Download Pedigree vs. Genomic Inbreeding

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