Use of AlphaDrop in the simulation approach to genomic selection and

mate allocation

Gregor Gorjanc

University of Ljubljana, Biotehnical faculty

Animal Science Department

Bologna, 2012

BF, Animal Science Department

„Revolution“ in animal breeding

• Classical approach (phenotype + pedigree)

• Genomic approach (phenotype + pedigree + SNP)

3 6 5 7

3 6 5 7

The key idea

Adapted from Karlsson &Lindblad-Toh (2008), Wang et al. (2009)

How to join „revolution“?

• Genotyping = €$£ • Test out different scenarios, methods, … using

simulation

AlphaDrop http://sites.google.com/site/hickeyjohn/alphadrop

Hickey J, Gorjanc G (2012) Simulated data for genomic selection and GWAS using a combination of coalescent and gene drop

methods. G3 (accepted)

AlphaDrop in a nutshell

• Simple program

• Coalescent simulation of haplotypes with MaCS (Chen et al., 2009) – mutation, recombination

• Dropping haplotypes through the pedigree – recombination, selection

• Result – SNP data and sequence data

(efficient internal compression: 01010110 long integer)

– QTL position and effect and genetic values

7

AlphaDrop parameter file example PedigreeStatus ,Internal

NumberOfSires ,50

NumberOfDamsPerSire ,10

NumberOfOffspringPerDam ,4

NumberOfChromosomes ,30

ChromosomeLengthMorgans ,1

NumberOfSnpChips ,1

nSnpPerChromosme ,2000

WriteFullSequenceOut ,No

MaxAlleleFreqForQTLForModel3And4 ,0.30

NumberOfQTLperChromosomeNormalDist ,300

NumberOfQTLperChromosomeGammaDist ,10

ShapeAndScaleOfGammaDistFor2And4 ,0.42,5.4

TraitHeritability ,0.75

NumberGenerationsBurnIn ,25

NumberGenerationsSelection ,0

SelectionMethod ,PedigreeBlup

SelectionTrait ,1

AlphaDrop output example 148K SimulatedPedigree.txt

1.2G Chip1Genotype.txt

2.3G Chip1Phase.txt

3.2M Chip1SnpIdAlleleFreqPhysicalPos.txt

5.6G Chip2Genotype.txt

12G Chip2Phase.txt

16M Chip2SnpIdAlleleFreqPhysicalPos.txt

1.7M PedigreePhenotypesTrueBreedingValues.txt

343 ProportionOfVariationExplainedByNumberOfQtl.txt

172M RestrictedCausitiveSitesAnimalGenotypes.txt

1.3M RestrictedCausitiveSitesChromIdSiteIdAlleleFreqPhys…

320 TraitVarianceComponents.txt

172M UnrestrictedCausitiveSitesAnimalGenotypes.txt

1.3M UnrestrictedCausitiveSitesChromIdSiteIdAlleleFreqPh…

Usage up to now

• Software development and testing Hickey – Alpha{Phase,Impute,Bayes}

• Genotyping strategies – Huang et al.: Assessment of Alternative Genotyping

Strategies to Maximize Imputation Accuracy at Minimal Cost

• Method development – Hickey et al.: Genomic evaluations using similarity between

haplotypes

– Yang and Tempelman: A Bayesian antedependence model for whole genome prediction

A particular simulation design (Hickey et al., Wang and Tempelman)

1

Genotype (G)

Pedigree

Phenotype (P)

Candidates (G, P)

2

3

4

5

6

7

8

9

10

Candidates (G, P)

Candidates (G, P)

Validation Calibration Gen.

Is AlphaDrop useful for RGB-Net?

• WG2 – Rabbit as a livestock

– T1: genotype/phenotype studies - YES

– T2: breeding plans - YES

– T3: biodiversity resources - ? – genotyping strategies

– mate allocation (dominance, inbreeding)

• Other WG?