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
The inbreeding coefficient is ½ the relationship of the parents
12.5% 25%
50% 25% 6.25%
3.125%
Full-sibs Half-sibs Half 1st cousins
Genomic inbreeding
12.5%
25%
25%
12.5%
Genomic inbreeding
12.5%
25%
25%
Genomic inbreeding
12.5%
25%
0%
Genomic Relationship
12.5%
25% 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
SNP10 B 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
zq
Correlations
0
5
10
15
20
25
30
35
40
0 10 20 30 40
Ru
ns o
f h
om
ozyg
osit
y (
%)
Pedigree inbreeding (%)
-30
-20
-10
0
10
20
30
40
0 10 20 30 40
Exp
ecte
d
ho
mo
zyg
ou
s (
%)
55
60
65
70
75
80
85
0 10 20 30 40
Perc
en
t h
om
ozyg
ou
s (
%)
-20
0
20
40
60
80
100
0 10 20 30 40
Gen
eti
c
rela
tio
nsh
ip (
%)
Pedigee inbreeding (%)
R=0.59
R=0.39
R=0.69
R=0.73
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
AB
AB AB
The lethal recessive variant is in 50% of his offspring
25% 50% 25%
BB AB AA
Affected Carrier Normal
Lethal recessive disease
% in population
CVM 2.5%
DUMPS 0.5%
Brachyspina 1.7%
BLAD 0.7%
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