The use of pedigree for measuring diversity

Utilisation and conservation of farm animal genetic resources 65 Chapter 3. What is genetic diversity? genetic variation is additive i.e. σ A 2 = σ G 2 . Note that in this approach the breed mean is the estimate of the allele frequency for the breed. As an example, if two breeds are ixed for diferent alleles then no diversity will be observed within breeds and all the diversity will lay between breeds. his is expanded upon below in paragraph 6 and in chapter 4. 2. he breed means for the frequencies of several alleles, usually from unlinked loci, are combined by some pre-deined function to measure what is called a genetic distance between the breeds. here are several such distance measures chapter 5 and they oten difer in principle from 1 because no explicit consideration is made of variance within breeds. his will be expanded upon in chapter 5. 3. Instead of using gene frequency, the frequency of heterozygotes may be measured. A heterozygote has two diferent alleles at a locus, and is function of the allele frequencies and non-randomness of mating and survival rates. he justiication for this is that in the absence of diversity there will be no heterozygotes in the population. Providing mating is at random, the heterozygosity increases with the number of alleles found in the population and with decreasing variation among the allele frequencies for the population. he assumption of random mating is important and is oten assumed to hold within a breed but deviations can be signiicant, particularly if there is relatively little exchange among breeders. If genotype data is available, the assumption of random mating can be tested by looking at the magnitude and signiicance of departures from Hardy-Weinberg equilibrium Falconer and Mackay, 1996; Lynch and Walsh, 1998. Nevertheless in the absence of random mating, both the observed and expected heterozygosity can be informative for studying diversity. Whatever result is calculated for the heterozygosity it will depend on the sample of loci used, and extension to inferences about the entire genome are diicult. For example, Toro et al. 2006 describes a remark attributed to Nei, that a irst approximation to the correlation between the heterozygosity of a sample of r loci and a genome of n loci is rn 12 i.e. for a sample of 20 loci from 20,000 the correlation might be expected to be 0.03. herefore reliable comparisons between breeds must be made on very dense sets of markers, which may be possible in some species, such as cattle where DNA chips can contain in excess of 50,000 markers. 4. A further simple but limited measure of diversity is counting the number of diferent alleles appearing in the population for a set of loci, with the more alleles the more diverse. Counting the number of alleles in each breed and the number shared with each other breed ofers an opportunity of examining diferences between breeds. A variation on this is to count the number of ‘private alleles’, where a ‘private allele’ 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;