Statistical identification of major genes in pigs

Litter size is an important characteristic in pig breeding. Apart from selection within available lines, also the development of a synthetic line with the Chinese Meishan breed could be an interesting approach to obtain a line with an increased level of litter size. To investigate genetic aspects of traits of interest in such a synthetic line, Dutch pig breeding companies have produced F 1 and F 2 Meishan x Western crossbreds. This thesis focusses on one important genetic aspect, the presence of major genes. In Chapters 2 to 4, statistical methodology to model a major gene inheritance is investigated and developed Chapters 5 and 6 consider analysis of data collected on the produced Meishan crossbreds for presence of major genes. To develop a synthetic line with Meishan, presence of major genes affecting litter size, growth and fatness is of interest. Additionally, the presence of major genes is investigated for meat quality traits.Statistical methodologyIn Chapter 2, the possibility to detect major genes by use of F 1 and F 2 is investigated. Here, special attention is paid to the situation where alleles at the major locus are fixed in the founder populations. Using 1000 F 2 observations, the power to detect major genes reaches more than 95% for additive and completely dominant effects (difference between homozygotes) of 4 and 2 residual standard deviations, respectively. When F, data is included, any increase in variance from F 1 to F 2 biases parameter estimates and leads to putative detection of a major gene. Also when in reality alleles at the major locus segregate in the founder populations, parameter estimates become biased, unless the average allele frequency in the founder populations is exactly 0.5. Use of data and use of a model in which alleles segregate in parents, e.g. F 3 data, is concluded to give better robustness and larger power. The latter is confirmed in a separate study, as referenced in Chapter 7, which shows that effects up to 4 times as small