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Genomics: It’s here to stay!

Genomics: It’s here to stay!. Presented to Dairy Conference Moncton, NB, November 2013 Valérie Tremblay, agr . Holstein Canada Training and Extension Coordinator. Genomic testing to improve Profitability ?. By doing a better selection

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Genomics: It’s here to stay!

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  1. Genomics: It’s here to stay! Presented to Dairy Conference Moncton, NB, November 2013 Valérie Tremblay, agr. Holstein Canada Training and Extension Coordinator

  2. Genomictesting to improveProfitability? • By doing a betterselection • By using the best geneticsavailable (males and females) • By having one more tool in yourtoolbox for decisionmakingprocess • To betterunderstand the geneticpotential of yourherd • By managinginbreedinglevels • By gainingknowledge on the geneticdiseases / traits affectingdairyherdprofitability

  3. The basics of the science We work with markers that are equally spaced along the genome

  4. Markers? Each marker is equally spaced along the genome like posts beside our highways that indicate each kilometer Markers are the “spots” where we verify if the animal carries 0, 1 or 2 copies of the gene at that specific location

  5. Markers? These markers werediscovered by making connections between the DNA sequence of the reference population (generations of proven sires) and data recorded on daughters (classification and milkrecording).

  6. Genotypes of proven bulls with highly reliability proofs were compared to the same DNA segments at specific markers for bulls with the same qualities/strengths. Reference population…?

  7. Overview Genotype = Phenotype - Environment Even for a cow with the most desirable genes, the environment she is in will affect the way she will « express » these genes

  8. Genotype or Phenotype? • Genotype = what we usually can’t see • Phenotype = the physical appearance; what we usually « see » Genotype or Phenotype???: • LPI 2523 • Classified GP-83 • Hind legs curved • Production at 3-4 10 543 kg - 4,1%F and 3,5%P • Red Carrier • Sire proof for udder +10

  9. Genotype or Phenotype? Genotype: • Genetic potential received by its ancestor • Genetic potential transmittable to progeny • Always estimated, never known completely Phenotype: • Dependant on the genotype, but highly influenced by management and environment • Each animal will convert its potential in different ways • Changes over an animal’s lifetime

  10. Why? To enable the ability to compare cows according to their genetic potential: • Ex: first lactation average of 8500 kg milk in an average-management herd versus 8500 kg milk in a herd with an excellent management Which cow has the best potential??? • We need to remove the management/environmental effect to know more about her genetic potential

  11. Therefore…knowledge of the DNAsequencehelpsmake the Genotype more accurate

  12. DNA GenotypeGenetic IndexesLPI EBV PA DGV …

  13. Abreviations GEBV/ EBV: (Genomic) EstimatedBreeding Value GLPI/LPI: (Genomic) Lifetime Profit Index GPA/PA: (Genomic) Parent Average DGV: Direct Genomic Value GMACE: (Genomic) Multi-Trait Across Country Evaluation

  14. What is an « EBV » and how do we work with it?

  15. When you look at a sire proof…

  16. …or when you look at a pedigree…

  17. EBVs • = Estimated Breeding Values • Defines the genetic merit - half of which will be passed on to its progeny. • Most EBVs are expressed in the units of measurement for each particular trait EBV EBV EBV of progeny 2

  18. EBVs • Provide a measure of the breeding potential of an animal for a specific trait. They take into account: • performance data collected on known relatives • the relationships between performance traits (correlations) • the degree to which traits are inherited from one generation to the next (heritability). • An animal will only pass on half of its genes to its progeny so its EBVs must be halved in order to estimate the average genetic worth of its progeny

  19. EBVs • Therefore, EBVs represent: • Information to select parents of the next generation: what we want the parents to transmit to the next generation for both females and males • NOT necessarily the animals own ability to perform

  20. WHAT IS « DIRECT GENOMIC VALUE » (DGV) ?

  21. Direct Genomic Value • Calculated using DNA/markers selected on the genome and the ‘value’ of those markers compared to the reference population • Interesting Predictor of genetic merit… BUT not as applicable and reliable as the blended proof • Weight (emphasis) in the blended proof decreases as we add phenotypic information (production and conformation) • Scale of expression is larger than that of the blended proof (more variation) – danger of overestimation for high end animals

