AlphaSim software for

Transcription

1 AlphaSim software for simulating plant and animal breeding programs Serap Gonen*, Mara Battagin, Diarmaid de Burca, Chris Gaynor, Janez Jenko, David L Wilson, Anne- Michelle Faux, Gregor Gorjanc and John M Hickey

2 AlphaSim: Philosophy (1) Simulate haplotype sequences* and initial pedigree * MaCS (Chen et al., 2009) Model haplotype structure given a specific population history Haplotypes can be: Externally supplied by user Internally simulated Wheat Maize Cattle Poultry Swine Rabbit

3 AlphaSim: Philosophy (2) Sample haplotypes for base generation Select marker and casual loci QTN QTN

4 AlphaSim: Philosophy (3) Simulate allele substitution effects for causal loci Additive effects Dominance effects + Allele substitution effects

5 AlphaSim: Philosophy (4) Drop base haplotypes to the first generation (5) Generate breeding values and phenotypes

6 AlphaSim: Philosophy (6) Select parents of next generation, generate gametes and drop haplotypes to next generation (7) Repeat!

7 AlphaSim: Parameters Biotechnology Selection Flexibility AlphaSim Parameters Traits Pedigree Genome Populations

8 AlphaSim: Parameters Start-stop simulation Internal and/or external training data Internal and/or external pedigrees Merging divergent populations Biotechnology Selection Flexibility AlphaSim Parameters Traits Pedigree Genome Populations

9 AlphaSim: Parameters Association mapping population Bi-parental family MAGIC Nested half- /full-sib structure Synthetic population Biotechnology Selection Flexibility AlphaSim Parameters Traits Pedigree Genome Populations

10 AlphaSim: Parameters Biotechnology Flexibility Pedigree Model species Selection AlphaSim Parameters Traits Genome Populations Animal Plant Human Wild Effective population size

11 AlphaSim: Parameters Biotechnology Selection Flexibility AlphaSim Parameters Traits Pedigree Populations Genome Sequence SNP and QTN Chromosome length Number of Chromosomes

12 AlphaSim: Parameters Biotechnology Selection Flexibility AlphaSim Parameters Traits Pedigree Genome Populations Genetic and residual correlations between traits Gamma or Gaussian distribution Additive and Dominance effects Simple and complex traits Heritability

13 AlphaSim: Parameters Biotechnology Flexibility Pedigree External SNP solutions Optimal contribution selection Random selection Truncation selection TBV Selection AlphaSim Parameters Traits Genome Populations Phenotypes gebv

14 AlphaSim: Parameters Gene drives Gene editing Recombination rate Double haploids Biotechnology Flexibility Pedigree Selection AlphaSim Parameters Traits Genome Populations

15 AlphaSim: Output Data AlphaSim Default Outputs Genome Selection

16 AlphaSim: Output Trait variance components and correlations Pedigree TBV, TDV, Phenotypes QTN additive and dominance effects Total additive and dominance genic variances in each generation Data Allele frequency and physical position of QTN and SNP across chromosomes Recombination positions for each individual AlphaSim Default Outputs Genome Selection

17 AlphaSim: Output Data Genome AlphaSim Default Outputs Selection Genomic relationship matrix Genotypes and phenotypes of training individuals and selection candidates TBV of the selection candidates Estimates of SNP effects gebv and accuracy Selection index

18 AlphaSim: Output Data Physical position and minor allele frequency of each segregating site, SNP and QTN AlphaSim Default Outputs Physical and genetic map Genome Selection SNP and QTN genotype and phased haplotypes of each individual

19 AlphaSim: Examples (1) Random Mating vs Genetic Selection Response to Selection Random mating Genetic Selection Genetic Variance Generation Generation

20 AlphaSim: Examples (2) Genome editing in animal breeding Jenko et al. GSE (2015) 47:55

21 AlphaSim: Examples (3) Selecting for recombination in animal breeding Battagin et al. GSE (2016) 48:44

22 AlphaSim: Examples (4) Introducing genomic selection in wheat Gaynor et al. In Preparation

23 AlphaSim: AlphaSuite

24 AlphaSim: GUI

25 Acknowledgements John Hickey Gregor Gorjanc Roberto Antolin Mara Battagin Diarmaid De Burca Andrew Derrington Chris Gaynor Paolo Gottardo Janez Jenko Daniel Money Roger Ros Freixedes Maria Sanchez Perez Masoud Shirali Adriana Somavilla Thank you!