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What’s Coming in Genomic Evaluations and How It Affects You G. R. Wiggans Animal What’s Coming in Genomic Evaluations and How It Affects You G. R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george. [email protected] usda. gov DHI-Provo Herd Management Conference (1) G. R. Wiggans 2008

What are genomic evaluations? l DNA extracted from blood, hair, or semen l ~40, What are genomic evaluations? l DNA extracted from blood, hair, or semen l ~40, 000 genetic markers (SNPs) evaluated l l l 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 DHI-Provo Herd Management Conference (2) G. R. Wiggans 2008

What is a SNP? l l l Single-nucleotide polymorphism Place on the chromosome where What is a SNP? l l l 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 DHI-Provo Herd Management Conference (3) G. R. Wiggans 2008

Genomic vs. traditional PTA l l l Genotype can be thought of as source Genomic vs. traditional PTA l l l 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 DHI-Provo Herd Management Conference (4) G. R. Wiggans 2008

What’s happened so far l l l Illumina Bovine. SNP 50™ Bead. Chip developed What’s happened so far l l l Illumina Bovine. SNP 50™ Bead. Chip 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 l Jersey results released in October l New results released every 2 months l Nearly 15, 000 animals genotyped through October DHI-Provo Herd Management Conference (5) G. R. Wiggans 2008

Genotyped animals (October 2008) Breed Holstein Jersey Brown Swiss Bulls 12, 275 1, 205 Genotyped animals (October 2008) Breed Holstein Jersey Brown Swiss Bulls 12, 275 1, 205 365 DHI-Provo Herd Management Conference (6) Cows 2, 445 369 3 Predictors 7, 821 1, 428 359 G. R. Wiggans 2008

How to get animals genotyped l l l Participating AI organizations have 5 -year How to get animals genotyped l l l 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 w Avoid duplication w Confirm l validity of ID and pedigree Breed associations developing cow genotyping service DHI-Provo Herd Management Conference (7) G. R. Wiggans 2008

What can go wrong l l l Sample doesn’t provide adequate DNA quality or What can go wrong l l l Sample doesn’t provide adequate DNA quality or quantity Genotype has many SNPs that can’t be determined (90% call rate required) Genotype conflicts with parent(s) w Pedigree error w Sample ID error w Laboratory error w Genotype checked against all others to find true parent DHI-Provo Herd Management Conference (8) G. R. Wiggans 2008

Collaboration with Canada l Semex w w l l Supported since beginning of genomics Collaboration with Canada l Semex w w l l 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 DHI-Provo Herd Management Conference (9) G. R. Wiggans 2008

Collaboration with Canada (cont. ) l l Canadian and U. S. evaluations of genotyped Collaboration with Canada (cont. ) l l 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 DHI-Provo Herd Management Conference (10) G. R. Wiggans 2008

DNA laboratories l l Research w Bovine Functional Genomics Laboratory (BFGL), USDA (Beltsville, MD) DNA laboratories l l Research w Bovine Functional Genomics Laboratory (BFGL), USDA (Beltsville, MD) w University of Alberta (Edmonton, AB, Canada) w University of Missouri (Columbia, MO) w Illumina (San Diego, CA) Commercial w Gene. Seek (Lincoln, NE) w Genetics & IVF Institute (Fairfax, VA) w Genetic Visions (Middleton, WI) w DNA Land. Marks (Saint-Jean-sur-Richelieu, QC, Canada) w Maxxam Analytics (Mississauga, ON, Canada) w ABS (De. Forest, WI, through Sy. Gen/PIC, Franklin, KY ) DHI-Provo Herd Management Conference (11) G. R. Wiggans 2008

Use of genomic evaluations l AI organizations determine which young bulls to buy l Use of genomic evaluations l AI organizations determine which young bulls to buy l Considered in selection of mating sires l Impact on bull dam selection will increase l May be used to market semen from 2 -year -old bulls DHI-Provo Herd Management Conference (12) G. R. Wiggans 2008

January 2009 l l l Genomic evaluations become official Genotyped ancestors contribute their evaluations January 2009 l l l 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 DHI-Provo Herd Management Conference (13) G. R. Wiggans 2008

Impact on producers l l l Young-bull evaluations will have accuracy of early first-crop Impact on producers l l l 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 DHI-Provo Herd Management Conference (14) G. R. Wiggans 2008

Schedule l l Calculate SNP effects with each of 3 annual traditional evaluations Calculate Schedule l l Calculate SNP effects with each of 3 annual traditional evaluations Calculate genomic evaluations once or more between traditional evaluations, monthly? w Recalculate SNP effects if significant number of predictor animals added w Use existing SNP effects if only young animals added DHI-Provo Herd Management Conference (15) G. R. Wiggans 2008

Improvements l l Require bar codes on sample containers to reduce errors and improve Improvements l l 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 l l Genotype more predictor bulls (most active bulls expected Plans to increase accuracy l l 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 DHI-Provo Herd Management Conference (17) G. R. Wiggans 2008

International implications l l All major dairy countries investigating genomic selection Interbull meeting in International implications l l 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 DHI-Provo Herd Management Conference (18) G. R. Wiggans 2008

Low-cost genotyping research l l l Develop a genetic test that’s cheap enough to Low-cost genotyping research l l l Develop a genetic test that’s cheap enough to enable use for most animals Provide parentage verification/discovery Provide genetic estimate useful for first-stage screening l 384 SNPs proposed for first test l High throughput procedures being developed DHI-Provo Herd Management Conference (19) G. R. Wiggans 2008

Longer-term possibilities l Determine inheritance of individual chromosome segments (haplotyping) w l l May Longer-term possibilities l Determine inheritance of individual chromosome segments (haplotyping) w l l 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 l l Extraordinarily rapid implementation of genomic evaluations Young bull acquisition and marketing Implications l l 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 DHI-Provo Herd Management Conference (21) G. R. Wiggans 2008

Financial support l l National Research Initiative grants, USDA NAAB (Columbia, MO) w ABS Financial support l l National Research Initiative grants, USDA NAAB (Columbia, MO) w ABS Global (De. Forest, WI) w Accelerated Genetics (Baraboo, WI) w Alta (Balzac, AB) w Genex (Shawano, WI) w New Generation Genetics (Fort Atkinson, WI) w Select Sires (Plain City, OH) w Semex Alliance (Guelph, ON) w Taurus-Service (Mehoopany, PA) l Holstein Association USA (Brattleboro, VT) l American Jersey Cattle Association (Reynoldsburg, OH) l Agricultural Research Service, USDA DHI-Provo Herd Management Conference (22) G. R. Wiggans 2008