102 Utilisation and conservation of farm animal genetic resources
Miguel Toro and Asko Mäki-Tanila
Rogers, A.R. and H. Harpending, 1992. Population growth makes waves in the distribution of pairwise genetic diferences. Molecular Biology and Evolution 9: 552–569.
Rosenberg, N.A. and M. Nordborg, 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics. 3: 380-390.
Rosenberg, N.A., T. Burke, K. Elo, M.W. Feldman, P. Friedlin, M.A.M. Groenen, J. Hillel, A. Mäki-Tanila, M. Tixier-Boichard, A. Vignal, K. Wimmers and S. Weigend, 2001. Empirical evaluation of genetic clustering
methods using multilocus genotypes from 20 chicken breeds. Genetics 159: 699-713. Rothschild, M., C. Jacobson, D. Vaske, C. Tuggle, L. Wang, T. Short, G. Eckardt, S. Sasaki, A. Vincent, D.
McLaren, O. Southwood, H. van der Steen, A. Mileham and G. Plastow, 1996. he estrogen receptor locus is associated with a major gene inluencing litter size in pigs. Genetics 93: 201-205.
Tajima, F. 1989. he efect of change in population size on DNA polymorphism. Genetics 123: 597-601. Tapio, M., N. Marzanov, M. Ozerov, M. Ćinkulov, G. Gonzarenko, T. Kiselyova, M. Murawski, H. Viinalass
and J. Kantanen., 2006. Sheep mitochondrial DNA variation in European, Caucasian and Central Asian areas. Molecular Biology and Evolution 23: 1776–1783.
Toro, M.A. and A. Caballero, 2005. Characterisation and conservation of genetic diversity in subdivided populations. Philosophical Transactions of the Royal Society of London B 360: 1367-1378.
Trut, L.M., 1999. Early canid domestication: the farm-fox experiment. American Scientist 87: 160-168.
Wall, J. D. and J.K. Pritchard., 2003 Haplotype blocks and linkage disequilibrium in the human genome. Nature Reviews Genetics. 4: 587-597.
Wiener, P., D. Burton, P. Ajmone-Marsan, S. Dunner, G. Mommens, I.J. Nijman, C. Rodellar, A. Valentini and J.L.Williams, 2003. Signatures of selection? Patterns of microsatellite diversity on a chromosome containing
a selected locus. Heredity 90: 350-358. Yancovich, A., I. Levin, A. Cahaner and J. Hillel, 1996. Introgression of the avian naked neck gene assisted by
DNA ingerprint. Animal Genetics 27: 149-155. Zeder, M.A., D.G. Bradley, E. Emshwiller and B.D. Smith., 2006. Documenting Domestication
: New Genetic and Archaeological Paradigms. University of California Press.
Zhang, K., J.M. Akey, N. Wang, M. Xiong, R. Chakraborty and L. Jin., 2003. Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drit. Human Genetics 113:
51–59.
Utilisation and conservation of farm animal genetic resources 103
Chapter 5. Measuring genetic diversity in farm animals
Herwin Eding
1
and Jörn Bennewitz
2 1
Federal Agricultural Research Centre, Institute for Animal Breeding, Höltystraße 10, 31535 Neustadt, Germany
2
Institute of Animal Breeding and Husbandry, Christian-Albrechts-University of Kiel, 24098 Kiel, Germany
Questions that will be answered in this chapter: Why measure genetic diversity?
What measures of genetic diversity are there and when are they appropriate? How are these measures related and interpreted?
What is Weitzman diversity, what is Core set diversity and which should one use?
Summary
In chapter 3 the general meaning of genetic diversity was explained, as well as the basic principles underlying the origin and inluence of genetic diversity within and
between breeds. In this chapter we will present a number of widely used methods to measure genetic diversity in farm animal species. hese range from genetic distances
and F-statistics to kinships as methods to estimate genetic diversity between and within populations. In the second part we will discuss two frameworks to summarise these
diversity measures: the Weitzman and the Core set method.
1. Introduction
In the last decades much research has been focused on the determination of genetic diversity and the uniqueness of breeds in order to decide on genetic conservation
priorities. Many of the measures are based on population genetic theory and are using molecular data. Such measures reveal genetic diversity with neutral genetic markers
chapter 3 and support conservation decisions aiming to maintain the genetic lexibility and potential for changes chapter 2. While genetic diversity can be deined
in a number of ways in terms of conservation of species or farm animal breeds or single alleles for this chapter the general objective is maintenance of the genetic variance in
the species.
• •
• •
104 Utilisation and conservation of farm animal genetic resources
Herwin Eding and Jörn Bennewitz
1.1. Why measure genetic diversity?
Within livestock species, the genetic diversity is most obvious as the spectrum and number of breeds. Breeds are deined as populations within a species of which the
members can be determined by a set of characteristics particular to the breed FAO, 1998, although there exist many alternative deinitions chapter 3. he FAO deinition
assumes that in phenotypes of characteristics or traits, there is a clear boundary between populations. his may be clear in Europe where separation of breeds from others was an
intentional process accompanied by the establishment of herd books, some 200 years ago Ruane, 1999. In other regions, e.g. in Africa, such a clear deinition of breeds is
not always possible, due to widespread crossing between populations. Assigning animals to breeds in these regions is subjective and oten questionable Scherf, 2000.
We want to have a more general picture of the variation and concentrate on variation in traits or genotypes in populations, whether they are breeds or sub-populations
within a livestock species. he genetic variance in a trait can be partitioned using the coeicient of kinship in between and within population components chapter 3. With
molecular genetic techniques, such as genotyping with microsatellite markers, genetic diversity between breeds is mostly studied using genetic distances or genetic similarities
and derived quantities molecular coancestries, marker estimated kinships. Genetic distances express the diferences between populations either in terms of numbers
of mutations or in terms of diferences in allele frequencies or genetic drit. Breed formation occurred recently on the evolutionary scale. For this reason, genetic diversity
between populations is usually quantiied using measures based on genetic drit only and ignoring the efect of mutation. Within a breed the diversity is usually directly
related to the rate of inbreeding within the breed, and expressed as heterozygosity, efective population size, efective number of alleles per locus or Wright’s F-statistics,
usually also calculated from marker allele frequencies.
Conservation eforts should be as eicient as possible, securing a maximum amount of genetic diversity with the available resources. To this end, breeds at risk need to be
evaluated for the amount of genetic diversity. he evaluation is very much dependent on the rationale for conservation Ruane, 1999 and may require balancing diversity
within and between populations.
here are two frameworks to quantify genetic diversity in a group of populations: the Weitzman diversity and the Core set diversity section 5.3. he two frameworks
rely on genetic distances or genetic similarities calculated from neutral marker allele frequencies. here are also other methods, such as cluster analysis briely discussed in
chapter 4, multivariate analysis and principle component analysis.
