Download - Foreign Collaborations 1

8/3/2019 Foreign Collaborations 1

1/22

G.R. WiggansAnimal Improvement Programs Laboratory

Agricultural Research Service, USDABeltsville, MD

[email protected]

2008G.R. WiggansDHI-Provo Herd Management Conference (1)

Whats Coming in

Genomic Evaluationsand How It Affects You


2/22

G.R. Wiggans 2008DHI-Provo Herd Management Conference (2)

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 theother is estimated

Genomic evaluation combines SNP effect

estimates with existing PA or PTA

Genomic data contribute ~11 daughterequivalents to reliability


3/22


What is a SNP?

Single-nucleotide polymorphism

Place on the chromosome where animals differ in thenucleotides (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 bothalleles well represented in population


4/22


Genomic vs. traditional PTA

Genotype can be thought of as source of informationlike parents, progeny, and records

Official PTA will have a indicator if they include agenomic contribution

One genotype is used to calculate genomicevaluations for all 29 traits

Genomic evaluations used the same way astraditional PTA

Expected to increase rate of genetic improvementbecause of a large decrease in generation interval


5/22


Whats happened so far

Illumina BovineSNP50 BeadChip developed

Accuracy of genomic information assessed by using2003 evaluations of bulls born before 2000 to predict2008 evaluations of young bulls

Test evaluations began to provide genomicevaluations of bull calves in April

Jersey results released in October

New results released every 2 months

Nearly 15,000 animals genotyped through October


6/22


Genotyped animals (October 2008)

Breed Bulls Cows PredictorsHolstein 12,275 2,445 7,821

Jersey 1,205 369 1,428

Brown Swiss 365 3 359


7/22G.R. Wiggans 2008DHI-Provo Herd Management Conference (7)

How to get animals genotyped

Participating AI organizations have 5-year exclusiveright to evaluate bulls genomically

Each AI organization genotypes first-choice flushes,thereby usually avoiding duplicate genotypes

Web-based system being developed to collectnominations

Avoid duplication

Confirm validity of ID and pedigree

Breed associations developing cow genotypingservice



What can go wrong

Sample doesnt provide adequate DNA quality orquantity

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 trueparent



Collaboration with Canada

Semex Supported since beginning of genomics

research

Contributed valuable genotypes to firstaccuracy test

Genotypes will be shared between AIPL and

Canadian Dairy Network

AIPL and University of Guelph collaboration



Collaboration with Canada (cont.)

Canadian and U.S. evaluations of genotypedanimals expected to have same accuracy becausesame set of predictor animals used

Canada expects official release of genomicevaluations in April 2009

Young animals expected to be evaluated only byone country

Common procedures between 2 countries assistin industry acceptance



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 )



Use of genomic evaluations

AI organizations determine which youngbulls to buy

Considered in selection of mating sires

Impact on bull dam selection will increase

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



January 2009

Genomic evaluations become official

Genotyped ancestors contribute theirevaluations to descendents

Evaluations of all genotyped females are public

Evaluations of males enrolled with NAAB or24 months old are public

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



Impact on producers

Young-bull evaluations will have accuracy of earlyfirst-crop evaluations

AI organizations may market genomicallyevaluated 2-year-olds

Genotypes for bull dams likely to be required

Rate of genetic improvement likely to increase byup to 50%

Progeny-test programs will change


15/22


Schedule

Calculate SNP effects with each of 3 annualtraditional evaluations

Calculate genomic evaluations once or more

between traditional evaluations, monthly?

Recalculate SNP effects if significantnumber of predictor animals added

Use existing SNP effects if only younganimals added


16/22


Improvements

Require bar codes on sample containers toreduce errors and improve lab efficiency

Establish routine system to detect, report, andresolve parent-progeny genotype conflicts

Enroll animals that might be genotyped at birthto minimize ID issues when genotyped

Reduce processing time by enabling labs toreport genotypes directly to AIPL


17/22


Plans to increase accuracy

Genotype more predictor bulls(most active bulls expected to be genotyped soon)

Reach 1,500 Brown Swiss through foreigncollaboration?

Increase genotyped Jerseys from both domesticanimals and possible foreign collaboration

Investigate across-breed analysis to allow datafrom Holsteins to improve accuracy for Jerseysand Brown Swiss


18/22


International implications

All major dairy countries investigating genomicselection

Interbull meeting in January to discuss howgenomic evaluations should be integrated

AI organizations need to find balance betweencompetitive benefits from treating genotypesas proprietary versus sharing

Importing countries must change rules to allowfor genomically evaluated young bulls


19/22


Low-cost genotyping research

Develop a genetic test thats cheap enough toenable use for most animals

Provide parentage verification/discovery

Provide genetic estimate useful for first-stagescreening

384 SNPs proposed for first test

High throughput procedures being developed


20/22


Longer-term possibilities

Determine inheritance of individualchromosome segments (haplotyping)

May allow better tracking of QTL

Approximate genotypes of missing ancestorsto increase predictor population

Increase number of SNPs or even use entireDNA sequence


21/22


Implications

Extraordinarily rapid implementation ofgenomic evaluations

Young bull acquisition and marketing

now based on genomic evaluations

Increase in diversity of bull dams

considered

Industry groups taking responsibility forgenotyping and validation


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G R Wiggans 2008DHI-Provo Herd Management Conference (22)

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

Download - Foreign Collaborations 1

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