Incorporation of Genomic Information into Selection Tools
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Transcript of Incorporation of Genomic Information into Selection Tools
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Incorporation of Genomic Information into Selection ToolsMike TessMontana State University
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OutlineWhere we areWhere we need to goEfforts to get there
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Where are we?
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Types of markersParentageDeterminationValidationTraceabilityGenetic ID tagManagement toolsPredict a future phenotypeSelection toolsPredict progeny performanceProduce genetic change
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U.S. Genomic CompaniesBovigenIgenityMMI
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DNA markers are evolvingSingle locus
Multiple loci
Panels of many loci
Whole genome scans
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The language of DNA markersGenotypesHaplotypesScoresScansStarsProfilesMolecular Genetic Values
Accuracy?Confusion!Units?
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Where we need to go
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DNA Technologies and Genetic ImprovementHow can we use DNA markers to achieve:Maximum speed?Minimum cost?Maximum control?Maximum choice?
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We need a common currency
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Multiple sources of information
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A common currencySINGLE estimate of breeding value based on all information availableDNA scoresPedigreePhenotypes
SINGLE measure of accuracy
Higher accuracy earlier in life
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Some traitsPhenotypesDNAMarkers
NOYESNO----YES
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Some traitsPhenotypesDNAMarkers
NOYESNO----YES
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A common currencyPedigreesPhenotypesEPD
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A common currencyPhenotypesDNAMarkers
NOYESNO----EPDYES
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Some traitsPhenotypesDNAMarkers
NOYESNO----EPDYES
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A common currencyBovigen ScoreIgenity ScoreMMI ScoreM-EPDMolecularTranslation (MT)
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A common currencyPhenotypesDNAMarkers
NOYESNO----EPDYESM-EPD
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Some traitsPhenotypesDNAMarkers
NOYESNO----EPDYESM-EPD
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A common currencyPedigreesPhenotypesDNA ScoresMA-EPD
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A common currency for selectionPhenotypesDNAMarkersSame units. Same measure of accuracy.
NOYESNO----EPDYESM-EPDMA-EPD
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Yearling BullsHow much would increased accuracy be worth?
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A suggested roadmap . . .
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DNA CompaniesReferencePopulationsPublicWebsite
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Validation and AssessmentIndependent verification
Does the test work?What else might change if I select based on this test?
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Reference PopulationsData = tissue (DNA), pedigrees, and phenotypesExisting dataHerds optimally designed and managed for current and future use
Representative of:Different breedsDifferent production environments
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DNA CompaniesReferencePopulationsBreedAssociationsBreeders &ProducersDatabaseDNA companiesBreed Assoc.ConsultantsBreedersProducersExtension
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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
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ChallengesQTL/DNA marker discovery50k 300k loci chipStatistical proceduresData required
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ChallengesDatabaseLocation(s)AccessData50-300k genotypes?
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ChallengesValidationDefinitionsStandardsResponsible organizationInternational scope
AssessmentResponsible organizationRelationship to discovery
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ChallengesEducationChanging technologyExploding terminologyVariation in understandingMultiple industry voicesCredibility at risk
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ChallengesDecision SupportDesigning breeding plansBio-economic objectivesSpeed versus directionChoosing selection tools
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Efforts to get there
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A Team ApproachGenomic companiesBreed associationsUSDA-ARSState Experiment StationsNBCECBIFCommission
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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
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Roles for the CommissionFacilitate meetings Encourage actionConduit for communication
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Validation and AssessmentBIF Commission
Responsible organization = NBCEC?
Recommended standards and procedures DefinitionsMultiple sources of informationPopulations and production/marketing systems
BIF RecommendationsInternational collaborations
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Education and Decision SupportBIF CommissionAssess needsEncourage development of materials and tools
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Reference PopulationsBreedsEnvironmentsProduction systemsTraits measured
USDA-ARSBreed Associations
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Reference PopulationsPhenotypesPedigreesDNA testingValidationValidated markersKey sires
Critical link in national cattle evaluation
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Statistics Commission/NBCECRohan Fernando Iowa State Univ.Steve Kachman Univ. NebraskaRob Templeman Michigan State Univ.Mark Thallman USMARCDick Quass Cornell Univ.
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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
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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
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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
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DNA CompaniesReferencePopulationsBreedAssociationsBreeders &ProducersDatabaseDNA companiesBreed Assoc.ConsultantsBreedersProducersExtension
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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 . . .
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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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