification/discovery Provide genetic estimate useful for first-stage screening 384 SNPs proposed for first test High throughput procedures being developed
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (19)

Longer-term possibilities

Determine inheritance of individual chromosome segments (haplotyping)

May allow better tracking of QTL

Approximate genotypes of missing ancestors to increase predictor population Increase number of SNPs or even use entire DNA sequence

DHI-Provo Herd Management Conference (20)

G.R. Wiggans

2008

Implications

Extraordinarily rapid implementation of genomic evaluations Young bull acquisition and marketing now based on genomic evaluations Increase in diversity of bull dams considered Industry groups taking responsibility for genotyping and validation
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (21)

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) Agricultural Research Service, USDA
G.R. Wiggans
2008

DHI-Provo Herd Management Conference (22)