  22. How do weinclude a DNA sequenceintothis?

  23. Inclusion of New DNA Contribution for Males

  24. Inclusion of New DNA Contribution for Females

  25. Genomics helps us… • Increase genetic evaluation accuracy • Increase the accuracy of selection AT A VERY YOUNG AGE • Speeds up genetic improvement

  26. Pathway for sires in AI – beforegenomic Time for gestation, birth of first daughters (approx. 150 registereddaughtersafter 18 months) Birth- Selectionwith pedigrees 1st proof: Bull isapprox. 5 years of age 0 1 2 5 yrs Sampledbetween 12-15 months Semensold as a young sire Thesedaughtersneed to calve. Production and classification performance are recorded

  27. Genomicscan help Birth- Selectionwith pedigrees + GENOMIC Time for gestation, birth of first daughters (approx. 150 registereddaughtersafter 18 months) 1st proof: Bull isapprox. 5 years of age Embryo 0 1 2 5 yrs Sampledbetween 12-15 months Semensold as a young sire Thesedaughtersneed to calve. Production and classification performances are recorded Genomic Genomic

  28. Moment of selection for females Timing for DNA test Calving Birth First selection: Before1st service - breeding Embryo Stage Second selection: Aftercalvingwith lactation records, classification

  29. RELIABILITY…WHAT DOES IT CHANGE?

  30. Reliability • Reliability of genetic indexes is influenced by different factors: • Quantity of data • Consistency of results • Heritability of the trait • Distribution (number of herds) • Indicates the possibility of variation in + or – as we add more data, pedigree or PA • Gives an idea of the risk taken • Comparison between different types of animals (heifers vs cows, young sires vs older sires)

  31. Reliability

  32. Reliability: Impact on Genomics • Variation of reliability for all traits • Brings an additional accuracy • If genetic index decreases, it DOESN’T mean the animal is not good anymore • Reduces the gap between estimated breeding values and true breeding values

  33. Understanding the spread of possibilities

  34. Helps Selection Genomics CANNOT predict which one will be the next Star brood Cow or next Show Queen. However…: • It helps differentiate between siblings: determine the ones that have the most potential • It will improve LPI reliability (more accurate selection and faster progress) • It can lead to the discovery of new and interesting cow families

  35. How do weperformthe test?

  36. Genotyping Services and prices

  37. Geno ID program • For herdsthat have unregisteredanimals • One step process for genotyping and registering animals with accuracy

  38. Hair, Nasal swabs or TSU? • Hair: • Follicle of the hair root is required • At least 40 hair follicles • Harder to get a good sample from young calves

  39. Hair, Nasal swabs or TSU? • Swabs: • Convenient and more effective for young animals • Careful for dirt (little is acceptable) • Have to order sample kits – 5$ each in groups of 10 • TSU= Tissue Sample Unit • Collect tissue in the ear, inserted in the punch devicethatcontainsliquid • 30$ for 10 or 75$ for 30 • Need to buy the appropriate tagger

  40. Moment of selection Calving Birth Second selection: Aftercalvingwith lactation records, classification First selection: Before 1st service - breeding Embryo Stage

  41. How do we use the results?

  42. Results

  43. Results Sortable and downloadable Excel file

  44. Use of genotype • Selection of elite females • Définition of “elite” • Herd management decision tool • More accurate genetic indexes to compare • Within herd • Within the breed • Intensify the choice of next generation dams • Better selection of ET donors • Differentiate full sisters • Value of elite females

  45. Use of genotypes ? • Sire selection • Divide the herdinto groups • Better use of « speciality sires » • Sexedsemen • Young sires • Elite sires for certain traits • Mating programs more accurate • Genomicevaluations are included for both males and females

  46. Use of Genomic Young Sires • Higher proofs with lower Reliability!! = MORE RISK but a chance of faster progress • Do not put all your eggs in the same basket! • Use several sires to spread the risk • The % of young sires to use in your herd depend on your herd objectives

  47. SomeFrequentlyAsked Questions…

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