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