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An experiment of divergent selection for intramuscular fat was carried out at Universitat Politècnica de València. The high response of selection in intramuscular fat content, after nine generations of selection, and a multidimensional scaling analysis showed a high degree of genomic differentiation between the two divergent populations. Therefore, local genomic differences could link genomic regions, encompassing selective sweeps, to the trait used as selection criterion. In this sense, the aim of this study was to identify genomic regions related to intramuscular fat through three methods for detection of selection signatures and to generate a list of candidate genes. The methods implemented in this study were Wright's fixation index, cross population composite likelihood ratio and cross population - extended haplotype homozygosity. Genomic data came from the 9th generation of the two populations divergently selected, 237 from Low line and 240 from High line. A high single nucleotide polymorphism (SNP) density array, Affymetrix Axiom OrcunSNP Array (around 200k SNPs), was used for genotyping samples. Several genomic regions distributed along rabbit chromosomes (OCU) were identified as signatures of selection (SNPs having a value above cut-off of 1%) within each method. In contrast, 8 genomic regions, harbouring 80 SNPs (OCU1, OCU3, OCU6, OCU7, OCU16 and OCU17), were identified by at least 2 methods and none by the 3 methods. In general, our results suggest that intramuscular fat selection influenced multiple genomic regions which can be a consequence of either only selection effect or the combined effect of selection and genetic drift. In addition, 73 genes were retrieved from the 8 selection signatures. After functional and enrichment analyses, the main genes into the selection signatures linked to energy, fatty acids, carbohydrates and lipid metabolic processes were ACER2, PLIN2, DENND4C, RPS6, RRAGA (OCU1), ST8SIA6, VIM (OCU16), RORA, GANC and PLA2G4B (OCU17). This genomic scan is the first study using rabbits from a divergent selection experiment. Our results pointed out a large polygenic component of the intramuscular fat content. Besides, promising positional candidate genes would be analysed in further studies in order to bear out their contributions to this trait and their feasible implications for rabbit breeding programmes.

The Iberian pig is one of the pig breeds that has the highest meat quality. Traditionally, producers have bred one of the available varieties, exclusively, and have not used crosses between them, which has contrasted sharply with other populations of commercial pigs for which crossbreeding has been a standard procedure. The objective of this study was to perform an experiment under full diallel design among three contemporary commercial varieties of Iberian pig and estimate the additive genetic variation and the crossbreeding effects (direct, maternal and heterosis) for prolificacy. The data set comprised 18 193 records for total number born and number born alive from 3800 sows of three varieties of the Iberian breed (Retinto, Torbiscal and Entrepelado) and their reciprocal crosses (Retinto × Torbiscal, Torbiscal × Retinto, Retinto × Entrepelado, Entrepelado × Retinto, Torbiscal × Entrepelado and Entrepelado × Torbiscal), and a pedigree of 4609 individuals. The analysis was based on a multiple population repeatability model, and we developed a model comparison test that indicated the presence of direct line, maternal and heterosis effects. The results indicated the superiorities of the direct line effect of the Retinto and the maternal effect of the Entrepelado populations. All of the potential crosses produced significant heterosis, and additive genetic variation was higher in the Entrepelado than it was in the other two populations. The recommended cross for the highest yield in prolificacy is a Retinto father and an Entrepelado mother to generate a hybrid commercial sow.

The objective of this work was to study the changes that, selecting for environmental variability of birth weight (BW), could bring to other interesting traits in livestock such as: survivability at weaning (SW), litter size (LS) and weaning weight (WW), their variability assessed from standard deviations of LS, standard deviation of WW (SDWW) and also the total litter weight at birth (TLBW) and total litter weight at weaning. Data were registered after eight generations of a divergent selection experiment for BW environmental variability in mice. Genetic parameters and phenotypic and genetic evolution were assessed using linear homoscedastic and heteroscedastic models in which the traits were attributed to the female, except BW and WW that were in some models also attributed to the pup. Genetic correlation between the trait and variability levels was -0.81 for LS and -0.33 for WW. Clear divergent phenotypic trends were observed between lines for LS, WW and SDWW. Although animals were heavier in the high line, TLBW and at weaning was greater in the low line. Despite the negative genetic correlation that was obtained, SDWW was also higher in the high line. Heritabilities were 0.21 and 0.06, respectively, for LS and SW. Both phenotypic and genetic trends showed clear superiority of the low line over the high line for these traits, but inferior for WW. Heteroscedastic model performed similar to the homoscedastic model when there was enough information. Considering LS and survival, the low line was preferred from a welfare point of view, but its superiority from the productivity perspective was not clear. Robustness seemed higher as shown by a low variation and having a benefit to the animal welfare, but this still remains unclear. It was concluded that low variation benefits the welfare of animals.

