Rotation Bounds for Hölder Continuous Homeomorphisms with Integrable Distortion.

We obtain sharp rotation bounds for the subclass of homeomorphisms f : C → C of finite distortion which have distortion function in L loc p , p > 1 , and for which a Hölder continuous inverse is available. The interest in this class is partially motivated by examples arising from fluid mechanics. Our rotation bounds hereby presented improve the existing ones, for which the Hölder continuity is not assumed. We also present examples proving sharpness.

Characterisation of sperm piRNAs and their correlation with semen quality traits in swine.

Piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs that are essential in the transcriptional silencing of transposable elements and warrant genome stability in the mammalian germline. In this study, we have identified piRNAs in porcine sperm using male germline and zygote datasets from human, mice, cow and pig, and evaluated the relation between their abundances and sperm quality traits. In our analysis, we identified 283 382 piRNAs, 1355 of which correlated with P ≤ 0.01 to at least one semen quality trait. Fifty-seven percent of the correlated piRNAs mapped less than 50 kb apart from any other piRNA in the pig genome. Furthermore, piRNA location was significantly enriched near long interspersed nuclear elements. Moreover, some of the significant piRNAs mapped within or close to genes relevant for fertility or spermatogenesis such as CSNK1G2 and PSMF1.

A targeted genotyping approach enhances identification of variants in taste receptor and appetite/reward genes of potential functional importance for obesity-related porcine traits.

Taste receptors (TASRs) and appetite and reward (AR) mechanisms influence eating behaviour, which in turn affects food intake and risk of obesity. In a previous study, we used next generation sequencing to identify potentially functional mutations in TASR and AR genes and found indications for genetic associations between identified variants and growth and fat deposition in a subgroup of animals (n = 38) from the UNIK resource pig population. This population was created for studying obesity and obesity-related diseases. In the present study we validated results from our previous study by investigating genetic associations between 24 selected single nucleotide variants in TASR and AR gene variants and 35 phenotypes describing obesity and metabolism in the entire UNIK population (n = 564). Fifteen variants showed significant association with specific obesity-related phenotypes after Bonferroni correction. Six of the 15 genes, namely SIM1, FOS, TAS2R4, TAS2R9, MCHR2 and LEPR, showed good correlation between known biological function and associated phenotype. We verified a genetic association between potentially functional variants in TASR/AR genes and growth/obesity and conclude that the combination of identification of potentially functional variants by next generation sequencing followed by targeted genotyping and association studies is a powerful and cost-effective approach for increasing the power of genetic association studies.

A genome-wide association analysis for carcass traits in a commercial Duroc pig population.

We performed a genome-wide association study to map the genetic determinants of carcass traits in 350 Duroc pigs typed with the Porcine SNP60 BeadChip. Association analyses were carried out using the gemma software. The proportion of phenotypic variance explained by the SNPs ranged between negligible to moderate (hSNP2= 0.01-0.30) depending on the trait under consideration. At the genome-wide level, we detected one significant association between backfat thickness between the 3rd and 4th ribs and six SNPs mapping to SSC12 (37-40 Mb). We also identified several chromosome-wide significant associations for ham weight (SSC11: 51-53 Mb, three SNPs; 67-68 Mb, two SNPs), carcass weight (SSC11: 66-68 Mb, two SNPs), backfat thickness between the 3rd and 4th ribs (SSC12: 21 Mb, one SNP; 33-40 Mb, 17 SNPs; 51-58 Mb, two SNPs), backfat thickness in the last rib (SSC12: 37 Mb, one SNP; 40-41 Mb, nine SNPs) and lean meat content (SSC13: 34 Mb, three SNPs and SSC16: 45.1 Mb, one SNP; 62-63 Mb, 10 SNPs; 71-75 Mb, nine SNPs). The ham weight trait-associated region on SSC11 contains two genes (UCHL3 and LMO7) related to muscle development. In addition, the ACACA gene, which encodes an enzyme for the catalysis of fatty acid synthesis, maps to the SSC12 (37-41 Mb) region harbouring trait-associated regions for backfat thickness traits. Sequencing of these candidate genes may help to uncover the causal mutations responsible for the associations found in the present study.

Canine Leishmaniasis Progression is Associated with Vitamin D Deficiency.

The relationship between vitamin D deficiency and the risk of suffering from a plethora of health disorders, ranging from autoimmune processes to infectious diseases has been widely described. Nonetheless, the potential role of vitamin D in visceral leishmaniasis remains uncharacterized. In the Mediterranean basin, where the dog is leishmania's main peri-domestic reservoir, control measures against the canine disease have shown beneficial effects on the incidence of human leishmaniasis. In this study, we measured the vitamin D levels in serum samples from a cohort of 68 healthy and disease dogs from a highly endemic area and we have also studied the relationship of these levels with parasitological and immunological parameters. The sick dogs presented significantly lower (P < 0.001) vitamin D levels (19.6 ng/mL) than their non-infected (31.8 ng/mL) and the asymptomatic counterparts (29.6 ng/mL). In addition, vitamin D deficiency correlated with several parameters linked to leishmaniasis progression. However, there was no correlation between vitamin D levels and the Leishmania-specific cellular immune response. Moreover, both the leishmanin skin test and the IFN-γ levels displayed negative correlations with serological, parasitological and clinical signs. Further studies to determine the functional role of vitamin D on the progression and control of canine leishmaniasis are needed.

