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2.1 Breeding objectives
2.2 Breeding structure
2.3 Inter-population gene flow
2.4 Population size
2.5 Monitoring genetic diversity

A central requirement for any action plan to respond to the current erosion of domestic animal biodiversity is the identification of key indicators through which this process can be monitored. These indicators should also be designed to facilitate evaluation of the effects of any corrective actions.

The process driving change in the genetic constitution of livestock populations is the economic and demographic change in society, and the resulting complex of change in farming systems. This process is already closely documented and monitored.

The five key points at which its impact on genetic diversity can be monitored are indicated by the letter M in figure 1. These are discussed in turn. In each case, the normal sense in which the term ‘population’ is used is to indicate a breed or landrace of animals of a particular species. In developed countries, breed definition is very clear, and usually includes a nucleus of registered animals and a wider body of non-registered animals which share a common pattern of use in agriculture, a degree of uniformity of phenotype, and a common gene pool. The breeders involved are usually organised in a voluntary society which supervises standards and provides services such as registration. Comparable populations in developing countries are often less well defined, and simply comprise the common type of animal traditionally used in a particular region. There is normally no formal organisation of breeders. For such populations, the term ‘landrace’ is often used, though they may equally be considered breeds.

2.1 Breeding objectives

For most populations of domestic animals, no formal breeding objectives exist. Generally, all females in the population are retained for breeding, so there is no effective selection on the female side. The proportion of males retained for breeding varies with the species and the population, but is generally less than one in 10. There is therefore the potential for considerable genetic change through selection on the male side. In practice however, this effect is often slight. Many traits of importance, for example female fertility and egg or milk production, can only be evaluated indirectly through the performance of female relatives. In the absence of extensive record-keeping, male selection is likely to be ineffective.

Figure 1 - Linkages between animal genetic diversity and environmental effects

Figure sent by fax 15/11 - will be sent by email as soon as available.

In populations where meat production is important (sheep, beef cattle, pigs, chickens) males will usually be selected for body size and external appearance. However, the effectiveness of selection is usually reduced by concern for balancing factors, such as ability to withstand difficult conditions, aesthetic considerations which have nothing to do with productivity, and the fact that growth and body shape can be subject to much non-genetic variation, and are assessed subjectively. The net effect is that in many such populations, genetic change is very slow, and is generally dominated by natural selection for health and fitness traits.

In such populations, monitoring change in breeding objectives is difficult, since they are in general non-documented. In most such cases, an initial benchmark study should be undertaken. This should include:

· an objective statement of the economic purposes for which the animals are kept

· a quantification of the main production parameters, including mature body weight of males and females, height at withers, average reproductive rate, generation length in males and females, and general descriptors such as coat colour, fleece type, presence of horns etc.

· average performance for special production traits, such as milk yield or egg production, in defined production conditions.

Such documentation should be repeated at regular (five-yearly) intervals. Each country that has ratified the Convention on Biological Diversity is required to implement a national Action Plan for the management of the country’s animal genetic resources. These population documentation exercises should be an essential part of such national plans. With the passage of time, many of these populations will gradually acquire a better quantified infrastructure, and the quality of data should improve. Particular attention should be paid to the documentation of special and potentially valuable characteristics, e.g. altitude, heat or cold adaptation; resistance to particular diseases or to internal, external or blood parasites.

For populations with formal breeding goals, monitoring changes in these objectives is easier. In many such cases, formal, quantified, selection indexes are used, in which individual traits are balanced for their economic value, degree of heritability and inter-relationships. The structure of these formal breeding programmes now generally facilitates the objective measurement of genetic change in the population, and this will increasingly be part of the routine annual documentation of the breeding programme.

2.2 Breeding structure

Changes induced in the breeding structure of populations should also be monitored. In breeds or landraces with little formal documentation, this could form part of the five-yearly survey undertaken to monitor changes in breeding objectives. Factors to be documented would vary with the species, but would include:

· replacement rates for males and females
· ratio of breeding males to females
· age structure of the population
· extent of natural vs artificial insemination
· pattern of acquisition of breeding material, i.e. from hatcheries or breeding companies.
For well documented populations, annual statistical reports normally include most of these factors.

Artificial insemination is used in breeding most dairy cattle in developed countries and a small but increasing proportion of buffalo and dairy cows in developing countries. One consequence is to greatly reduce the number of males required. While this can increase selection efficiency, it can also rapidly narrow the genetic sources in a population. This is exemplified in a recent study of North American Holstein population7.

2.3 Inter-population gene flow

Probably the most important factor affecting the genetic constitution of populations has been the movement of genetic material between populations. This can most often take the form of cross-breeding, with the introduction of males from outside. For each population, it is important to monitor in particular the inward gene-flow. As for other elements of genetic change, the requirements for monitoring are different for well-documented breeds and for undocumented landraces. In the latter case, regular (five-yearly) analyses should be done of the pattern of genetic movement into the population. This should include an estimation of:

· extent of crossbreeding (generally proportion of females mated to males from outside the population)

· the source of external genetic material

· nature of the crossbreeding. In some cases, this may be terminal crossing to produce slaughter animals, with no permanent genetic effect on the population. In other cases it may be a pattern of continuous crossing, in which the population’s genetic resources are gradually replaced. It can also take the form of partial or complete replacement of existing breeding structures by a planned provision of hybrids.

