Chapter 8 Breeding Programs

1. Chapter 8Breeding Programs

2. Breeding program • What are reasons to start a breeding program? • Genetic conservation • Genetic selection • What information do you need to make a breeding program? • Select best animals for next generation… EBV!

3. Structure of breeding programs • Define the breeding goal • Record data on selection candidates • Estimate breeding values • Mating design with selected individuals • Disseminate genetic progress • Evaluation breeding scheme

4. Structure of breeding programs • Define the breeding goal • Record data on selection candidates • Estimate breeding values • Mating design with selected individuals • Disseminate genetic progress • Evaluation breeding scheme

5. Define the breeding goal • A breeding goal indicates the desired direction of change over generations • Examples: • Increased milk yield • Increased egg production • Reduced leg problems

6. Breeding goals: • Include more than 1 trait • Inclusion of traits depends on importance, not on heritability! • Defining breeding goals is about predicting the future! • Breeding goals should be expressed as a single value: ranking of individuals

7. Breeding goal defined as: • The weighted sum of economic values and breeding values or • Set of desired gains for each trait, based on marketing considerations of breeding companies

8. Economic model Figure 8.1. The use of a profit function to derive economic values. The economic value (EV) of a trait is the increase in profit that results from a single unit increase of the trait value.

9. Economic Model • The economic value vi is used as weight in the breeding goal: H = A1v1 + A2v2 + A3v3 + …. + Anvn • H is the weighted sum of TRUE breeding values

10. Estimating a BV for H • Index I to estimate H I = b1P1 + b2P2 + b3P3 + …. + bnPn • b can be obtained by linear regression • For a single trait I = H’ = EBV

11. Breeding goals: economic values or desired gains? • Some traits cannot be expressed in economic values: • Competitive position vs. profitability (Breeding company want to predict market in long term) • Consequences of negative correlated responses (fertility, health, or welfare)

12. Defining breeding goals for the future • Economic profit farmer • Competitive position breeding company • Country/ production system • International trade restrictions? • Production quota

13. Desired direction of change • Animal welfare: • Disease resistence, stress tolerance, longevity, fertility and functional traits • Undesired correlated responses to selection • Adaptation to alternative management • Product quality: • Fat production • Nutrient value, fatty acid and protein compositions of output products

14. Structure of breeding programs • Define the breeding goal • Record data on selection candidates • Estimate breeding values • Mating design with selected individuals • Disseminate genetic progress • Evaluation breeding scheme

15. Data recording systems • Who collects the data? • Farmers • Breeding company • Test stations • Data on selection candidates or on sibs/progeny? • Depends on traits!

16. Structure of breeding programs • Define the breeding goal • Record data on selection candidates • Estimate breeding values • Mating design with selected individuals • Disseminate genetic progress • Evaluation breeding scheme

17. Breeding Value estimation • Structure of breeding program depends on species and traits: Dairy Cattle: few offspring/ female identification at birth sex limited traits Layer Hens: more progeny/ female identification at birth reproduction vs production Progeny Testing Line Crossing

18. Breeding Value Estimation Fish: Many offspring/ female No identification at birth Production Own Performance/ Sib Testing

19. Structure of breeding programs • Define the breeding goal • Record data on selection candidates • Estimate breeding values • Mating design with selected individuals • Disseminate genetic progress • Evaluation breeding scheme

20. Selection and Mating • Selecting parents determines genetic improvement over time • Mating parents determines combination of maternal and paternal alleles

21. Structure of breeding programs • Define the breeding goal • Record data on selection candidates • Estimate breeding values • Mating design with selected individuals • Disseminate genetic progress • Evaluation breeding scheme

22. Dissemination • Dairy Cattle: straws • Pigs: piglet producers and fattening farms • Chicken: Only crossbreds • Fish: monosex or sterile fry

23. Structure of breeding programs • Define the breeding goal • Record data on selection candidates • Estimate breeding values • Mating design with selected individuals • Disseminate genetic progress • Evaluation breeding scheme

24. Evaluation of breeding programs • Things that can go wrong: • Wrong models, eg no inclusion of systematic environmental effects: common environment! • Overestimation genetic parameters • Preferential treatments • Unexpected correlated responses • Selection response • Inbreeding and Genetic diversity • Costs

25. Summary Breeding program • 4 steps to a successful program: • Define a breeding goal • Make a base population and estimate genetic parameters • Estimate breeding values • Assess quality: genetic progress, rate of inbreeding and costs

26. Chapter 8Genotype x Environment Interaction

27. Breeding program • Different genotypes show different sensitivity to changes in the environment • Are the animals (or breed) we selected based on their genotype in one environment also the best animals (or breed) in another environment? • no GxE interaction: Yes • large GxE interaction: Maybe

28. GxE interaction • Do we need different animals (selection directions) for: • High input conditions vs organic farming systems? • Production in temperate environments vs production in tropical environments?

29. A tropical fenotype: Nelore short hair, skin folds, long ears, no body fat reserves, long legs

30. A temperate fenotype: Red Agnus Coarse hair, subcutaneous fat, short stature

31. Crossbreeds show wide variation

32. But you can get the best of both worlds!

33. GxE interaction • Ranking of breeding values change with change in environment (re-ranking) • Average value of a trait does not change • Between breeds: some fit better to certain environments (countries) than others • Within breed: some genotypes less (more) sensitive to variation in environment • > Within country >Between countries

34. G x E interaction P P strong strong E E P P weak none E E

35. How to detect GxE • Between breeds: test different breeds in different environments, and rank. • Within breeds: test progeny groups in different (2 or more) environments, and calculate genetic correlations between the two “traits”

36. G x E interaction: btw. breeds No GxE GxE 1 1 1 1 2 2 P 2 P 2 3 3 4 4 5 5 5 5 6 6 6 6 E1 E2 E1 E2

37. G x E interaction: within breeds R <0.8:GXE R>0.8: no GXE X(E2) X(E2) X(E1) X(E1)

38. Conclusions Problems: • 1) breeding goals may differ (populations) • 2) breeding values can differ (within breeds) Examples: • Feed intake groups vs individuals • SPF environments vs on-farm conditions • Test station performance vs commercial fattening

39. GxE

40. GxE

41. exercise: Tabular method… V Fv=0.3 U W aji = ½ asi + ½ adi ajj = 1 + ½ asd = 1 + Fjj X Y Z Calculate the inbreeding coefficient of animal Z using the Tabular method. Note that animal V is inbred.

42. aji = ½ asi + ½ adi ajj = 1 + ½ asd = 1 + Fjj Exercise: Tabular method ? 1 ? 0 1.3 ? ? 0 ? 0 ? 1 0.5 ? 0.65 ? 0 ? ? 1 ? 0 ? 0.65 0.5 ? 0.325 ? ? 1 0.25 ? 0.65 ? 0.25 ? ? 0.66 ? 0.66 1.16 ?