Conservation genetics of cattle, sheep, and goats - Globaldiv

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Conservation genetics of cattle,

sheep, and goats

Pierre Taberlet

Laboratoire d'Ecologie Alpine, CNRS UMR 5553

Université Joseph Fourier, Grenoble, France

Conservation genetics of

cattle, sheep, and goats

•! Introduction on conservation genetics

•! History of cattle, sheep, and goats

•! Conservation issues

–! The FAO/UNEP strategy

–! Facts

–! Threats on genetic resources

•! Towards a sustainable management of

genetic resources

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–! Facts



genetic resources

Conservation

genetics

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Conservation

genetics

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Molecular Ecology (2008) 17, 275-284

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Effective population size (Ne)

•! Definition –! "the number of breeding individuals in an idealized

population that would show the same amount of

dispersion of allele frequencies under random genetic

drift or the same amount of inbreeding as the population under consideration" (Wright 1931, 1938)

•! The 50/500 rule-of-thumb (Franklin 1980) –! In the short term Ne should not be less than 50

(increased probability of extinction because of genetic

effects)

–! In the long term Ne should not be less than 500

The

extinction

vortex

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The

extinction

vortex

Extinction







–! Facts



genetic resources

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Farm animal history

present 5,000 BP 10,000 BP

Domestication of cattle, sheep,

and goats in Middle East

Cattle domestication (1)

•! Wild ancestor now extinct: auroch (Bos primigenius)

•! Domestication: 10500 BP (Helmer et al. 2005)

•! For domestic cattle, the common usage accepts two taxa

(Bos taurus, B. indicus)

•! Mitochondrial DNA polymorphism: two main lineages

corresponding to two domestication events (Loftus et al.

1994; Bradley et al. 1996)

•! Eighty four percent of the mtDNA variation is partitioned

among continents (Bradley et al. 1996)

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Sheep

A

B

!"

!"!!#

!"!!#

CattleBos indicus

Bos taurus

!"!$

GoatD

F

C

B

A G

Cattle domestication (2) Mitochondrial DNA polymorphism

85% among continents

Sheep domestication (1)

•! Wild ancestor(s): Ovis orientalis

•! Domestication: 10500 BP (Peters et al. 2005)

•! Domestic species: O. aries

•! Mitochondrial DNA polymorphism: four main lineages (Tapio et al. 2006)

•! Thirty five percent of the mtDNA variation is partitioned among continents (Townsend 2000)

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Sheep

A

B

!"

!"!!#

!"!!#

CattleBos indicus

Bos taurus

!"!$

GoatD

F

C

B

A G

Sheep domestication (2) Mitochondrial DNA

polymorphism 35% among continents

No relationship

with breeds

Goat domestication (1)

•! Wild ancestor: Bezoar (Capra aegagrus)

•! Domestication: 10500 BP (Peters et al. 2005)

•! Domestic species: Capra hircus

•! Mitochondrial DNA polymorphism: six main lineages (Naderi et al. 2007)

•! Ten percent of the mtDNA variation is partitioned among continents (Luikart et al. 2001)

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Sheep

A

B

!"

!"!!#

!"!!#

CattleBos indicus

Bos taurus

!"!$

GoatD

F

C

B

A G

Goat domestication (2)

Mitochondrial DNA

polymorphism 10% among continents

No relationship with breeds

Domestication in the Fertile Crescent,

about 10,500 years ago

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Domestication of cattle,

sheep, and goats

•! Multiple maternal origins

•! High level of nuclear DNA polymorphism

•! No evidence of bottleneck during the domestication

(sheep and goats)

•! Maybe a bottleneck during the domestication of

cattle, but evidence of introgression from aurochs

later on

•! Very large gene pools on which human induced-

selection was acting to produce the diversity of

breeds we observe today

Farm animal history




Spread of cattle, sheep,

and goats in Europe

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Dispersal from the

domestication centers

10,500

8,200

7,100

7,600

7,400

7,500

8,000

Danubian route

Mediterranean route

Farm animal history




Emergence of the breed concept Spread of cattle, sheep,

and goats in Europe

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Paulus Potter (1625-1654)

