Genomic selection applies to synthetic breeds

Genomic selection applies to synthetic breeds Jérémie Vandenplas, Mario P.L. Calus 21 November 2015

Traditional selection Aim Selection of the best animals to create the next generation Based on estimated breeding values (or PTA) calculated from phenotypic records (e.g., milk yield) pedigree heritability

Traditional selection Successful in many breeds/species Slow! Girolando Bull Progeny Test At least 5-6 years for the first results of the progeny

Traditional selection Successful in many breeds/species Slow! Girolando Bull Progeny Test At least 5-6 years for the first results of the progeny Introduction to genomic selection

Genomic selection: how does it work?

Genomic selection: how does it work? Selection based on DNA profiles (SNP genotypes)... A T T C T A G G... A T A C T A G G...... A T A C T A G G... A T A C T A G G... (~50,000 genetic markers)

Genomic selection: how does it work? Reference population Estimation of the effect of each SNP, based on phenotypes and genotypes of proven sires + Prediction equation G - milk yield: -0.1kg - protein yield: +0.5kg A T T C T A G G A T A C T A G G T - milk yield: +0.5kg - protein yield: +0.1kg

Genomic selection: how does it work? Reference population Selection candidates + Prediction equation Genomic breeding values for selection candidates

Genomic selection: how does it work? Reference population Selection candidates + Prediction equation Selected animals Using genomic breeding values

Genomic selection: how does it work? Accuracy of genomic breeding values depends on: Characteristics of the trait E.g., heritabily Characteristics of the genome E.g., QTL, linkage disequilibrium (Reference) population E.g., number of genotyped and phenotyped animals Statistical methods... Hayes et al. 2009. J. Dairy Sci. 92:433-443

Genomic selection: benefits

Genomic selection: benefits A T T C T A G G A T A C T A G G?

Genomic selection: benefits A T T C T A G G A T A C T A G G? T - milk yield: +0.5kg - protein yield: +0.1kg

Genomic selection: benefits A T T C T A G G A T A C T A G G? Hardly/not possible to distinguish related animals (e.g., full sibs) without genomic information

Genomic selection: benefits A T T C T A G G A T A C T A G G? A T T C T A G G A T T C T A G G A T T C T A G G A T A C T A G G Possibility to distinguish related animals (e.g., full sibs) with genomic information

Genomic selection: benefits Can improve selection response by Decreasing the number of animals selected as potential parents Selection candidates Traditional selection Genomic selection

Genomic selection: benefits Can improve selection response by Decreasing the number of animals selected as potential parents Identifying animals with superior genetic merit at a young age (even before the birth!) Much less than 5-6 years Reducing risk from using young genotyped bulls Increase in reliability of GEBV over parent average EBV! Schaeffer. 2006. J. Anim. Breed. Genet. 123:218-223

Genomic selection: benefits Can improve selection response by Decreasing the number of animals selected as potential parents Identifying animals with superior genetic merit at a young age (even before the birth!) Much less than 5-6 years Reducing risk from using young genotyped bulls Increase in reliability of GEBV over parent average EBV! Can potentially double the rate of genetic gain Schaeffer. 2006. J. Anim. Breed. Genet. 123:218-223

Genomic selection: benefits Applicable without pedigree Especially useful for traits that Are difficult or expensive to measure Are measured late in life or after the death Have a low heritability E.g., carcass traits, feed efficiency Need to phenotype everybody is reduced Costs are (highly) reduced

Genomic selection: within-breed Successful in dairy cattle! E.g., Holstein in the Netherlands Wide range of traits Milk production Longevity Fertility Udder health (e.g., somatic cell score) Health traits (e.g., claw health)...

Genomic selection: the Netherlands Holstein Introduction of genomic selection de Jong and Stoop. 2014. Interbull Workshop, Verden

Genomic selection: the Netherlands Holstein Accelerated genetic progress de Jong and Stoop. 2014. Interbull Workshop, Verden

Genomic selection: the Netherlands The generation interval is reduced Mainly for bulls sires: <7y <4 y de Jong and Stoop. 2014. Interbull Workshop, Verden

Genomic selection: the Netherlands Holstein Accelerated genetic progress Reduced generation interval Mainly for bulls sires (<7y <4y) de Jong and Stoop. 2014. Interbull Workshop, Verden

Genomic selection: the Netherlands Holstein Accelerated genetic progress Reduced generation interval Mainly for bulls sires (<7y <4y) >50% AI done with genotyped bulls de Jong and Stoop. 2014. Interbull Workshop, Verden

Genomic selection Successful in many countries/breeds/...

Genomic selection Successful in many countries/breeds/... And still room for improvement Reduced genotyping costs Improved knowledge...

Genomic selection in Girolando?

Genomic selection in Girolando? Girolando = synthetic breed Take the best characteristics from Holstein (milk production) Gyr (heat and decease resistance)

Genomic selection in Girolando? Girolando = synthetic breed Take the best characteristics from Holstein (milk production) Gyr (heat and decease resistance) Differences with common implementations Multiple breeds / crossbreeding Animals with different breed compositions...

Genomic selection in Girolando? Girolando = synthetic breed Take the best characteristics from Holstein (milk production) Gyr (heat and decease resistance) Opportunities

Genomic selection: opportunities

Genomic selection: opportunities Holstein already based on genomic selection! Indirect use Ibanez-Escriche et al. 2009. Genet. Sel. Evol. 41:12 Odegard et al. 2009. Genetics 181:737-745

Genomic selection: opportunities Holstein already based on genomic selection! Indirect use Many genotypes already available! Ibanez-Escriche et al. 2009. Genet. Sel. Evol. 41:12 Odegard et al. 2009. Genetics 181:737-745

Genomic selection: opportunities Holstein already based on genomic selection! Indirect use Many genotypes already available! Increase the genetic progress Mainly by using young genotyped bulls (reducing the generation interval) Mate selection Ibanez-Escriche et al. 2009. Genet. Sel. Evol. 41:12 Odegard et al. 2009. Genetics 181:737-745

Genomic selection: opportunities Select for the best characteristics of Holstein and Gyr Select for more uniform Girolando animals Optimize the genome of Girolando animals Ibanez-Escriche et al. 2009. Genet. Sel. Evol. 41:12 Odegard et al. 2009. Genetics 181:737-745

Genomic selection: opportunities Genotyping females? Advantages of genomic information More reliable information

Genomic selection: opportunities Genotyping females? Advantages of genomic information More reliable information Cows replacement strategy Selection of the best cows as potential parents Selection of the best heifers for herd replacements Greater genetic progress in the herd

Genomic selection: opportunities Genotyping females? Possible higher market values for genotyped heifers More accurate genomic breeding values

Genomic selection: opportunities Genotyping females? Possible higher market values for genotyped heifers More accurate genomic breeding values Can be included in the reference population Possibility to increase the accuracy

Genomic selection: opportunities Others Identification of alleles linked to genetic diseases Help the breeders in the choice of the parents Parentage identification Unknown pedigree, errors,...

Opportunities for Girolando Genomic selection can increase the genetic progress for a wide range of traits! Successful in many situations Opportunities for synthetic breeds Also advantages for females

Acknowledgments

Acknowledgments Questions?

http://www.funpecrp.com.br/gmr/year2006/vol3-5/gmr0250_full_text.htm http://www.interbull.org/static/web/7_3_dejong.pdf http://girolando.com.br/baixar.php?arquivo=arquivossit e/progenie/girolando_breed_genetic_summary_180.pdf