Genetic evaluation for three way crossbreeding
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1 Genetic evaluation for three way crossbreeding Ole F. Christensen Aarhus University, Center for Quantitative Genetics and Genomics EAAP 2015, Warszawa
2 Motivation (pigs) Crossbreeding is predominant in the production. Commonly: Crossbred sows from two dam lines Crossbred production pigs from sire line and crossbred sows. Genomic selection implemented for purebreds, but also gives options for crossbreds Ideally: Include records on crossbreds Compute breeding values for crossbred performance. Aim here: develop methods Three-breed terminal crossbreeding Additive relationships from pedigree and marker genotypes
3 Scenario Three breeds, A, B and C Breeds A and B are mated to produce AB sows Breed C boars are mated to AB sows to produce C(AB) crossbreds Phenotypes on purebreds A, B and C and crossbreds C(AB). Pedigree information exist and some animals are genotyped.
4 Previous work (two way crossbreeding) (Wei and van der Werf, 1994, Christensen et al., 2014) y A = X A β A + Z A a A + e A, y B = X B β B + Z B a B + e B, y AB = X AB β AB + g AB + e AB, where BVs for purebred performance: a A, a B. Relationships defined according to breed of origin. BVs for crossbred performance: g A, g B. Genetic correlation between purebred and crossbred performances.
5 Model for three way crossbreeding Model y A = X A β A + Z A a A + e A, y B = X B β B + Z B a B + e B, y C = X C β C + Z C a C + e C, y C(AB) = X C(AB) β C(AB) + g C(AB) + e C(AB), where BVs for purebred performance: aa, a B, a C. BVs for crossbred performance: g A, g B, g C. Relationships need to be defined!
6 Model for three way crossbreeding BVs for crossbred performance g A are correlated with with genetic effects g C(AB) (relationships) and BVs for purebred performance a A (genetic correlation). Supports a breeding goal with both purebred and crossbred performances. Allows different genetic variances in three breeds. Genetic correlation < 1: dominance effects and different genetic background, G E Relationships defined such that the model can be fitted using standard animals breeding software.
7 Additive genetic relationships Relationships can be defined either within or across breeds. Within breed: Partial relationship matrices (Garcia-Cortes and Toro, 2006): 3 breed specific matrices, 1 breed segregation matrix. Having marker genotypes on crossbreds: split according to breed of origin, construct marker-based partial relationship matrices. Across breeds: Pedigree relationships on founders within breeds and across breeds (Legarra et al. 2015). Estimate founder relationships from marker genotypes. presented here!
8 Genetic relationships across breeds Relationships between base individuals: γ A γ A,B γ A,C Γ = γ A,B γ B γ B,C γ A,C γ B,C γ C. Pedigree relationships defined recursively: A(Γ) Genomic relationships: G = mm T. Estimate Γ by matching G and A(Γ) 22. Combined relationships: H(Γ) where [ (H(Γ)) = 0 G 1 (A(Γ) 22 ) 1 ] + (A(Γ)) 1, Usual procedure for computing (A(Γ)) 1 and A 22 (Γ).
9 Variance-covariance of genetic effects Var a A a B a C g A g B g C g AB g = Σ H(Γ),
10 Variance-covariance of genetic effects Variance-covariance of genetic effects equals Σ H(Γ) where Σ = 10 genetic parameters. σa,a 2 σ a,a,b σ a,a,c σ ag,a σ a,a,b σa,b 2 σ a,b,c σ ag,b σ a,a,c σ a,b,c σa,c 2 σ ag,c σ ag,a σ ag,b σ ag,c σg 2. BLUP, REML available using standard animal breeding software (input: inverse relationship matrix).
11 Conclusions Methods for genetic evaluation for three-way crossbreeding are available. Relationships either within or across breed Implemented in standard animal breeding software First step!!
12 Acknowledgements Co-authors: Andres Legarra, Mogens Lund, Guosheng Su Project: Developing genomic selection for a pig breeding system based on crossbreeding Funding: through Green Development and Demonstration Programme (GUDP) by Danish Ministry of Food, Agriculture and Fisheries, Pig Research Centre and Aarhus University.
13 Future work Analyse data from Danish Duroc (Landrace Large White). Can the 10 genetic genetic parameters be estimated accurately?
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The Theory of Evolution Mechanisms of Evolution Notes Pt. 4 Population Genetics & Evolution IMPORTANT TO REMEMBER: Populations, not individuals, evolve. Population = a group of individuals of the same