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3 Measurement and Use of Genetic Variation A large part of observed variation in livestock species is ge- netic-that is, it arises from differences in the genes carried by various individuals. Genetic variation can be quantified at several levels: among species, among major types within a species, among breeds within a major type, between breeders' lines within a breed, and among individuals. Thus, for example, differences be- tween sheep and goats (species), between hair sheep and wool sheep (types), between Dorset and Merino sheep (breeds), between com- merc~al stocks or strains of Merino sheep (breeders' lines), and be- tween individuals of the Merino breed can all be attributed to varia- tion at the level of the gene. The term genetic diversity is used to express the degree of this variation. In animal agriculture, manipulation of genetic variation by con- trolling reproduction (through selection and crossbreeding) has been the foundation for improving livestock populations. The responsive- ness of a population to artificial selection and to changes in environ- ment or selection goals ultimately depends on a reservoir of genetic .' . ,, variation. ~ ~ 1 THE INFLUENCE OF HUMAN SOCIETY Domestic animal species in almost all cases do not exist as single, uniform breeds. Instead, their association with humans has encour- aged the development of a highly complex overall population struc- ture and the existence of many different crossbreeds. In many cases 63

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64 / Livestock crossbreeds have developed fortuitously as a by-product of the mi- gration of human populations; in others, they have developed as a result of human preferences for certain types of animals. The migration of human populations across the globe resulted in a parallel migration of their domestic animals, and it encouraged the introduction of domestic species into regions they would not likely have colonized successfully without human assistance. Once a spe- cies was introduced, the process of selective adaptation to the new environment began, and in many cases it was furthered by isolation of the newly established population from its parent population. Over time, the joint effects of selection and isolation led to populations that gradually became genetically distinct from other populations maintained in different environments. For each domestic species the geographic centers of initial domestication can be identified, and the distribution of breeding populations about those centers, with atten- dant adaptation to different environments, can be traced. Human needs and preferences also encouraged more varied popu- lations of domestic species. The development of wool sheep, of dairy cattle and goats, and of chickens and ducks with enhanced egg-lay- ing capacity provides examples of domestic populations bred to meet specific needs. When such developments are coupled with prefer- ences for different color patterns or morphological types, the result is another rich source of differentiation among livestock populations. Subdivision into Breeds The subdivision of domestic species in response to different hu- man preferences reached its zenith in the 1800s with the formation of breed societies in western Europe and in the regions colonized by western Europeans. The concept of breed identity rested on the idea that uniformity of type was an important goal in livestock produc- tion and could only be achieved by controlled matings involving ani- mals of known parentage. Thus, initial entry into breed society records was restricted on the basis of color or morphological type. Contin- ued recognition of breed membership required documentation of an- cestry. The power of breed isolation can best be seen in the tremen- dous genetic diversity in horses and dogs; breed isolation also brought forth the rich array of livestock in western Europe. Breed designation is primarily a western European and North Ameri- can concept, but it is often applied to any reasonably identifiable live- stock population. In reality, breed designations cannot be accurately used in much of the developing world, where pedigreed adherence to breed identity is not maintained, and controlled mating is not usu

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Measurement and Use of Genetic Variation / 65 A chicken flock of mixed origin are fed outside a henhouse in Burkina Faso. Credit: Food and Agriculture Organization of the United Nations. ally followed. In these countries, distinct, identifiable populations are likely the result of geographic isolation or phenotypic selection. Even in developed countries the designation of breed identity does not carry with it the unambiguous distinction of genetic unique- ness that is often assumed. Breeds have historically been combined with, or absorbed by, other breeds to obtain rearrangements of the gene pool. Specific genes are not lost in this process; they are just transferred into new populations. In the U.S. beef cattle herd, for example, many animals express apparent phenotypic breed identity (usually as a result of color), but only about 5 percent of the total are registered and possess pedigree-documented breed membership (Hawkins, 1988~. Thus, the genes and gene combinations carried by most breeds almost certainly also exist in the overall cattle popula- tion. An advantage of breed identity is the concentration of specific genes at high frequency and the ability to locate them reliably within those populations. In contrast, selection and screening would be required to extract the same genes from a highly heterogeneous cattle population.

