Analysis of the within-population genetic diversity and the effective size based on different kinds of information in selected animal populations

The scientific purpose of the thesis is twofold: (i) to investigate in details the links between criteria originating from different kinds of information, such as molecular markers, pedigrees, or phenotypes for quantitative traits, (ii) to go further in the examination of the joint evolution of the neutral variability and the selected variability. According to the kind of information, genetic diversity and its evolution are described through various parameters dealing with more or less complex underlying model, thus, we will have more or less realistic representation of the genetic diversity. On one hand, analysis of polymorphism gives a direct overview of the diversity: genotypes and allele frequencies of candidate gene or molecular markers will give access to specific polymorphism of known areas in the genome, whereas pedigrees will give access to anonymous polymorphism of neutral unknown areas in the genome. On the other hand, analysis of phenotypes gives a general overview of genetic diversity, assuming the model of representation to be more complex. The principal methods that are available for the analysis of genetic diversity and those used along this thesis, using different kinds of information are presented in chapter 1. Chapter 2, 3 and 4 deal with a valorisation of different kinds of information from experimental chicken lines, selected for immune response traits, for the integrate analysis of genetic variability. Genetic gain and genetic diversity based on performances and pedigree data were analysed in chapter 2. The observed evolutions of inbreeding and genetic gain were compared to values predicted by some theoretical models. The deterministic methods compared yielded results that were close to those observed in real data and differences between theoretical predictions and experimental results mainly arise from differences between the true and the assumed selection scheme, and from mathematical simplifications applied in the prediction methods. Effect of selection scheme on inbreeding and other criteria of genetic variability, based on pedigree data, was also investigated. The effective number of ancestors appeared to be the most relevant parameter in monitoring genetic diversity using pedigree information since it takes into account the loss of genetic diversity due to genetic drift occurring during the pedigree development. Estimation and evolution of genetic parameters and polymorphism evolution of a candidate gene were handled in chapter 3. Confrontation of different theoretical predictions with observed evolution of the polymorphism within lines and analysis of variance coponents were undergone to check the neutrality of MHC for the traits in our selected populations. But beyond the interest of MHC effect in immune responsiveness, this study has highlighted the interest of combining various approaches to assess the effect of a candidate gene and the evolution of its polymorphism, especially in the case of rare alleles. Changes in additive genetic variance during the course of the experiment were also investigated and we examined the cope of the underlying model (polygenic infinitesimal model) used for the estimation of the genetic parameters. Increasing the number of generation or taking subsets of generations using REML may be an appropriate method in monitoring genetic diversity over time and infer about the effect of selection on reduction of additive genetic variance. Evolution of polymorphism of supposedly neutral or selected molecular markers was analysed and compared in chapter 4. Different methods were combined, statistical analysis as well as modelling and simulations, to detect signature of selection left by QTL. Pictures of genetic diversity were drawn from polymorphism evolution of markers located in QTL regions and supposedly neutral markers, which may be considered as a reference. This study has shown that QTLs are very sensitive to the trait they related to and that a marker should be very close to a QTL to experience hitchhiking, since selective sweep occurs at a very short distance. Throughout the chapter, modelling was confirmed to be an efficient approach to make useful predictions of the evolution of selected populations although the basic assumptions considered in the models (polygenic additive model, normality of the distribution, base population at the equilibrium, etc.) are not met in reality. The effective size (Ne) of the population is a key parameter for estimation of genetic variability and was estimated using either pedigree information or variance in allele frequencies over time in the experimental chicken lines. Estimated effective size of the population based on the pedigree approach was always lower than estimated effective size based on the temporal variation approach, whatever the loci that were considered: candidate gene, supposedly neutral or selected markers. But, estimation using genotype information from supposedly neutral marker was lower than estimation using genotype information from markers under selection: genetic diversity in regions under selection is weaker than those of the whole genome. Chapter 5 was not a direct analysis of genetic diversity but an evaluation of risks consequently to reduction of genetic diversity. The study focused on abnormalities in populations that have experimented a strong bottleneck, such as the French Holstein dairy cattle population. Through simulations, we showed that appearance of genetic defects was due to the reduced and unbalanced use of bulls. We also investigated the consequences of counter-selection against the deleterious alleles identified in short and long-term.