60 Utilisation and conservation of farm animal genetic resources
John Woolliams and Miguel Toro
in lower σ
B 2
, i.e. a potential reduction in loss of genetic variation, particularly for itness in environments with low to medium inputs.
he diferences between breeds will have developed through a combination of four evolutionary forces: genetic drit, migration, selection and mutation Falconer and
Mackay, 1996. Genetic drit is a term for the random luctuations of allele frequencies
due to random sampling processes involved when genes are passed from parent to ofspring, and is one of the phenomena linked to inbreeding. Over time genetic drit
will lead to increasing genetic diferences between two breeds drawn from the same population and then maintained in isolation. he
migration of individuals moving from one breed to another, acts against inbreeding, since it lessens the genetic diferences
that exist between the breeds, and increases the variation within the recipient breed. If
selection occurs, carriers of favourable alleles have a selective advantage in the next generation, and the scale of diferences between two breeds will not necessarily relect
the degree of isolation. Selection may favour convergence or divergence depending on the selection taking place in each breed. In livestock, selection can be both artiicial and
natural; for example, natural selection will have played an important role in improving adaptive itness for particular breeds kept over many generations in environments with
speciic challenges e.g. periodic droughts. In general,
mutation in the genome increases the genetic diferentiation between breeds and creates genetic diversity. However,
mutation occurs with a low frequency chapter 8 and, in the absence of selection, the inluence of mutation becomes measurable only over a relatively large number of
generations. However at some point in the past, mutation has been responsible for creating the polymorphisms that lie at the heart of all genetic diversity.
3. The use of pedigree for measuring diversity
We can estimate the degree of diversity between breeds by simple, oten costly, experiments in which animals of diferent breeds are kept together in the same
environment. Providing 1 the numbers of animals per breed are suiciently large, so that the errors in estimating the breed mean are negligible compared to the scale
of diferences between breeds, and 2 the breeds are a fully representative sample of
half the total genetic variation. In the absence of information to the contrary it is reasonable to assume that this fraction will be applicable to a broad range of traits, including itness for
production in low- to medium-input environments with their associated stressors. If crises were to occur that required livestock production to adapt quickly to new challenges then it is the value
of g
2 2
that will be important, which will be σ
B 2
σ
B 2
+σ
W 2
. herefore conserving breeds with diversity of characteristics is a rational and important strategic response to the environmental
uncertainties of today.
Utilisation and conservation of farm animal genetic resources 61
Chapter 3. What is genetic diversity?
the breeds available, the variance σ
B 2
can be derived from the breed means. Which environment for testing and how diferent the answers would be in other environments
are important research questions that have global implications for agriculture, the environment and conservation. Given this uncertainty, it is important that testing
environments are directly relevant to the intended environment for implementation.
Quantifying the amount of genetic variation in a trait within a breed is more diicult and involves associating known genetic similarities between individuals with similarities
in phenotypes. he expectation is that more related individuals will resemble each other more closely than two individuals picked at random from the breed. Falconer and
Mackay 1996 show how the relationship between individuals can be related to the magnitude of the covariance in their performance, and how this allows the estimation
of the heritability, h
2
. A major source of the reliable information on the kinship is the pedigree, i.e. a record of sire and dam for each individual, accumulated over generations.
In practice, the most informative relationships are oten paternal half-sibs individuals sharing the same sire since the high reproductive rate of males in livestock species
makes them relatively abundant, and they have a covariance ¼σ
A 2
that is readily interpretable. In the absence of detailed information on DNA from individual animals,
which will continue to be the case for most populations for some time into the future, there is a need to identify these relationships through observing and recording the
pedigrees of animals, at least in suicient detail to identify sires.
4. The impact of DNA information
he last decade has seen the cost of genotype information reduced by orders of magnitude, making such information much more afordable for science and for
commercial applications. his is opening up new opportunities for evaluating diversity. A number of diferent marker types have been used in scientiic studies and their
popularity has changed with advances in technology. Box 3.3 provides a short review of important properties for markers and how well the diferent types match up to these
properties.
Informative DNA markers can therefore help the measurement of diversity as described in paragraph 3 in two ways. he irst way is to overcome the problem that in some
species it may be impossible or very costly to observe pedigree directly, e.g. in many ish species; and by genotyping a small number of markers say 5 to 10, chosen to be
informative, on all ofspring and all possible parents then it is possible to identify the sires and dams of almost all the ofspring. he second involves the extensive genotyping
across all chromosomes of genome in order to estimate the actual proportion of DNA shared by sibs or other relatives more precisely than simply using the expectation that
62 Utilisation and conservation of farm animal genetic resources
John Woolliams and Miguel Toro
Box 3.3. he attributes and advantages of types of DNA markers. Marker Attributes:
he following desirable attributes for a marker type can be identiied. Widely distributed. Wide distribution of markers throughout the genome allows the mapping
of the whole genome and tracking of gene low in populations, although maybe with only low resolution.
Locally dense. Ability to ind many markers within small genomic regions for the purpose of ine mapping.
Ability to localise. he marker can be placed at a physical location in the genome. Highly polymorphic. he utility of a marker depends on its ability to distinguish between
segments of homologous chromosomes. his will depend on the frequency of heterozygosity, which increases with the number of alleles at the marker locus and the more equal they
are in frequency. he amount of information contained by a marker is oten deined by its information content Lynch and Walsh, 1998.
Co-dominant. Ideally, both alleles at a marker locus can be distinguished. For some types of marker the individuals carrying 1 or 2 copies of an allele cannot be distinguished.
Low Mutation Rate. For many uses of marker information the long-term stability of the marker over generations is important for inferences about identity by descent IBD. he higher the
mutation rate, the less certain the inferences become. It is oten desirable for the marker locus to have a mutation activity that is representative of coding or regulatory sequences.
High hroughput. Determined by a number of elements, including the amenability to PCR, which allows more genotypes to be obtained from the same quantity of DNA, ability to
automate and multiplex assay procedures, and speed of assay. Low Technical Cost. Expressed per genotype.
Repeatable. Assays should be highly repeatable, both between assays within laboratories and between laboratories.
Types of Marker Mini-satellites MiniS. A sequence of DNA base pairs, typically of containing 10’s of base
pairs, repeated a variable number of times. DNA Fingerprints. Classically a multiple array of mini-satellites.
Restriction Fragment Length Polymorphism RFLP. An early bi-allelic marker type based on recognition sites for restriction enzymes.
Randomly Ampliied Polymorphic DNA RAPD. Markers formed from an arbitrary set of PCR primers, resulting in a random set of ampliied segments.
Micro-satellite MicroS. Based upon sites in which the same short sequence is repeated multiple times.
AFLP. AFLPs are a multiple array of RFLPs displayed in a single gel. Single Nucleotide Polymorphism SNP. Point mutation in the genome sequence, pre-
dominantly bi-allelic, but feasible to have 4 alleles, with each of the 4 nucleotide bases appearing in the same location.
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