the dangers of inbreeding in the arabian horse · 2019-02-12 · the danger of inbreeding in the...

The dangers of inbreeding in the Arabian horse

Dr. Steven JanssensLivestock genetics

ECAHO, Prague06 feb 2015

Livestock GeneticsDivision Gene Technology, Dep. BiosystemsKU Leuven

http://[email protected]

Kasteelpark Arenberg 30 – 2456B-3001 HeverleeBelgium

Tel: +32 (0)16 32 85 96 Fax: +32 (0) 16 321 994

6 febr. 2015 S. Janssens ECAHO 2

Introduction

Diversity between breeds

• The species (Equus Caballus) covers a large number of breeds that differ in many characteristics (e.g. body size)

• Breeds were linked to geographical location � studbooks

• Studbooks organise selection(impose restrictions on reproduction)

• � Selection causes a reduction in the genetic variationin breeds


Subdivision of the breed may further reducediversity• Sporthorses

show jumping <-> dressage

• In Arabians breeding for:

morphology <-> endurance <-> recreation, ….

keeping original maternal strains pure (RASANs???)


Why do we need to bother about geneticdiversity?

• Capacity to adapt(= can a population respond to natural and human selection)

• Linked to fitness(= capacity to produce fertile offspring)

� Studbooks need to monitor the genetic diversity of breeds toguarantee survival in the long run


The origin of geneticvariation

Nuclear DNA

96 febr. 2015 S. Janssens ECAHO

The horse genome• 62 autosomes + 2 (XX or XY)

• 2,7 109 basepairs (Wade et al. 2009)

• 20322 genes

• 3 106 locations of variation (2012) inthe genome !!!


Inheritance

• Chromosomes exist in pairs (2n)

• One comes from stallion, other from mare

⇒Horses have 2 copies for every gene, each horse is unique

Genes can have several variants due to mutations �

alleles

⇒Some alleles are no longer functional, some have advantages….

⇒Estimated 1 recessive, deleterious allele/animal


Mitochondrial DNA…..maternal inheritance

• mtDNA is passed on onlyfrom mare to all the offspring

• Maternal lineages share the same mtDNA


Genetic variation

• Is caused at the level of the DNA(also mtDNA)

• Genes exist in (many) variants, some advantageous, somedeleterious (1 recessive deleterious allel per individual)

• Genetic variation causes phenotypic variation,but not all variation at DNA level is known (currently)

• Variation affects adaptation capacity and fitness of population


Measures of diversity

COI – Coefficient of inbreeding (F)

• The probability that 2 genes at any locus in the genomeare identical by descent and results from matingindividuals related by common ancestors (=inbreeding)


The biological mechanism..

• Mating halfsibs• Each gene has 50%

probability to pass on• F = total prob. for

offspring to behomozygous(red or blue)

1/21/2

1/21/2

P(homozygous red) = 1/2*1/2*1/2*1/2 = 0.0625P(homozygous blue) = 1/2*1/2*1/2*1/2 = 0.0625

F=0.125


Close matings

Combinations Relationship COI of offspring (F)

Sire - daughter 0.50 0.250

Grandsire -granddaughter

0.25 0.125

Brother-sister(full sibs)

0.50 0.250

Halfsibs 0.25 0.125


Compute F from a pedigree

Foal

Stallion

Mare

Grandsire

Grandmother

Grandsire

Grandmother

Common ancestor

11

2

m n

F+ +

=

∑


Find “loops” that connect the sire and dam-side

5 individuals are in the path => F= 0,55=0,0325

Foal

Stallion

Mare

Grandsire

Grandmother

Grandsire

Grandmother

Common ancestor


Reduction of fitness due to inbreeding

• Increased homozygosity(for desirable traits)

• Unmasking of recessive deleterious alleles(estimates in man and mice indicate that on averageeach individual carries 1 lethal mutation)

• Reduced allozyme variablity(even if genes are not the same, they can work in the same way)


Inbreeding depression• Mostly on reproduction and fitness traits

(fertility, survival, disease resistance, …)• Typically 1% decrease in fitness per 1% increase in

inbreeding

Example: pregnancy rate

F=0, non inbred: 80%

F=0,125 (parents were halfsibs): 70%


Inbreeding depression in horses• In Friesians, strong relationship of F of the foal on

« retained placenta » at parturition

• In Polish Arabians, no effect of inbreeding on body measurements (height at withers, chest and cannonbone circumference)