· the extent to which breeding animals are produced at home or provided by outside breeding companies or organisations.

· the use of DNA techniques to track the nature and extent of gene infusion (see below).

In documented breeds, annual statistics covering the same range of factors can be, and generally are, produced. Because gene movement between populations is well documented in these cases, the use of DNA techniques may be less informative, and therefore less necessary.

2.4 Population size

Because population size is a key element in ensuring the genetic survival of a population, it should be carefully documented. This becomes progressively more necessary for smaller populations. At a minimum, approximate numbers of breeding males and females need to be recorded. From this, the effective population size can be calculated. This should be done on a regular basis, and in small populations, annually. In order to evaluate the risk to a breed or population, a number of other factors also need to be taken into account:

· whether the population is increasing or decreasing
· whether the number of herds is decreasing
· the extent of cross-breeding
Thresholds recommended4 for these factors include the following:
· effective population size drops below 50

· population size (number of females) decreases by more than 10% per year

· number of breeding herds decreases below 10

· proportion of matings to animals from outside the population exceeds 10%

2.5 Monitoring genetic diversity

The primary purpose of the preceding activities is to monitor factors which have an impact on genetic diversity in the population. It is also possible to measure changes in genetic diversity directly. This can be done at a number of levels.

Genetic parameters: The amount of genetic variation for a trait in a population is normally measured as its heritability. This is the ratio of the additive genetic variance to the total phenotypic variance. The primary concern would be for a narrowing of the genetic variance, though experimental and field data have shown that this is surprisingly well maintained even in populations under intense selection. In well documented populations, these statistics are routinely calculated, while in many landraces or local breeds, there are seldom suitable data available.

Where these statistics can be calculated with reasonable accuracy and precision, and at reasonable cost, they should be. In other cases, at least the phenotypic variance should be calculated. On a case by case basis, genetic variances also should be calculated, though it is generally not justified to set up special experiments or data collection schemes solely for this purpose.

Measurement of genetic trend: Genetic response to selection in a population is a function of the selection goals pursued, and of the heritability of these goals, the genetic variance for the traits concerned and the selection intensity applied. In many modern populations, these factors are all quantified as part of the process of calculating breeding values for individuals. The routine tracking of genetic trend in the population is therefore now feasible. In those cases it should be part of the annual reporting for the population.

In undocumented populations, measurement of genetic change in this way will not generally be feasible. However, benchmarking of the population against other populations (see below) may be useful.

Monitoring inbreeding: As populations become smaller, average inbreeding increases. This can be accentuated by deliberate patterns of mating related individuals, or by isolation of the population into subgroups. Because increased inbreeding is associated with a decline in a range of fitness factors, it can be an important determinant of a population’s prospects for survival. It is therefore a key indicator. In most circumstances, calculation of effective population size will permit a good estimate of the rate of inbreeding. However, this should be supplemented by periodic analyses of pedigree data to measure directly the accumulation of inbreeding in the population. This will take account of mating patterns, genetic grouping within the population, and non-random variability in family size.

Measuring genetic diversity at the DNA level: DNA techniques developed within the past 5 years now make feasible the routine monitoring of genetic variability within a population at the molecular level. In particular:

· the Polymerase Chain Reaction (PCR) permits the extraction and rapid multiplication of selected segments of DNA from very small samples of tissue, including blood, hair and milk

· the discovery of microsatellites, highly variable repeat segments of non-functional DNA, has uncovered a huge reservoir of genetic variability which is useful in tracking genetic change within and between populations

· rapid, cheap sequence analysis makes possible the evaluation of genetic differences between individuals in the structure of functional genes, at reasonable cost.

The methodology surrounding these methods is evolving rapidly. The techniques have a wide variety of uses in monitoring genetic change. The genetic consequence of inbreeding is an increase in homozygosity within individuals. Using these techniques, this can now be measured directly. The degree and nature of variability within a population can tell a great deal about its past evolutionary history, and about its relationship to other populations. This can be extremely important information in planning conservation programmes.

Monitoring inter-population differences: Perceived genetic differences between populations give rise to a great deal of gene-flow between populations, and can have a big impact on genetic diversity. It is therefore important that genetic differences between populations should be carefully documented. This is seldom the case, and comparisons often include many environmental factors in addition to genetic ones.

Inter-population genetic comparisons can be made at two levels. The first is carefully controlled experimentation in which breeds, and sometimes their crosses, are compared for a range of production traits. The second is the use of DNA techniques to document the extent of their common or divergent genetic heritage.

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