1. Using recombination to maintain genetic diversity
D. Segelke1, J. Heise² & G. Thaller3
1) Vereinigte Informationssysteme Tierhaltung w.V. (vit), Verden/Germany
2) University of Goettingen, Animal Breeding and Genetics, Göttingen/Germany
3) Institute of Animal Breeding and Husbandry, Christian-Albrechts-University,
Kiel/Germany

2. Understanding recombination important for:
Background
Meiotic recombination is a process by which pieces of DNA are broken and recombined to produce new combinations of alleles. (
Increasing number of genotyped animals, allows to study the mechanism and characteristics of recombination
Understanding recombination important for:
Imputation
Genomic evaluation
Genomic mating
Genetic diversity
 Higher probability to generate extreme positive offsprings

3. Materials & Methods Derivation global number of recombination
Genotypes imputed & phased with Fimpute
Identify the paternal & maternal haplotype within the offspring (# conflict)
Comparing the offspring’s paternal haplotype to the two haplotypes of the parent
In the offspring haplotype a recombination event was defined as a transition from the parents paternal to maternal haplotype or vice versa
Strand A:
Parent
Strand B:
Strand A:
Offspring
Strand B:
Strand A:
Parent
Strand B:
Strand A:
Offspring
Rec.

4. Materials & Methods Derivation global number of recombination
Reduction false positives by:
Recombination event surrounded by 3 informative SNPs
Recombination events in 2-Mb windows with recombination rate per parent significantly >5% were ignored
Sire and dam must be genotyped unless they have more than 10 offspring
Sire and/or dams with only 1 offspring were ignored
Studied phenotype: global number of recombination events (BTA 1-29)
Male recombination: Sire – offspring pairs
Female recombination: Dam – offspring pairs

5. Materials & Methods Genetic parameter & GWAS
Genetic parameter & breeding value estimation using VCE & PEST
Animal repeatability model
Y= µ + chiptype + PE + animal + e
GWAS and dominance GWAS were performed using GCTA
Additive GWAS:
y = a + bx + g + e
y: male or female EBV, a:mean term, b: additive effect candidate SNP, x : genotype indicator variable, g: polygenic effect (genomic relationship matrix), e: residual
Dominance GWAS:
y: mean deviation per parent, a:mean term, b: dominance effect of the candidate SNP, x : SNP genotype indicator variable, g:dominance relationship matrix, e:residual ,

6. Average number of male recombination: 23.4 ± 4.97 (n= 248,554 animals)
Results
Average number of male recombination: 23.4 ± 4.97 (n= 248,554 animals)
Kadri et al. (2016): 23.3
Ma et al. (2015): 25.5
Average number of female recombination : 23.8 ± 5.5 (n= 31,079 animals)
Kadri et al. (2016): 21.4
Ma et al. (2015): 23.2
Heritability male recombination: 0.13 ± 0.01
Kadri et al. (2016): 0.13 ± 0.03
Heritability female recombination: 0.06 ± 0.01
Kadri et al. (2016): 0.08 ± 0.02 ,

7. Results GWAS for female & male recombination nmale=3. 918; nfemale=6

8. Results Dominance GWAS for female & male recombination nmale=3
Results Dominance GWAS for female & male recombination nmale=3.918; nfemale=6.706

9. Results Trends in male & female recombination

10. Results Genetic correlation between single chromosomes for male

11. Results Different variation of breeding values of sire progeny groups
AI company: Sires showing high variation
Increased probability to find extreme positive candidates
Production herds: Sires showing less variation
Uniform progeny groups are better to manage
Prediction the variability of future offspring groups using SNP data
Cassano:
- mean: 32 kg
- variation: 16.5 kg
- p(>70kg): 1.1%
Alexander:
- mean: 33 kg
- variation: 19.5 kg
- p(>70kg): 2.8%

12. Results Genomic mating tool (gBAP)
Recombination-Map is used to identify bulls with higher probability of extreme offspring

13. Global number of recombination differs between male & female
Conclusion
Recombination is a biological process which can be used to maintain genetic diversity
Global number of recombination is heritable & allows breeding for recombination
Interesting for AI companies
Global number of recombination differs between male & female
Global number of recombination is mainly influenced by some major genes
Dominance
Further research needed to understand recombination
Gene editing

14. Thank you for attendance!
Acknowledgements
This project was funded by the German ministry
Entwicklung eines Anpaarungsprogramms mit zusätzlicher Nutzung genomischer Informationen (gBAP)
Thank you for attendance!
6. Dezember 2018