Mating structures for genomic selection breeding programs in aquacultue

1. Mating structures for genomic selection breeding programs in aquacultue Anna Sonesson & Jørgen Ødegård

2. Introduction • Important processes for breeding • Estimating breeding values of selction candidates • Selection of parents • Mating of parents • Two important results • Genetic gain • Rate of inbreeding DF (related to effective population size)

3. Control rates of inbreeding • Select parents with a constraint on rates of inbreeding • Avoid mating full/half sibs

4. Sire:Dam mating ratio • Traditionally 1:2 (sires:dams) mating designs • The 2 dams are needed to estimate family tank effects • Woolliams (1989) advocated factorial mating designs • E.g. 2:2, 10:10, 100:100 or Nsires:Ndams in aquaculture • More mates increases accuracy of breeding values • Fewer parents selected with limitation of number of family tanks - increased rates of inbreeding

5. Breeding values • Own phenotypic record • Best Linear Unbiased Prediction (BLUP) breeding values (Henderson, 1984) • Utilise family information, especially for traits not recorded on the candidates, e.g. disease resistance and fillet quality traits • High accuracy of breeding values and high rates of inbreeding • Genome-wide breeding values (Meuwissen et al., 2001)

6. Genome-wide estimated breeding values Chromosome 1 xx 2 3 ------ ------- ------------ ------- ------ ------- ------------ ------- Markers Estimate marker effects (Meuwissen et al., 2001) Genome-wide breeding value =sum av marker effects (additive inheritance)

7. Sibs of candidates are used to estimate the marker (SNP) effects for disease resistance and fillet quality traits Parents (Genotype) Test individuals (søsken) (Genotype +Phenotype) Candidates (Genotype)

8. Accuracy genomic breeding values heritability =0.4 og 40 sibs/family in test • Conventional BLUP breeding values: ca 0.57 • Genome-wide breeding values: 0.82 (Nielsen, et al, 2010) • ’Pooled genomic selection’: 0.60-0.82 depending on no. markers (Sonesson et al., 2010) G=r i sg Increases genetic gain with genomic selection

9. Genomic selection • Daetwyler et al., (2007): ’Genomic selection increases importance of the Mendelian sampling term and reduces the importance of family compared to traditional BLUP breeding values’ • More information on individual performance/genotype reduce rates of inbreeding • Maybe also mating designs are less important for genomic selection

10. Aim Compare different degrees of factorial mating designs in traditional BLUP and genomic selection on genetic gain for one growth trait and one disease trait and rates of inbreeding

11. Material & Methods • 2 traits Growth: h2=0.25, measured on 6000 candidates Disease: h2=0.25 measured on 3000 sibs of candidates • 100 or 200 sires and 100 or 200 dams selected • 100, 200 or 1000 families • Mating ratios 1:1, 2:2, 10:10 or 1:2

12. Material & Methods • Traditional BLUP (Henderson, 1984) • Genomic selection • 5000 SNP (biallelic) markers, 1000 QTL spread on 10 chromosomes • GS-BLUP breeding values (Meuwissen et al., 2001) • Truncation selection • With 10 or no restriction on no. selected offspring per parent • 10 discrete generations

13. No restriction on no. selected offspring per parent

14. Max. 10 selected offspring per parent

15. Hieracrchical mating and max 10 selected offspring per parent

16. Conclusion • Genomic selection has equal DGGROWTH and DGDISEASE is 69-170% higher than traditional BLUP selection • Traditional BLUP • The DF is reduced with 50% when going from 1:1 to 10:10 mating (100 to 1000 families) without restriction • No change in DGGROWTH but DGDISEASE is increased in concordance with decrease in DF when going from 1:1 to 10:10 mating • Genomic selection • Only DF is reduced with ~50%, and no effect on genetic gain when going from 1:1 to 10:10 mating

17. Conclusion • Traditional BLUP selection • Higher mating ratio important to reduce DF and increase genetic gain for the sib-trait (DISEASE here) • Alternatively, use a constraint on how many offspring are allowed to be selected from each parent • Genomic selection • Mating ratio only important to reduce DF, but DF were very low for the pop. sizes we used here

18. Conclusion genomic selection • Genomic selection powerful method to improve traits that are not recorded on selection candidates • Factorial mating very powerful for genomic selection • SNP chip development limitation of implementation of genomic selection

19. THANK YOU FOR YOUR ATTENTION!! This work has been done in NRC projects 190442 and 186862 (co-financed by AquaGen AS, Geno and Norsvin)