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Pedigree vs. Genomic Inbreeding Tara Carthy Teagasc, Moorepark ICBF industry meeting 02/02/2016 Inbreeding • Inbreeding arise due to mating of closely related animals • Offspring have a greater likelihood of having two copies of the same variant (homozygous ) AA or BB • Homozygous variant arise due to • Identical by state • Identical by decent Pedigree inbreeding Half-sibs Full-sibs 6.25% 25% 50% 25% Half 1st cousins 12.5% 3.125% The inbreeding coefficient is ½ the relationship of the parents Genomic inbreeding 25% 25% 12.5% 12.5% Genomic inbreeding 25% 12.5% 25% Genomic inbreeding 25% 12.5% 0% Genomic Relationship 25% 12.5% The genomic relationship of these two animal is 0 Measure of genomic inbreeding SNP1 B B SNP2 B A SNP3 A B SNP4 B B SNP5 A A SNP6 B B SNP7 A B SNP8 A A SNP9 A B • Percentage homozygous • The proportion of the genome that have the same variant • 60% homozygous • Adjusting for base level of homozygosity in population • 10% homozygosity • Runs of homozygosity • The proportion of the genome that have consecutive variant that are the same • 30% in ROH Genetic relationships • Using genotypes rather than pedigree information to measure relationship of an animal to itself • Homozyosity rather than traditional inbreeding is measured • “Inbreeding” can be less than zero • Adjustments to genomic inbreeding to reflect actually inbreeding Correlations Expected homozygous (%) Percent homozygous (%) 85 R=0.59 80 75 70 65 60 55 0 10 20 30 40 R=0.39 60 40 20 0 -20 0 10 20 30 Pedigee inbreeding (%) R=0.69 0 Runs of homozygosity (%) Genetic relationship (%) 100 80 40 30 20 10 0 -10 -20 -30 40 zq 10 40 35 30 25 20 15 10 5 0 20 30 40 R=0.73 0 10 20 30 Pedigree inbreeding (%) 40 Inbreeding depression The effect of inbreeding is dependent on what part of the DNA is inherited from the common ancestor Both animals are 25% inbreed Affected by inbreeding Not affected by inbreeding Inbreeding depression • Lethal recessive diseases The lethal recessive variant is in 50% of his offspring AB AB Lethal recessive disease % in population AB CVM 2.5% DUMPS 0.5% Brachyspina 1.7% BLAD 0.7% 25% 50% 25% BB AB AA Affected Carrier Normal Sire advice • Currently sire advice is based on pedigree information • Where both sire and dam are genotyped genomic relationships can be used more accurately than pedigree relationships • With genomics • Avoid mating carriers lethal disease • Mate animals with complementary genotypes for best production Conclusion • Genomic information can be used to • More accurate define the relationship between animal • Provide a more accurate measure of the inbreeding of an animal • Not all inbreeding has a negative effect on performance • Sire advice will be updated to include genomic information