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66 / Livestock The crossing of breeds to obtain more heterogeneous populations does not, in itself, lead to reduced genetic diversity. The genes from the combined populations should still exist within the overall popu- lation, although they could subsequently be lost through selection, continued crossing back to one of the parent breeds, or random chance if resulting populations are small. The introduction of imported stocks into a nation is often viewed as a source of genetic diversity that can subsequently be used in population improvement. WHAT IS A LIVESTOCK BREED? The term breed as a formal designation often has little meaning out- side areas of Western influence, where pedigree recording is often non- existent. For the purposes of this report, the term breed means any recognizable interbreeding population within a livestock species. A degree of mixing may occur among different breeds where mating is not strictly controlled. However, recognizable, regional stocks or pop- ulations exist worldwide that are analogous to Western breeds. The concept of a livestock breed, in which all members of the popu- lation have a pedigree tracing their ancestry to animals of the same breed, was developed primarily in Western Europe during the eigh- teenth century. In its strictest sense, a breed designates a closed popu- lation-mating pairs are drawn only from within the population and relationships among individuals are documented by recorded pedigrees for all animals. Its members share certain recognizable phenotypic characteristics, such as color, horn shape, and body type, that are a feature of their breed. Members of a breed share a common ancestry and selection history. For example, the Holstein breed of dairy cattle, developed from the Dutch Black Pied breed, have been selected to produce large quantities of relatively low-fat milk, while the jersey breed of dairy cattle, from the Channel Islands, has been selected to produce smaller quantities of richer, high-fat milk. In general, the term breeding population refers to an interbreeding group with some identifiable common appearance, performance, ancestry, se- lection history, or other feature. Without good measures of genetic distance between groups, ad hoc judgments must be made about which individuals constitute a breeding population. With a good sampling procedure and by keeping individual samples separate, however, re- classification can be done retrospectively if better information accrues. Most livestock populations are outbreeding, so individuals chosen at random should be representative of the population and of its genetic variation. What may be uncertain is the extent of gene flow between different subpopulations, such as geographic groups or breed subtypes.

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Measurement and Use of Genetic Variation / 67 With breed preservation, however, the packaging as well as the overall maintenance of genetic diversity are important. Genes and gene combinations are usually more readily accessible in relatively fixed populations than in large, heterogeneous populations. In milk production in cattle, for example, the Holstein breed is widely recog- nized as superior in terms of total volume of milk produced per lactation. Although the genes controlling lactation clearly exist in other breeds and, over time, could be identified and their frequency increased to yield a genetic capacity for high milk production, a simi- lar result could be obtained much more rapidly by crossing other breeds with the Holstein to achieve a rapid adjustment in the fre- quency of alleles conducive to high levels of milk production. A strong argument for breed preservation, then, is the need not just to maintain genetic diversity but also to maintain its accessibility in predictable source populations. FACTORS AFFECTING GENETIC VARIATION Allelic frequencies are altered by four forces: selection, migration or gene flow, mutation, and random genetic drift. Of the four, muta- tion is the only force that produces new genetic variation (in the form of new alleles). The other forces may alter the genetic composition or structure of a population. Selection Selection can be either natural or artificial (imposed by humans); both are strong forces that alter the genetic composition of many livestock populations. Natural selection is a continuous process re- flecting environmental pressures, and occurs when a certain geno- type confers a reproductive advantage on an individual relative to other genotypes in that population. Artificial selection is superim- posed on natural selection by animal breeders in an effort to change various traits in preferred stocks. The rate of response to selection of either kind depends on the variation in the population. More vari- able populations are expected to produce more extreme types that can be selected or identified and propagated to produce more rapid genetic changes. In livestock improvement, selection has operated historically at the level of the phenotype. In recent decades, however, methods such as progeny testing have been developed to estimate the genetic merit of an individual based on the performance of its offspring. Now, molecular methods for discerning the genotype are opening up