• In Norwegian trotters, negative effect of inbreeding on racing performance

• In Belgian Warmbloods also a negative effect of F on show jumping performance


Control of inbreeding short and long term

• Avoid high individual F’s

• Monitor and conserve the geneticvariation of the breed

change of average F of the population


COI in Friesians

Sevinga et al. 2004


Rate of inbreeding (ΔF) in Friesians


Inbreeding rate and effective size

• Effectieve population size = number of animals in ideal population with same rate of inbreeding as the studied population

• Rule of thumb:

Ne ≥ 100 or ΔF=0,005 per generation

Ne < 50 danger � ΔF ≥ 0,01 per generation


Populationunderstudy

foals/yearNe F

Friesian 52392 3000 27 0,15

Belgian Draught 5900 800 80-100 0,03

Arabians(Spain, 2011)

14247 ??? 39 0,09

Arabians(Poland, 2005)

706 ??? -- 0,01

Arabians(Belgium)

4056 350 ?? 0,00


Ne reflects mating practice in the breed

• Based on number of breeding mares and stallions

1Ne

14Nf

14Nm

Stallions (Nm) Mares (Nf) Ne

Belg. Arabian 836 1860 2307

Belgian Draught 446 384.6 1597


Ne and mating practice

• Unbalanced use of stallionsand/or mares

V is variance in family size forstallions and mares

Var. Of family size stallions(Vf)

Var. Of family size mares(Vm) Ne

Belg. Arabian 232 3,89 135,3

Belgian draught 1853 2,8 41,6

Ne8N

4 Vf Vm


Pedigree analysis can reveal much more…

• Number of founders, number of ancestors, number of founder genomes, generation interval ….

• Requires correct and complete pedigree file

�t his feature is expressed in Complete Generation Equivalents


• Pedigree complete over 4 generations� CGE = 4

• Number of ancestors / generation

21, 22, 23, 24, …

Complete Generation equivalents

6 febr. 2015S. Janssens ECAHO

32

• Incomplete pedigree� CGE = 3.56

• Animals with low CGE� common ancestors less likely

� seem less related

� probably: real inbreeding > calculated


33

Pedigree completeness

• Belgian Arabians

CGE = 2,5

� Conclusions forBelgian Arabiansare very preliminary

• Spanish study

CGE = 7,7


34

Alternative…..molecular tools

• Use of genetic markers to assess breed diversity

• 2 main indicators of molecular diversity- rate of heterozygosity (H)- allelic richness (Ar)

• We need DNA from a representative group of horses

• Tracking of maternal lineages using mtDNA


Observedheterozygosity

Expectedheterozygosity

Allelicrichness

Belgian Draught 0,663 0,657 6,7

Arabians(Spain, 2011)

0,533 0,636 3,41

Arabians(Algeria, 2014)

0,718 0,731 6,43


• Comparison of observed heterozygosity (number of heterozygotes = HO) to the expected heterozygosity (under HWE = HE) � estimate of the degree of inbreeding

• Population inbreeding coefficient (Fis)o Number between -1 and 1

• FIS = 0 � no inbreeding (population HWE)• FIS > 0 � heterozygote deficit (inbreeding)• FIS < 0 � heterozygote excess

� could indicate possible bottleneck, outbreeding,small sample size!

Fis � 1 ��

��


Relationship between Arabian breeds andstrains


Maternal lineages can be questioned basedon mtDNA


Conclusions

The danger of inbreeding in the Arabian horse

• Inbreeding results in:

- inbreeding depression (fitness and reproduction)

- unmasking of deleterious alleles

• In several horse breeds, negative effects of inbreedinghave been demonstrated

• Inbreeding is not only an issue for each individual but should also be handled at population level


What to do…

• Monitor the breedIf pedigree’s are avalaible this is method of choice. Otherwise, molecular methods can be used

• Ne is a good basic measure to express genetic diversitya value of 100 is desirable for survival of the breed

• Scientific tools exist to optimize breedingaim at equal contributions of parents to next generation

• Carefully think about use of genetic tests !!Exclusion of carrier animals might lead to “bottleneck” thatwill generate new problems in 3 or 4 generations.


Molecular tools

• Based on markers present in nuclear or mitochondrial DNA

• Requires biological sample and representative number of horses

• No pedigree data needed

• Many applications (within and between breeds)

• Technology evolves fast….applications will follow the coming years. It is a good idea to collect biologicalsamples routinely and more important, record anyinteresting phenotype (disease, color, performance, ….)


Thank you for yourattention

Acknowledgements

Ministry of the Flemish communitydep. sustainable agricultural development&Flemish Pig Breeding association

the dangers of inbreeding in the arabian horse · 2019-02-12 · the danger of inbreeding in the...

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