Studies on breeding schemes in a closed pig population

G. de Roo

Research output: Thesisinternal PhD, WU


<p>Size of a population in genetic terms is a function of number of male and female individuals used for breeding over a generation. A breed can be small because of a small total number of individuals but also because of a small number of individuals of one sex. According to this definition, many breeds of livestock, pets and zoo animals are small populations.<br/>Breeding scheme designed for finite populations sometimes primarily aim at conservation of animal genetic resources. In most cases, however, the breeding program should lead to continuous genetic improvement over a period of time of interest to breeders. Available additive genetic variance, therefore, should be used efficiently. This is not straightforward because selection in one generation affects the additive genetic variance in the next generation. A second complication is the increase in additive genetic relationship between animals, which is inevitable in a finite population. Inbreeding reduces additive genetic variance available for selection and, secondly, has a negative effect on the mean of traits subject to dominance.<p>The aim of this thesis was optimization of breeding schemes in finite populations. Attention was focussed on breeding schemes in a closed swine herd as an example of a finite population in which selection and inbreeding are both relevant. The outcome of a breeding scheme for such a herd is affected by many factors as, for example, population size and structure, founder population size and selection and mating strategies. Effects of variation in a number of these factors on selection response and rate of increase in inbreeding coefficient (F) were studied.<p>The genetic model used was highlighted in the first chapter. This model applied to quantitative traits and assumed that many loci of small effect each affected a trait. To prevent confounding of effects of inbreeding on the additive genetic variance and on the mean, an additive genetic model was used in chapters 3 to 5. Effects of inbreeding depression were considered in chapter 6.<p>A stochastic model of a closed swine herd was described in chapter 2. This model measured genetic changes in production and reproduction traits and F over a period of 25 years. Growth rate (23 to 100 kg), feed intake, lean percentage, litter size and interval from weaning to oestrus were incorporated in the model because of their economic relevance to pig breeding. The model included overlapping generations, continuous mating and farrowing and weekly selection of boars and sows. Week was the unit of time. This model was used in subsequent chapters. The parameters used applied to a sire line.<p>Population size at the nucleus level is an important factor with respect to costs and benefits of pig breeding. Selection response is dependent on number of boars and of sows available for selection and on number of each sex used for breeding. Effects of variation in population size and in intensities of selection on selection response and rate of increase in F were reported in chapter 3. Results were compared to expectations from selection theory and from theory of effective population size.<br/>Advantages of intense selection in short-term response were less than expected because assumptions of independent observations and constant variance were violated. Selection induced linkage disequilibrium and reduced the additive genetic variance. Intensity of selection was reduced because of small numbers of families. Comparison of alternative breeding schemes should include a correction for the amount of linkage disequilibrium caused by each breeding scheme. The equilibrium additive genetic variance should be used in the calculation of expected response to selection. When number of families is small, as in many practical situations, selection intensities used should also be corrected for family size, except when available family information is included in the index and selection intensities are based on number of families.<br/>Response was curvilinear with time, and curvilinearity increased with intensity of selection. Increased relationships between animals caused reduced variance available for selection and diminished response. When the time period included in the evaluation of breeding schemes increased, optimal annual number of boars also increased.<br/>Equations were derived to describe cumulative response in year 25 as a function of size of the sow herd and annual number of boars. With 25, 50, 100 and 150 sows, 52, 66, 75 and 84 percent of maximum response with an infinite number of sows was attained. Optimal annual number of boars depended on size of the sow herd: when herd size increased, optimal annual number of boars increased to 15.<br/>Drift caused considerable differences in response between replicates. These differences, however, were small compared to differences in means between sow alternatives. Splitting of a line into independent sublines, therefore, is unadvisable because of reduced expected response due to smaller population size.<p>The design of a mating system for selected animals needs special attention. Mating policy includes the choice whether and to what extent mating of relatives should be avoided. It also implies choice of number of boars to be used simultaneously for breeding. In chapter 4 alternative mating policies were compared.<br/>Under the additive genetic model followed, cumulative response over a period of 25 years was generally highest with 3 boars used simultaneously and no avoidance of mating of relatives. With avoidance of mating of relatives, number of offspring of sires with few relatives was increased. These sires probably were not as good genetically as sires with many relatives, because selection was on phenotype alone. With avoidance of mating of relatives breeding values of mates will be more diverse and the additive genetic variance among offspring will be less than without avoidance of mating of relatives. Unequal numbers of offspring of sires also contributed to a lower additive genetic variance and, thus, to a lower response to selection for alternatives with avoidance of mating of relatives. It should be noted that inbreeding depression was not a consideration in this chapter.