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68 / Livestock new possibilities for artificial selection based on the actual genes car- ried by an individual. Natural selection applies selection pressure on a population for certain characteristics, and it may or may not be antagonistic to artifi- cial selection. Likewise, environments vary widely, and a genotype that is at a selective advantage in one environment may lose that advantage or actually be at a disadvantage under different condi- tions. For example, the small goats living in the tsetse fly zones of East and West Africa are much more resistant to trypanosomiasis than imported European breeds. This phenomenon eventually leads to the development of genetically distinct populations adapted to specific environments. Genotype-by-environment interactions main- tain allelic diversity if subpopulations of a species are raised under a wide range of production systems. Breeding goals have changed over the years, and artificial selec- tion practiced by animal breeders has varied accordingly. Currently, a range of selection goals can be identified for almost all livestock species; the most pronounced differences are found for ruminants raised for their meat. In chickens separate breeds and crossbreeds have been selected for eggs (layers) and meat (broilers). Even within the highly selected lines derived from these commercial breeds, goals have not remained constant over time. In broilers, for example, the emphasis has moved away from birds with faster growth rates to those with more desirable body composition or those that use feed more efficiently. Migration Migration or gene flow occurs as a result of the movement of individuals between populations. In livestock production, crossbreeding (mating among two or more different breeds) and backcrossing (mat- ing the crossbred progeny back to one of the parental breeds) are used to move favorable alleles from one population into a second population and can result in extremely rapid changes in gene fre- quencies. Crossbreeding, however, can break up favorable combina- tions of alleles that can only be reconstituted through further breed- ing and selection. Mutation Mutation refers to a structural change in a gene, and it is thought to be a random occurrence. The probability of improving a gene function as the result of a mutation is extremely small. The genetic

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Measurement and Use of Genetic Variation / 69 variation that has accumulated over many thousands of generations, however, reflects not only the environmental conditions to which that population was exposed but also the mutations that have been re- tained in the gene pool. An important consideration in conserving genetic diversity re- lates to the extent to which mutation is a factor in maintaining and creating genetic variation over time. Selection responses in livestock populations may continue in part because of genetic variation con- tributed by mutation (Enfield, 1988; Hill, 1982; Hill and Keightley, 1988~. Testing the value of new or newly recognized mutations, how- ever, can be time consuming. In contrast, previously existing muta- tions in the population presumably have already been studied and may be of greater value as a genetic resource. Genetic Drift Genetic drift refers to the random changes in allele frequency. When population sizes are small, random genetic drift can lead to loss of alleles owing simply to chance, particularly if they are present at low frequencies. A practical consequence is that the number of breeding individuals maintained in a preserved population must be sufficiently large to avoid the potential for decreased genetic varia- tion resulting from genetic drift. Guidelines for the number of ani- mals required in breeding populations to minimize this risk have been discussed (Smith, 1984b). GERMPLASM USE Management programs for genetic resources are influenced by the ways in which genetic diversity is used. In general, germplasm use follows one of two patterns. The first pattern pertains to pro- grams for industrialized stocks of poultry, pigs, and dairy cattle, which occur primarily in developed countries but which are also being ag- gressively marketed for use in developing nations. The second is more appropriate for grazing ruminants worldwide and is generally applicable to any stock maintained under extensive conditions. Industrial Stocks The development of industrialized stocks of poultry, pigs, and dairy cattle has been predicated on the ability to achieve uniform, high-quality conditions in a production environment. When achieved, this environmental stability means that minimal selection effort is

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70 / Livestock Genetically improved Bos taurus cattle, such as these Hereford in Kenya, are particularly desired by farmers because they are more productive than indig- enous breeds. However, highly productive grade cattle are also susceptible to tick-borne diseases, such as theileriosis, a debilitating and often fatal dis- ease caused by a protozoan parasite. Sprays and dips to keep the animals free of ticks and drugs to control the parasite in infected animals are costly and difficult to administer. Credit: International Laboratory for Research on Animal Diseases. necessary for environmental adaptation. It also facilitates the devel- opment of specialized stocks of very high genetic merit for specific production traits, such as egg production in layer strains of poultry or milk production in Holstein cattle. Breeders of the industrialized livestock populations have tended to move toward development of one (in the case of Holstein dairy cattle) or a few (in the case of poultry) highly selected strains that have come to dominate production. Depending on the fecundity of the species, purebred lines (in dairy cattle) or specific crossing of specialized sire and dam lines (in poultry) may be used. A relatively wide array of germplasm may have been sampled, or at least com- paratively evaluated, in the early formation of the populations. Cur- rent emphasis, however, is on selection within existing industrialized stocks; the focus is normally on a small set of traits, and the goal is to achieve maximum rates of genetic change. Selection has been effec- tive, and the industrialized stocks are now clearly differentiated from the original stocks. The possibility of drastic changes in production and marketing conditions, and the need to return to, or sample genes from, Reindustrialized stocks, cannot be totally discounted. More perti