An experiment of a 2×2 full diallelic cross between two contemporary Iberian pig strains (Retinto: RR, and Torbiscal: TT) was conducted to estimate the crossbreeding effects for growth and carcass traits. Phenotypic records were obtained under intensive management and consisted of two different data sets. The first set comprised growth traits until weaning and was collected at two different farms (6236 and 1208 records, respectively). Specific data included individual piglet weight at birth and at weaning at 28 days and average daily gain from birth to weaning at 28 days (ADG28) for both RR and TT and their reciprocal crosses. The second set comprised growth data from birth to slaughter (~340 days and ~160 kg) and carcass traits from 349 individuals (randomly) sampled at weaning from the first dataset. Data were analyzed through a Bayesian analysis by using a reparameterization of Dickerson's model that allowed estimation of the posterior distributions of the following crossbreeding effects: average maternal breed effect (gM), average paternal breed effect (gP) and individual heterosis (hI). Results showed that the relative magnitude of crossbreeding effects depends on the trait analyzed. Crosses where Torbiscal strain was used as mother (RT and TT) achieved the greatest performance for all growth traits at weaning, leading to remarkable gM effects. The most outstanding example is the case of ADG28 where the probability of relevance was one. In contrast, TR cross showed the greatest differences from RR cross for all growth at slaughter and carcass traits. These differences were mainly due to hI and gP crossbreeding parameters. In particular, the posterior mean of hI was more noticeable for live weight at slaughter, average daily gain at slaughter and carcass length, while gP was more relevant for hams (kg) and loins (kg) representing from 3% to10% of average performance of traits. Hence, growth traits at weaning did not reveal any notable advantage of the crossbreeding scheme because of the superiority of the Torbiscal strain with respect to its mothering ability and the small hI. However, results from growth and carcass traits at slaughter would support the implementation of a TR crossbred system. It would allow exploitation of both the gP of the Torbiscal strain and the hI between these two Iberian pig strains. Additionally, gP estimates and phenotypic differences between reciprocal crosses might suggest signs of the presence of paternal genetic imprinting in primal cuts traits.

Differential gene expression analyses typically focus on departures across mathematical expectations (i.e. mean) from two or more groups of microarrays, without considering alternative patterns of departure. Nevertheless, recent studies in humans and great apes have suggested that differential gene expression could also be characterized in terms of heterogeneous dispersion patterns. This must be viewed as a very interesting genetic phenomenon clearly linked to the regulation mechanisms of gene transcription. Unfortunately, we completely lack information about the incidence and relevance of dispersion-specific differential gene expression in livestock species, although a specific Bayes factor (BF) for testing this kind of differential gene expression (i.e. within-probe heteroskedasticity) has been recently developed. Within this context, our main objective was to characterize the incidence of dispersion-specific differential gene expression in pigs and, if possible, providing the first evidence of this phenomenon in a livestock species. We evaluated dispersion-specific differential gene expression on ovary, uterus and hypophysis samples from 22 F2 Iberian × Meishan sows, where a total of 15,252 probes were interrogated. For each tissue, heteroskedasticity of probe-specific residual variances was evaluated by three pairwise comparisons involving three physiological stages, that is, heat, 15 days of pregnancy and 45 days of pregnancy. Between 2.9% and 37.4% of the analyzed probes provided statistical evidence of within-tissue across-physiological stages dispersion-specific differential gene expression (BF >1), and between 0.1% and 3.0% of them reported decisive evidence (BF >100). It is important to highlight that <8% of the heteroskedastic probes were also linked to differential gene expression in terms of departures among the probe-specific mathematical expectation of each physiological stage. This discarded the disturbance of scale effects in a high percentage of probes and suggested that probe-specific heteroskedasticity must be viewed as an independent phenomenon within the context of differential gene expression. As a whole, our results report a remarkable incidence of dispersion-specific differential gene expression across the whole genome of the pig, establishing a very interesting starting point for further studies focused on deciphering the genetic mechanisms underlying heteroskedasticity.

This work presents an analysis of heterogeneity of environmental variance for slaughter weight (175 days) in pigs. This heterogeneity is associated with systematic and additive genetic effects. The model also postulates the presence of additive genetic effects affecting the mean and environmental variance. The study reveals the presence of genetic variation at the level of the mean and the variance, but an absence of correlation, or a small negative correlation, between both types of additive genetic effects. In addition, we show that both, the additive genetic effects on the mean and those on environmental variance have an important influence upon the future economic performance of selected individuals.