66 Utilisation and conservation of farm animal genetic resources
John Woolliams and Miguel Toro
is deined as an allele found in one breed but in no other. However the heuristic diversity between breeds will be determined not only by whether or not alleles are
shared between breeds but also by whether those shared are at similar frequencies within each breed. herefore the counting approach to measuring diversity appears
less valuable than measuring the allele frequencies themselves. Nevertheless observations on private alleles can be very useful in other ways, for example in
traceability schemes.
he items 1 to 4 above give some simple ideas about how molecular diversity might be measured. It is a reasonable question to ask what the relationship between molecular
and quantitative measures of variation might be, and whether these tell the same or diferent stories. he answer appears to suggest that the stories are not the same: in a
meta-analysis Reed and Frankham 2001 suggest that the mean correlation between molecular and quantitative estimates of diversity is weak 0.22 ± 0.05, indicating that
molecular measures of diversity only explain 4 of the variation in quantitative traits. his estimate will include studies that pre-date much of the explosion of molecular data,
with the design shortcomings that follow from this limitation. herefore the question remains open and it is very possible that as dense genome information becomes more
available over the next decade, and we gain experience in interpreting it, then our predictions may should improve.
5. Genome-wide patterns of diversity
In paragraph 4 the ways in which information on DNA sequences expanded our views of diversity were explored. However whilst the approaches described above could be
applied to any set of markers, the interpretation of the outcome will depend on the positioning of the DNA markers used. he ‘functional’ DNA in the genome comprises
less than 5 of the total DNA e.g. Federova and Federov, 2005. his includes coding regions for amino acids to be used in proteins, and promoter regions, which control the
transcription of the coding DNA. he remaining anonymous DNA includes regions that science has yet to ind a purpose for, and may include DNA that is truly without
function. For some loci in functional regions an allele may confer a selective advantage on carrier individuals so that the allele will most likely increase in frequency over time
and become ixed in the population. It is typically assumed in publications that markers using anonymous DNA are neutral i.e. are not associated with alleles that confer
signiicant selective advantage. he issue over the neutrality of the markers is important since it is assumed that these markers change in frequency only by genetic drit, rather
than by drit
and selection. he neutrality of a locus may difer between breeds since: 1 one breed may have important alleles segregating that are not segregating in another;
Utilisation and conservation of farm animal genetic resources 67
Chapter 3. What is genetic diversity?
and 2 diferent livestock breeds will be subject to diferent selection criteria, with these largely dominated by the selection objectives of the breeders concerned.
he genome is organised into chromosomes and this introduces the phenomenon of linkage Box 3.5. One consequence of linkage is that alleles that are on the same
chromosome and close to a new favourable mutation will be tend to increase in frequency alongside the mutation in a process termed ‘hitch-hiking’ Maynard-Smith
and Haigh, 1974. It is very likely that the alleles very closely linked to the mutation will also become ixed in the population. herefore this region of the chromosome, very
close to the locus under selection, will display very low diversity in the neighbouring loci within a breed. An examination of allelic diversity throughout the genome may
Box 3.5. Chromosomes and linkage. During fertilisation an individual receives two copies of DNA at each locus, ignoring sex-linked
loci, with one copy passed in the gamete received from each parent. he loci are passed in discrete blocks of DNA called chromosomes, and the chromosome passed from the sire and the
corresponding chromosome passed from the dam are termed a homologous chromosome pair. he number of human chromosome pairs, including the sex-linked pair, is 23, and the corresponding
number in cattle is 30. he chromosomes passed by the parent will be a random choice among the pair of homologous chromosomes it carries, either its own paternally-inherited or maternally-
inherited chromosome. he choice is made during the process of gamete formation, called meiosis. he process of meiosis involves crossovers, in which segments of the two homologous
chromosomes carried by the parent are exchanged. As a result, new gene sequences may arise. However there are relatively few crossover events relative to the total number of genes and so
paternally or maternally inherited alleles at neighbouring loci on a chromosome are more likely to be passed to ofspring together on the same gamete. However the further away the loci are on
the same chromosome, the closer the probability of these alleles being passed together resembles ½ i.e. the probability appropriate for loci on diferent heterologous chromosomes, since there is
an increasing chance that an odd number of crossovers has occurred between them. his tendency for paternally or maternally inherited alleles on the same chromosome to be passed together is
called ‘linkage’, and two loci on the same homologous chromosomes are said to be linked. Linkage is measured in Morgans M, or centi-Morgans cM, and a chromosome’s length is deined by the
linkage of two loci at either end of the chromosome. A total chromosome length x M is expected to have x crossovers during meiosis, although the number that actually occurs is a random variable
see Lynch and Walsh, 1998 for further information on linkage and measuring linkage. A typical mammalian chromosome has a length of 1 M. Two loci a distance of 0 M apart indicates that
the same parent’s alleles are invariably passed together, and an ininite distance apart indicates a probability of ½ of being passed together.
68 Utilisation and conservation of farm animal genetic resources
John Woolliams and Miguel Toro
therefore show patterns of regions of high diversity punctuated by regions of relatively low diversity. his pattern of diversity
within the genome is called a selection footprint and may indicate loci important for domestication, or for the characteristics of particular
breeds e.g. Wiener et al., 2003, or simply highly-conserved regions for the genus as a
whole, whether wild or domesticated. hese regions will be further discussed in more detail in chapter 4. Efective searching for selection footprints is only just beginning in
livestock species with the availability of dense, afordable, genome-wide markers such as SNPs.
More generally, the expansion in DNA information will allow the diversity of allelic combinations at loci distributed throughout the genome to be studied. his type of
diversity within breeds will depend not only on the allele frequencies but also on the extent of linkage disequilibrium LD that is observed. his LD may arise from the
breed history of census size and management over time, including bottlenecks or introgression. However this form of diversity, both between and within breeds, may
indicate the presence of epistatic interactions afecting performance. In summary, the study of genetic diversity will extend to diferences in genomic patterns between and
within breeds.
6. Measuring changes in diversity
So far we have simply considered measuring the amount of diversity present in a population. his will relect events in the history of the population or the breed,
oten long ago, and the information on the diversity may illuminate the breed origins. However, sustainable management of genetic resources is concerned with managing
the diversity that is present today. It is important to realise that some genetic variation is inevitably lost in each generation due to the inherent randomness in the passing of
alleles from parent to ofspring. It is impossible to ensure that every distinct variation at each of ~ 3x10
9
base pairs of a genome can be replicated in the individuals selected as replacements for the current generation. Nevertheless in each generation there is
potentially new variation entering the population as a result of mutation, immigration if the population is not closed or the inluence of epistatic interactions uncovering
new variations Carlborg et al., 2006 in selected populations. herefore the sustainable
management is more concerned with maintaining the expected rate of loss of existing variation to a sustainable level, justiied in more detail by Woolliams
et al. 2002. herefore what is required is a means of measuring or predicting the rate of loss.
he important concept in measuring the rate of loss is the idea of inbreeding. To measure inbreeding we identify a reference point in the history of a population, called
the base generation, when we assume that all the alleles at an assumed neutral locus