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Measurement and Use of Genetic Variation / 71 nent, however, is the fact that the large differences in production between industrial and nonindustrial stocks will likely require that the capture and use of genes residing in nonindustrialized stocks of livestock species be achieved through marker-assisted selection and, perhaps, molecular isolation and transfer of individual genes inde- pendent of the remainder of the genome. These technologies are being developed now (see Chapter 4), and they provide strong justi- fication for the preservation and characterization of the genetic re- sources of poultry, pigs, and cattle. Nonindustrial Populations For extensively managed ruminant species raised for meat and fiber, and for nonindustrialized populations in general, germplasm .~ . .~_ i . -_ .: . - :':: R _ _ _ = Introduced animals with superior production characteristics are often cross- bred with indigenous breeds to confer disease resistance and adaptation to environmental extremes. Pictured is a cross between the Landim landrace of Mozambique and a breed of the Alpine group of dairy goats. Credit: Inter- national Livestock Center for Africa.

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72 / Livestock use differs markedly from that for industrialized stocks. In exten- sively managed populations the ability of individual animals to in- teract effectively with their environment, to forage for feed, and to deal with climatic stress is critical. Generally, the efficiency of graz- ing ruminants can be increased by improving their ability to adapt to their environment. The existence of many distinct populations, each adapted to a particular environmental niche, can best ensure the capability to im- prove meat and fiber ruminant species. Because many of these niches occur repeatedly around the globe, several regional populations adapted to similar niches may exist at any given time. Environmental stabil THE PACKAGING OF GENETIC INFORMATION A gene, in the classical sense, is the basic unit of heredity, and it has one or more specific effects on the organism. Genes are segments of DNA (deoxyribonucleic acid) in the nucleus of the cell, linearly ar- ranged to form threadlike structures called chromosomes. The term locus refers to the position of a gene on the chromosome, and it is sometimes used interchangeably with the term gene to refer to particu- lar segments of DNA that influence a trait. Alternate forms of a gene found at the same locus are called alleles. Some genes have many alleles, while for others only a single allele is known. Multiple alleles result in multiple phenotypes for a particular trait; that is, the trait will vary depending on which allele is present at the locus. Multiple alleles, for example, have been identified for many of the genes that code for blood proteins. The allelic frequency refers to the proportion of loci in the population as a whole occupied by each allele. A gene for which there is more than one allele is called poly- morphic. Livestock animals are diploid-that is, they carry two copies of each gene. If both copies are the same allele, the individual is said to be homozygous; if the two copies are different alleles of the gene, the individual is heterozygous for that locus. An individual's genetic com- position or genotype, in conjunction with the environment in which that individual is found, determines the phenotype or observable char- acteristics. DNA is the chemical that carries genetic information in almost all living organisms. The DNA molecule itself is an elongated double helix, often compared to a long, twisted ladder. Corresponding to the rungs of the ladder are two bases, a base pair. The sequence of base pairs at a given locus confers the specificity required for transmitting information by means of the genes. Owing to variability of the base

