NORTH-SOUTH CENTRE - ETH - North-South Centre North-South ...

Estimating effective population size for
the conservation of African cattle breeds
Demographic information is often lacking for livestock
breeds of the developing world. Therefore, effective population
size – a major criterion to assess the degree of breed
endangerment – cannot be calculated. However, basic
population information is crucial for priority-setting and
decision-making in livestock conservation, and consequently,
for a sustainable management of local breeds. In this
project, a molecular method for the efficient estimation
of effective population size is proposed. We are investigating
the use of genome-wide Single Nucleotide Polymorphisms
(SNPs) to estimate the effective population size of
two indigenous African cattle populations and one reference
population.
The new method was elaborated in a research partnership
between the Swiss College for Agriculture (SHL), Zollikofen,
Switzerland, the International Livestock Research Institute
(ILRI), Nairobi, Kenya, and the Institute of Animal Breeding
and Genetics of the University of Goettingen, Germany. The
partnership is expected to contribute profound knowledge
regarding animal breeding in developing countries, molecular
genetics and conservation of animal genetic resources.
In early 2009, further analysis of the full genotyping results
was conducted. The genotyping results were merged with
the bovine genome assembly 4. In total 53 903 SNPs (on the
29 autosomes) became useable for final analyses. The genotyping
results served for the estimation of local recombination
rates for each chromosome and each breed. As expected,
the estimation of recombination rates for each
breed was time-consuming. In total, the jobs were running
over four months. In April 2009, Miika Tapio spent two
weeks in our group at SHL. This visit allowed for interesting
discussions on the results, on additional analyses and the
planning of further steps.
In a first publication, the feasibility of the method was
proven for the reference population (a local Swiss breed).
With a second publication on the use of genome-wide
SNP-data for the conservation of two African cattle breeds,
this project will reach a successful end.
70 Research fellow
Christine Flury, SHL, Switzerland
Capacity development
Research fellowships
Supervisors
Stefan Rieder, SHL, Switzerland;
Olivier Hanotte, University of Nottingham, UK;
Henner Simianer,
University of Goettingen, Germany
Collaborator
Miika Tapio, ILRI, Kenya
Duration
February 2007 – March 2010
Effective population size (Ne)
Generations ago
Reference breed N’Dama Sheko
Effective population size for the three breeds using the estimated
genetic map distance for all 29 autosomes