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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 pr

We performed a whole-genome scan with 110 informative microsatellites in a commercial Duroc population for which growth, fatness, carcass and meat quality phenotypes were available. Importantly, meat quality traits were recorded in two different muscles, that is, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), to find out whether these traits are determined by muscle-specific genetic factors. At the whole-population level, three genome-wide QTL were identified for carcass weight (SSC7, 60 cM), meat redness (SSC13, 84 cM) and yellowness (SSC15, 108 cM). Within-family analyses allowed us to detect genome-wide significant QTL for muscle loin depth between the 3rd and 4th ribs (SSC15, 54 cM), backfat thickness (BFT) in vivo (SSC10, 58 cM), ham weight (SSC9, 69 cM), carcass weight (SSC7, 60 cM; SSC9, 68 cM), BFT on the last rib (SSC11, 48 cM) and GM redness (SSC8, 85 cM; SSC13, 84 cM). Interestingly, there was low positional concordance between meat quality QTL maps obtained for GM and LTL. As a matter of fact, the three genome-wide significant QTL for colour traits (SSC8, SSC13 and SSC15) that we detected in our study were all GM specific. This result suggests that QTL effects might be modulated to a certain extent by genetic and environmental factors linked to muscle function and anatomical location. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Teat number is an important trait in sows that should accompany the increase in litter size that has been achieved in the last decades through selection. We have previously identified a genome-wide significant QTL for teat number in porcine chromosome SSC5 by means of an experimental Meishan by Iberian F 2 intercross population. In the present report, we have studied the porcine parathyroid hormone-like hormone (PTHLH) gene, which maps to SSC5, as a candidate gene for this trait, as PTHLH is involved in nipple formation during embryogenesis and nipple development during pregnancy and lactation. We have found that porcine PTHLH gene is transcribed into three mRNA species differing in the 5'UTR region. Two of these variants are reported in pigs here for the first time one was similar to variant 1 described in humans while the other, which was generated by the retention of two small introns, has not been identified before in any other species. In addition, mRNA expression profile for two of the mRNA variants was assessed in 19 pig tissues. Porcine PTHLH showed a widespread expression as it was present in all tested tissues and relative expression of each variant was tissue dependent. Finally, we have performed an association study between a non-synonymous mutation in the coding region of this gene and sow teat number. The PTHLH polymorphism was segregating in our Meishan by Iberian F 2 population at intermediate allelic frequencies. We compared here six different statistical models to choose the one with a better fit and a lower degree of complexity. However, despite the potential negative effect of the PTHLH mutation in the signal peptide of this protein, we did not detect any association between the PTHLH genotype and the sow teat number phenotype, concluding that the causal mutation of the observed QTL is very likely not related to this gene. © 2011 Blackwell Verlag GmbH.

Intramuscular fat (IMF) storage is a biological process with a strong impact on nutritional and technological properties of meat and also with rel- evant consequences on human health. The genetic ar- chitecture of IMF content and composition phenotypes has been thoroughly studied in pigs through the iden- tification of QTL and the estimation of genetic param- eters. A question that has not been elucidated yet is if the genetic determinants of IMF-related phenotypes are muscle specific or, conversely, have broad effects on the whole skeletal muscle compartment. We have ad- dressed this question by generating lipid QTL maps for 2 muscles with a high commercial value, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), in a Duroc commercial population (n = 350). Our data support a lack of concordance between the GM and LTL QTL maps, suggesting that the effects of poly- morphisms influencing IMF, cholesterol, and fatty acid contents are modulated to some extent by complex spa- tial factors related to muscle location, metabolism, and function. These results have important implications on the implementation of genomic selection schemes aimed to improve the lipid profile of swine meat. © 2011 American Society of Animal Science, All rights reserved.

The objective of this experiment is to study genes and proteins differing across reproductive stages in swine. RNA from ovary, from sows on heat, 15 and 45 days of pregnancy have been hybridised in porcine oligonucleotide microchips to characterize changes in gene expression profile between different reproductive stages. Expression differences in 281 genes (posterior probability <10-11) have been found between expression at different stages in ovary. One of these genes, vinculin, showed 100 times more expression on heat than at 45 days of pregnancy, so we chose that gene for immunohistochemistry and western blot analysis. On immunohistochemistry we found that ovaries of sows on heat showed stronger vinculin staining than ovaries stroma of sows at 30 days of pregnancy. On western blot, significant differences appeared only between heat and 45 days of pregnancy.