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Measurement and Use of Genetic Variation / 73 ity, however, is rapidly falling victim to human technology. Environ- mental niches can change rapidly as conditions are improved or de- graded. The continued adaptation of grazing ruminants to these changing environments can be achieved by selection, but it is often accom- plished more efficiently by recombining several existing populations to form a new germplasm base consistent with the new production conditions. Thus, Sahiwal cattle from the Indian subcontinent have contributed to milk-producing stocks in Africa and Australasia; pro- lific Finnish Landrace sheep have contributed to the development of several new breeds worldwide for example, the Polypay sheep for use in improved grazing areas of North America; and Africander pairs, the number of different alleles that could theoretically be formed from even a short piece of DNA is extremely large. For instance, a segment of DNA with only 10 base pairs could have over a million different codes. Genes average about 1,000 base pairs, but some are in excess of 100,000 base pairs; thus, the DNA structure provides for an amazing amount of variation. The difference between two alleles is often as simple as a substitution of a single base pair, but that may correspond to a significant difference in the phenotype resulting from those alleles. Certain traits are controlled by a single gene; these are referred to as qualitative or Mendelian traits. Red versus black coat color in cattle, for example, is controlled by a single locus. Many characteristics, how- ever, are influenced by a larger number of genes; these are called quan- titative or polygenic traits. The cumulative action of these genes influ- ences the expression of the trait, but the effect of any single gene is small and cannot generally be isolated in the phenotype. Important production traits, such as rate of weight gain, milk yield, and litter size, are examples of polygenic traits. Occasionally, a major gene, one having a stronger influence on the trait, can be detected, but there is nevertheless modification of the trait by other loci that have smaller effects. An understanding of the extent of allelic or genetic variation is a key factor in conservation genetics. For some loci it is possible to estimate allelic frequencies for a group of animals, such as a breed. The number of loci for which allelic frequencies have been quantified, however, is but a handful of the estimated 50,000 to 100,000 genes operative in most mammalian genomes. Alleles contributing to polygenic traits cannot generally be identified, and measurements of their frequencies have not been feasible. Allelic frequencies undoubtedly vary among sub- populations within a species, but the extent and significance of that variation are not usually known.

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74 / Livestock cattle from southern Africa have become a part of the Barzona breed for use in the arid regions of the United States. RECOMMENDATIONS Globally, a vast amount of diversity exists: among habitats or ecosystems, among the species found within an ecosystem, and among the individuals of a given species (Office of Technology Assessment, 1987; Wilson, 1988~. Variation among individuals of a species leads to differences in their ability to respond to the environment, to differ- ential reproductive success, and, ultimately, to continued evolution and adaptation of the species. The status of unique populations should be-monitored carefully, and when necessary, appropriate action should be taken to prevent loss. Rich diversity exists within domestic species and reflects genetic differences among the populations. Breed preservation protects ge- netic diversity and enables more rapid use of conserved genes. Loss of unique breeds or populations implies loss of unique alleles or allelic combinations. Existing breeds and populations should be evaluated to the extent pos- sible to assess their potential to contribute to livestock improvement. The genetic characterization of large numbers of indigenous breeds is costly and time consuming, but the evaluation of promising breeds is a critical part of livestock improvement efforts. The general use of unimproved or undeveloped germplasm as a source of genes for im- provement is less likely for modern industrialized and intensively managed livestock than it is for improvement of nonindustrialized, extensively managed livestock, such as the grazing ruminants. How- ever, the possible value of specific genes from unimproved breeds that are adapted to certain environments is a strong future possibil- ity. For example, genes for disease resistance or ability to survive with less water may be incorporated into intensively managed breeds to adapt them to harsher environments. The degree of differentiation between the industrialized stocks and other populations of the same species has now progressed to the point that use of genetic material from nonindustrialized or preserved stock is no longer considered attractive in conventional breeding meth- ods, barring major changes in the production system. However, use- ful individual genes or gene complexes, such as those that confer disease resistance, exist in nonindustrialized stocks. The cost of in- serting those genes by traditional crossing and backcrossing tech- niques is considered prohibitive. Advances in molecular biology may

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Measurement and Use of Genetic Variation / 75 foster, through gene transfer, the use of unique genes from unim- proved stocks. In grazing ruminants, it is possible that a number of existing breeds may have much to contribute to current commercial stocks, either in crosses or as purebred lines. The evaluation of these breeds, then, becomes a priority. The potential of preserved breeds to con- tribute to future production systems is also greater for the grazing ruminants because the global range in production environments en- compasses such a wide range of conditions and because highly spe- cialized, industrialized stocks do not yet exist for these species.

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