Incorporation of Genomic Information into Selection ToolsMike TessMontana State University

OutlineWhere we areWhere we need to goEfforts to get there

Where are we?

Types of markersParentageDeterminationValidationTraceabilityGenetic ID tagManagement toolsPredict a future phenotypeSelection toolsPredict progeny performanceProduce genetic change

U.S. Genomic CompaniesBovigenIgenityMMI

DNA markers are evolvingSingle locus

Multiple loci

Panels of many loci

Whole genome scans

The language of DNA markersGenotypesHaplotypesScoresScansStarsProfilesMolecular Genetic Values

Accuracy?Confusion!Units?

Where we need to go

DNA Technologies and Genetic ImprovementHow can we use DNA markers to achieve:Maximum speed?Minimum cost?Maximum control?Maximum choice?

We need a common currency

Multiple sources of information

A common currencySINGLE estimate of breeding value based on all information availableDNA scoresPedigreePhenotypes

SINGLE measure of accuracy

Higher accuracy earlier in life

Some traitsPhenotypesDNAMarkers

NOYESNO----YES

Some traitsPhenotypesDNAMarkers

NOYESNO----YES

A common currencyPedigreesPhenotypesEPD

A common currencyPhenotypesDNAMarkers

NOYESNO----EPDYES

Some traitsPhenotypesDNAMarkers

NOYESNO----EPDYES

A common currencyBovigen ScoreIgenity ScoreMMI ScoreM-EPDMolecularTranslation (MT)

A common currencyPhenotypesDNAMarkers

NOYESNO----EPDYESM-EPD

Some traitsPhenotypesDNAMarkers

NOYESNO----EPDYESM-EPD

A common currencyPedigreesPhenotypesDNA ScoresMA-EPD

A common currency for selectionPhenotypesDNAMarkersSame units. Same measure of accuracy.

NOYESNO----EPDYESM-EPDMA-EPD

Yearling BullsHow much would increased accuracy be worth?

A suggested roadmap . . .

DNA CompaniesReferencePopulationsPublicWebsite

Validation and AssessmentIndependent verification

Does the test work?What else might change if I select based on this test?

Reference PopulationsData = tissue (DNA), pedigrees, and phenotypesExisting dataHerds optimally designed and managed for current and future use

Representative of:Different breedsDifferent production environments

DNA CompaniesReferencePopulationsBreedAssociationsBreeders &ProducersDatabaseDNA companiesBreed Assoc.ConsultantsBreedersProducersExtension

ChallengesMultiple companies marketing markers for the same traits.Overlapping informationDynamic individual DNA testsIncreasing number of lociIncreasing accuracy

Animals evaluated for the same traits at different points in time

ChallengesQTL/DNA marker discovery50k 300k loci chipStatistical proceduresData required

ChallengesDatabaseLocation(s)AccessData50-300k genotypes?

ChallengesValidationDefinitionsStandardsResponsible organizationInternational scope

AssessmentResponsible organizationRelationship to discovery

ChallengesEducationChanging technologyExploding terminologyVariation in understandingMultiple industry voicesCredibility at risk

ChallengesDecision SupportDesigning breeding plansBio-economic objectivesSpeed versus directionChoosing selection tools

Efforts to get there

A Team ApproachGenomic companiesBreed associationsUSDA-ARSState Experiment StationsNBCECBIFCommission

BIF CommissionRonnie Green USDA-ARSRonnie Silcox University of GeorgiaDarrell Wilkes ABS GlobalJim Wilton University of GuelphMike Tess Montana State University

Bill Bowman American AngusChair BIF Emerging Technologies Committee

Roles for the CommissionFacilitate meetings Encourage actionConduit for communication

Validation and AssessmentBIF Commission

Responsible organization = NBCEC?

Recommended standards and procedures DefinitionsMultiple sources of informationPopulations and production/marketing systems

BIF RecommendationsInternational collaborations

Education and Decision SupportBIF CommissionAssess needsEncourage development of materials and tools

Reference PopulationsBreedsEnvironmentsProduction systemsTraits measured

USDA-ARSBreed Associations

Reference PopulationsPhenotypesPedigreesDNA testingValidationValidated markersKey sires

Critical link in national cattle evaluation

Statistics Commission/NBCECRohan Fernando Iowa State Univ.Steve Kachman Univ. NebraskaRob Templeman Michigan State Univ.Mark Thallman USMARCDick Quass Cornell Univ.

Statistics and Software Recommended standards for estimating and reporting:DNA marker effects Units of the traitAdditive genetic valueDNA marker accuracy

Procedures for mining information from large SNP panels

Statistics and Software Procedures for melding information from multiple markers into a single M-EPD with a corresponding accuracyMolecular translation

Procedures for incorporating M-EPD into national genetic evaluation systemsDNA-markers, phenotypes, pedigree

Goal Delivery of M-EPD or MA-EPD to producers soon after completion of DNA tests

Updated as new information is added to the databaseDNA scores of relativesIndividual performancePerformance of relatives

DNA CompaniesReferencePopulationsBreedAssociationsBreeders &ProducersDatabaseDNA companiesBreed Assoc.ConsultantsBreedersProducersExtension

In closing . . . ..DNA technologies have always offered great promise . . .

DNA is always more complicated than it seems at the time

Confusion within industry is high . . .

In closing . . . ..Credibility of genetic research and genetic tools at risk

Lines between research, technology transfer and education need to blur

We must walk before we can run

Good things are on the horizon

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