Responses in growth rate, food conversion efficiency, carcass composition, residual food intake, meat quality and reproduction traits to selection in pigs for four years, for high or low post-weaning growth rate on a fixed but restricted ration were measured in progeny grown on either restricted, ad libitum individual or ad libitum group feeding regimens. Genetic and phenotypic correlations among the traits were also examined on animals whose full pedigrees comprised a total of 5324 animals. Substantial divergent response was achieved from selection for high vs. low growth rate on restricted feeding, with the genetic means of daily gain diverging by 81.25 g or 2.78 genetic standard deviations (SigmaG). The high and low growth rate lines also differed in ultrasonic backfat and food conversion efficiency by 1.12 SigmaG and 0.84 SigmaG, and by 0.88 SigmaG, 1.10 SigmaG, and 1.14 SigmaG for carcass weight daily gain, carcass fat and lean percentage, respectively. These responses were consistent with the moderately to highly, favourable genetic correlations among and between performance and carcass composition traits. Genetic changes in growth rate, ultrasonic backfat, food conversion ratio, carcass daily gain, carcass fat and lean percentage when measured on ad libitum individual feeding were all economically beneficial. The high growth line had a significantly lower voluntary daily food intake and residual food intake than the contemporaneous low line, indicating a reduced energy requirement for maintenance in the high relative to the low line. Genetic correlations between either growth rate or backfat and carcass traits were favourable but unfavourable between daily food intake and carcass fat or lean percentage, implying that selection strategies which place emphasis on increased leanness and decreased fatness would result in a decline in voluntary food intake of the animals. The descendants of breeding pigs selected for high post-weaning daily gain on restricted feeding showed significantly increased growth rates, slaughter weights and carcase lean percentages and reduced fatness when grown in group housing with ad libitum feeding. This suggests that restricted feeding is an effective performance testing approach for seedstock lines supplying commercial regimens with group housing and ad libitum feeding. Carcase lean pH values measured 24 hours post-mortem (pH24) were not statistically different between the selected lines, suggesting that an increase in basal metabolic rate due to increased rate of lean deposition in the high relative to the low line may have been compensated for by a reduction in heat production from other sources such as physical activity. Such a reduction was evidenced by a lower residual food intake in the high than the low growth lines. This supports the hypothesis that selection for high growth rate on restricted feeding does not have detrimental effects on pork quality. The sows of the high growth line produced more piglets with significantly heavier weights at birth, giving a potential for better post-natal growth and higher yield of pork weaned per sow per year than the low growth sows. Body weights of the high line sows prior to mating were also significantly higher than those of low line sows suggesting earlier age of sexual maturity. A non-significant tendency for high line sows to have a lower voluntary food intake than low line sows pointed to the possibility that their lower maintenance requirement as growers was carried over to the lactational phase of life. It is concluded that selection for high growth rate on a restricted ration of fixed amount will produce pig strains with a high genetic potential for lean growth, reduced energy requirement for maintenance and improved reproductive performance, and which will be suitable for growing under a wide range of commercial feeding environments.

Artificial divergent selection of chickens for high and low body weight at 8 weeks of age has produced two lines: the high (HWS) and low (LWS) body weight chicken lines. In addition to the difference in body weight, the lines show extreme differences in feeding behaviour and body composition. The aim of this study was to uncover the genetic and molecular factors that contribute to and determine these differences, especially regarding body energy regulation and appetite. In papers I and II, genome-wide gene expression in a brain sample containing hypothalamus and in dissected hypothalamus was analysed using DNA microarray and qRT-PCR. We found that levels of differential expression were generally moderate, which was consistent with the idea that polygenic factors were involved in the establishment of the chicken lines. Genes associated with neural plasticity, lipid metabolism and body energy regulation were differentially expressed. This result indicated that the neural systems regulating feeding behaviour and body weight were altered in the chicken lines. However, genes that were involved in the central melanocortin system were not systematically differentially expressed. Interestingly, the biggest differences in expression between the lines found in endogenous retrovirus sequences of the ALV subgroup E. Thus, in paper III, we characterized the number of integrations, the expression of ALVE retroviral elements and their effects on body weight. A significant correlation between low body weight and high ALVE expression was observed in female F9 birds from an HWS x LWS advanced intercross line. This implied that ev-loci contributing to increased ALVE expression levels were genetically linked to loci influencing the low body weight of the pullets. In paper IV, the carnitine palmitoyltransferase-1b gene (CPT1B), which was highly differentially expressed in the hypothalami, was investigated. We mapped chicken CPT1B to the distal tip of chromosome 1p. The levels of CPT1B mRNA in the HWS line were higher in the hypothalamus and lower in muscle than in the LWS line. This pattern of differential expression indicates that this gene could contribute to the remarkable phenotypic differences between HWS and LWS chickens. However, comparison with quantitative trait loci data showed that the expression of CPT1B is a trans effect, rather than a direct causative locus. In conclusion, the data suggested that the long-term selection for body weight resulted in differential gene expression in the brains of the selected chicken lines. These results may have relevance for the poultry industry and will also contribute to increasing knowledge about human diseases such as obesity and anorexia.

In this thesis, I examine variation in occurrence and performance of glabrous and trichome-producing plants of the perennial herb Arabidopsis lyrata. I combine field studies and genetic analysis to (1) examine the function of trichomes as a resistance character in natural populations, (2) compare the magnitude of population differentiation in trichome-production and at putatively neutral marker loci, (3) examine the molecular genetic basis of trichome-production, and (4) quantify the effects of herbivore removal on population growth and relative performance of glabrous and trichome-producing plants. In a survey of 30 populations of A. lyrata in Norway and Sweden, I documented spatiotemporal variation in damage from insect herbivores. With few exceptions, glabrous plants were more damaged by herbivorous insects than trichome-producing plants in polymorphic populations. Damage levels varied substantially among populations and among years. The intensity of herbivory quantified as mean leaf removal to glabrous plants was higher in polymorphic populations than in monomorphic glabrous populations. Within the Swedish range, populations were more strongly differentiated at the locus coding for glabrousness than at eight putatively neutral isozyme loci. This is consistent with the hypothesis that trichome production is subject to divergent selection. A study of the genetic basis of trichome production showed that glabrousness was associated with mutations in an orthologue to GLABROUS1, a regulatory gene known to cause glabrousness in A. thaliana. Comparative data indicate that the genetic basis of glabrousness varies among populations. Experimental removal of insect herbivores in a natural A. lyrata population increased population growth rate and the relative fitness of the glabrous morph. The results suggest that insect herbivory may influence both population dynamics and selection on trichome production in A. lyrata.

Establishing group structure in complex networks is potentially very useful since nodes belonging to the same module can often be related by commonalities in their biological function. However, module detection in complex networks poses a challenging problem and has sparked a great deal of interest in various disciplines in recent years [5]. In real networks, which can be quite complex, we have no idea about the true number of modules that exist. Furthermore, the structure of the modules may be hierarchical meaning they may be further divided into sub-modules and so forth. Many attempts have been made to deal with these problems and because the involved methods vary considerably they have been difficult to compare [5]. The objectives of this thesis are (i) to create and implement a new algorithm that will identify modules in complex networks and reconstruct the network in such a way so as to maximize modularity, (ii) to evaluate the performance of a new method, and compare it to a popular method based on a simulated annealing algorithm, and (iii) to apply the new method, and a comparator method, to analyze the metabolic network of the bacterial genus Listeria, an important pathogen in both agricultural and human clinical settings.