Anthonie van Borssum

(1630/31-1677)

Rosa Bonheur (1822-1899): 1849

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The breed concept

•! About 200 years ago

•! At the same time that the industrial

revolution

•! Standardization of phenotypes and

performances

•! Corresponds to the fragmentation of the

initial gene pool

Farm animal history




Emergence of the breed concept

Beginning of intensive selection

Spread of cattle, sheep,

and goats in Europe

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Artificial insemination

Strong reduction of the effective population size

•! About 10000 years ago: farmers started to control the reproduction of their farm animals in a traditional way

•! About 200 years ago (2% of the history): standardization of the color, morphology, and performance

•! Reproduction among different phenotypes was seriously reduced

•! About 50 years ago (0.5% of the history): the selection pressures strongly increased

Summary of the history

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–! Facts



genetic resources

The FAO/UNEP strategy in

the seventies •! The first joint project was launched in 1974 with the title

"Conservation of animal genetic resources (pilot study)". A survey of

the cattle breeds of Europe and the Mediterranean countries revealed

that of 149 indigenous breeds in this area only 33 are holding their

own and the others are declining in numbers. For the rest of the

world, and the non-bovine species in Europe, the report gives a brief

survey of breeds which appear to be in danger of eventual extinction.

•! The FAO/UNEP collaborative project on the Conservation of Animal Genetic Resources, which is now coming to an end, has clearly

shown the growing need for strengthening activities on the evaluation

of animal genetic resources at the national level and for monitoring

genetic changes. This need is further highlighted by the growing

evidence that critical shortages of suitable livestock resources have

appeared over the last decade in a number of regions.

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Current status Cattle Sheep Goats

Population size (billion) 1.4 1.1 0.7

Current number of breeds 1224 1313 570

Number of extinct breeds 254 181 17

% of extinct breeds 17 12 3

!"#$%&'()*'*+%),-."!%/01112%






!"#$%&'()*'*+%),-."!%/01112%

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!"#$%&'()*'*+%),-."!%/01112%






!"#$%&'()*'*+%),-."!%/01112%

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Threats on industrial breeds (1)

•! Artificial insemination strongly decreases the

genetic diversity

•! Germany: Ne = 52 for Holstein

•! France: Ne = 46 for Holstein

•! France: Ne = 27 for Tarentaise

•! Japan: Ne = 17 for Japanese Black


•! Emergence of new genetic diseases –!Bovine leukocyte

adhesion deficiency

–!Achondroplasia

–!Complex vertebral malformation (CVM)

•! Rapid decline in fertility –!USA, 1951: 65%

–!USA, 1996: 40%

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•! Introgression from highly productive breeds

•! New selection pressures (e.g. on coat colour)

Abondance

Montbéliarde

Threats on traditional breeds •! Already extinct: 17% of cattle breed and 12%

of sheep breed

•! Often low population size, with problem of

inbreeding

•! Competition with industrial breeds

•! Crossbreeding with industrial breeds

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In a few decades, we might lose

most of the highly valuable genetic

resources that humanity has

gradually selected over the past

10,000 years







–! Facts



genetic resources

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Towards a sustainable

management of genetic resources

•! Better characterization at the genetic level –! Problem of the ascertainment bias of microsatellites

and SNPs

–! Availability of whole genome sequences

–! Wild relatives / traditional breeds from the

domestication centre

•! Implementation of conservation strategies –! Genomic selection taking into account biodiversity

–! In the short term, very important to monitor the spread

of industrial breeds

–! The socio-economic aspect is crucial

Thank you for your attention


Conservation genetics of cattle, sheep, and goats - Globaldiv

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