Innovative indicator of molecular genetic diversity Danchin-Burge Coralie1, Moureaux Sophie1,2, Boichard Didier2, Baur Aurélia2,3, Fritz Sébastien2,3 1 Institut de l'Elevage, Paris, France - coralie.danchin@idele.fr 2 INRA GABI, Jouy en Josas, France 3 ALLICE, Paris, France

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Genetic abnormalities in Brown Swiss cattle Spiderleg Weaver Spinal Dysmyelination Spinal Muscular Atrophy Embryo mortality 1 & 2 Congenital nasolacrimal duct fistula … to be continued !

Kinship coefficient X is the common ancestor Z is inbred A and B are related X A B The kinship coefficient between A and B is equal to Z inbreeding coefficient Z

Calculation of kinship coefficients based on pedigree information Data available on line (http://www.idele.fr) Kinship coefficients averaged over a population Young AI bulls compared with Active female populations Total AI population + quality control (pedigree depth)

Let’s have an example JACKSON AG - BSWFRAM001534192414 Male kinship (%) 5.4 Pedigree depth: 7.0 Female kinship (%) 3.5 JEROBOAM - BSWFRAM002130591415 Male kinship (%) 4.6 Pedigree depth:6.7 Female kinship (%) 2.8

Fmoy population = 0.5 / σmoy = 0.1 Calculation of kinship coefficients based on molecular information – ORI (1) SNP frequencies are averaged over a population type Example: all AI bulls less than 5 years old Fmoy population = 0.5 / σmoy = 0.1 First allele Fqcy 1 Second allele Fqcy 2 SNP1 A 0.6 T 0.4 SNP2 C 0.9 0.1 SNP3 0.3 G 0.7

CHAMPION’s Fmoy= 0.6 - ORI indicator = - (0.6-0.5) / 0.1 = -1 Calculation of kinship coefficients based on molecular information - ORI (2) SNP frequencies are calculated for each individual and compared with the population frequencies Example: one AI bull, “CHAMPION” First allele Fqcy 1 Second allele Fqcy 2 SNP1 A 0.6 SNP2 C 0.9 T 0.1 SNP3 0.7 CHAMPION’s Fmoy= 0.6 - ORI indicator = - (0.6-0.5) / 0.1 = -1 ORI > 0 => Original bull (compared with the population type) ORI < 0 => Bull carrying the same alleles as the population type

Main advantage of the ORI method 0.6 0.6 0.4 0.6 0.8 0.2 0.2 0.2 0.9 0.1 0.9 0.1 Full sibs don’t have the same ORI indicator f = 0.533 f = 0.4 0.6 0.8 0.9 0.2 0.1 0.4 f = 0.533 f = 0.4

Comparing the pedigree and molecular method

Perspectives

TMIO(3) = TMI+3xORIT+3xORIC+3xORIF A new Total Merit Index ? A simulation of 3 different selection processes TMI of the actual 17 bulls sold in 2015; 17 best bulls according to their Total Merit Index in 2015; 17 bulls with a new total merit index TMIO3. TMIO(3) = TMI+3xORIT+3xORIC+3xORIF

Results

Conclusion ORI index are innovative and performant genetic variability indicator ORI are more accurate than pedigree indicators, even more so in the case of an international breed (loss of pedigree information) … Now it’s up to you, the breed’s managers to decide how to implement it in a new TMI ! Pour les 17 taureaux mis en marché Réponse > 1 spop sur l’ISU Réponse < 0 pour tous les indicateurs de variabilité génétique Pour la formule actuellement utilisée, ISUO (4) : Perte de 0.13 spop sur ISU par rapport à scénario max (ISU2015) Gain de 0.29 spop sur p_mal et 0.17 spop sur p_fem par rapport à scénario max (ISU2015)

Thank you for your attention 3G Thank you for your attention Contact: coralie.danchin@idele.fr