<br/>Avoiding mating of relatives initially postponed the increase of F. Rate of increase in F after year five, however, was rather independent of mating policy. Differences in F in year 25 between alternatives with and without avoidance of mating of relatives were considerable and ranged from 2.1 percent for 100 sows, 20 boars annually and 10 boars at a time to 6.9 percent for 100 sows, 5 boars annually and 3 boars at a time. The risk of an unexpected high level of F was also higher when there was no avoidance of mating of relatives. A mating system with avoidance of mating of close relatives only probably is optimal.<p>At the start of a new line, the question of size of the founder population arises. The founder population should have a high mean breeding value and contain a substantial amount of genetic variation. Effects of changes in size of the founder population, in effective population size after the foundation period and in intensity of selection of founder animals from a base population were evaluated in chapter 5.<br/>Determination of optimal size of the founder population implies a balancing of mean breeding value and additive genetic variance in the founder group. Optimal number of founder animals depends on differences in estimated breeding values between animals, on the accuracy of these estimates and on the risk of low response a breeder is willing to take. This risk increases at a decreasing number of founder animals.<br/>Use of five founder boars provided, on average, good responses. The established level of additive genetic variance offered good possibilities for further selection and fast reduction of this variance in the early years of the breeding program was prevented.<br/>Optimal number of founder sows depended on desired size of the herd. A gradual increase of number of sows towards the desired size of the herd was optimal. This strategy implies culling of sows with a low performance, even if the desired size of the herd is not reached yet. Selection of sows should be mild, because build up of the sow herd should be done reasonably fast. A herd of 100 sows could be founded acceptably by 25 founder sows.<br/>Effects of a temporary restriction of population size on selection response depend on number and genetic relationships of remaining animals. A fast increase in effective population size after such a bottleneck can limit the rate of increase in F and the negative effects on response.<p>The level of F is relevant to breeders because it affects the additive genetic variance. Direct inbreeding depression effects on production traits are less important in a sire line because a loss in heterozygosity will be regained in hybrid slaughter animals. Inbreeding depression, however, might also affect selection response indirectly. Through its effect on fertility, inbreeding depression will affect number of animals available for selection and, thus, selection response. Effects of inbreeding depression were investigated in chapter 6.<br/>Three sets of partial regression coefficients of F on litter size at birth and at weaning and on growth rate were considered: no inbreeding depression, a set based on literature and a set of values twice as large as indicated by literature. Two sizes of the sow herd were considered, 25 and 100, and annual number of boars varied from 5 to 20.<br/>Inbreeding depression induced a negative correlation between performance and F and, therefore, slightly diminished rate of increase in F when animals available for selection differed in F. Mild selection for litter size improved breeding values and, simultaneously, limited inbreeding depression for the trait. Selection counteracted inbreeding depression most effectively with a low rate of increase in F.<br/>Inbreeding depression affected response for production traits most through its effect on the mean. Reduction in litter size had a limited effect on intensity of selection, because only two boars per litter were tested. This effect might be larger with other testing strategies or less prolific species. Response was reduced when animals available for selection differed in F, because of a bias in estimated breeding values. Data to be used in estimation of breeding values, therefore, should be corrected for differences in F between animals.<br/>Optimal annual number of boars was largely unaffected by degree of inbreeding depression. The main effect of inbreeding depression was to reduce response of alternatives with five boars annually relative to other boar alternatives. Even without inbreeding depression, number of boars used annually should be larger than five.<p>Effects of opening of the nucleus and breeding programmes that aim at conservation of animal genetic resources were considered in chapter 7. Implications of the study for the design of breeding schemes in general and, more specific, for selection in some livestock species were also discussed.<br/>Introduction of new breeding animals from outside the nucleus is only worthwhile occasionally. The effect on selection response and F will be limited and the selection policy followed in the nucleus will be of major importance to the benefits of the breeding scheme.<br/>With maintenance of genetic variance as the main objective of breeding, emphasis should be on limiting the rate of increase in F. Differences in contributions of animals to the next generation of offspring should be minimized. Use of within-family selection, therefore, is advisable. Number of sires and dams used per generation should be as equal as possible. This can be realized at relatively low costs by a fast turn-over of sires and a long herd life of dams.<br/>Many populations of livestock are small in genetic terms because effective number of sires is small. With differential numbers of matings per sire, effective number of sires is considerably smaller than actual number of sires. Use of a very small number of sires will limit genetic improvement and will cause a high rate of increase in F. Optimization of breeding schemes not only implies intense selection of breeding stock but also in cludes use of a sufficient number of sires to insure continuous<br/>genetic improvement over the period of time of interest to breeders.<p><TT></TT>
Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Politiek, R.D., Promotor, External person
  • van der Steen, H.A.M., Promotor, External person
Award date19 Feb 1988
Place of PublicationS.l.
Publication statusPublished - 1988


  • animal breeding
  • improvement
  • inbreeding
  • pigs
  • resistance
  • selection

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