Copy number variation in the genomes of domestic animals.

Copy number variation (CNV) might be one of the main contributors to phenotypic diversity and evolutionary adaptation in animals and plants, employing a wide variety of mechanisms, such as gene dosage and transcript structure alterations, to modulate organismal plasticity. In the past 4 years, considerable advances have been made in the characterization of the genomic architecture of CNV in domestic species. First, low-resolution CNV maps were produced for cattle, goat, sheep, pig, dog, chicken, duck and turkey, showing that these structural polymorphisms comprise a significant part of these genomes. Furthermore, CNVs have been associated with several pigmentation (white coat in horse, pig and sheep) and morphological (late feathering and pea comb in chicken) traits, as well as with susceptibility to a wide array of diseases and developmental disorders, for example osteopetrosis, anhidrotic ectodermal dysplasia, copper toxicosis, intersexuality, cone degeneration, periodic fever and dermoid sinus, among others. In the future, development of high-resolution tools for CNV detection and typing combined with the implementation of databases integrating CNV, QTL and gene expression data will be essential to identify and measure the impact of this source of structural variation on the many phenotypes that are relevant to animal breeders and veterinary practitioners.

Characterization of OAR1 and OAR18 QTL associated with muscle depth in British commercial terminal sire sheep.

This study aimed at verifying previously identified QTL affecting growth and carcass traits on ovine chromosome 18 (OAR18) in Texel sheep (n = 1844), and on OAR1 in Charollais (n = 851) and Suffolk (n = 998) sheep. The QTL were investigated using regression and variance component mapping (VCA) of body weight, muscle and fat depth measurements. In addition, the mode of inheritance of the Texel OAR18 QTL was explored, using data from 4376 Texel sheep, fitting VCA models testing for additive and imprinting effects. We also simulated a 480-sheep population with different QTL imprinting models and various available levels of marker information to understand the behaviour of the VCA results under different assumed genetic models. In summary, the previously identified QTL were successfully verified using both interval mapping and VCA in the three breeds. We propose a polar overdominance mode of inheritance for the OAR18 QTL in Texel sheep, and we present methods to dissect the QTL mode of inheritance, using the Texel OAR18 QTL as an example.

Short communication: genetic variability in the predicted microRNA target sites of caprine casein genes.

The main goal of the current work was to identify single nucleotide polymorphisms (SNP) that might create or disrupt microRNA (miRNA) target sites in the caprine casein genes. The 3' untranslated regions of the goat alpha(S1)-, alpha(S2)-, beta-, and kappa-casein genes (CSN1S1, CSN1S2, CSN2, and CSN3, respectively) were resequenced in 25 individuals of the Murciano-Granadina, Cashmere, Canarian, Saanen, and Sahelian breeds. Five SNP were identified through this strategy: c.175C>T at CSN1S1; c.109T>C, c.139G>C, and c.160T>C at CSN1S2; and c.216C>T at CSN2. Analysis with the Patrocles Finder tool predicted that all of these SNP are located within regions complementary to the seed of diverse miRNA sequences. These in silico results suggest that polymorphism at miRNA target sites might have some effect on casein expression. We explored this issue by genotyping the c.175C>T SNP (CSN1S1) in 85 Murciano-Granadina goats with records for milk CSN1S1 concentrations. This substitution destroys a putative target site for miR-101, a miRNA known to be expressed in the bovine mammary gland. Although TT goats had higher levels (6.25 g/L) of CSN1S1 than their CT (6.05 g/L) and CC (6.04 g/L) counterparts, these differences were not significant. Experimental confirmation of the miRNA target sites predicted in the current work and performance of additional association analyses in other goat populations will be an essential step to find out if polymorphic miRNA target sites constitute an important source of variation in casein expression.

Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds.

We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite, and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populations. The analysis of nuclear markers evidenced the existence of a close genetic relationship between Near Eastern and European wild boars making it difficult to infer their relative contributions to the gene pool of modern European breeds. Moreover, we have shown that European and Far Eastern pig populations have contributed maternal and paternal lineages to the foundation of African and South American breeds. Although West African pigs from Nigeria and Benin exclusively harbored European alleles, Far Eastern and European genetic signatures of similar intensity were detected in swine breeds from Eastern Africa. This region seems to have been a major point of entry of livestock species in the African continent as a result of the Indian Ocean trade. Finally, South American creole breeds had essentially a European ancestry although Asian Y-chromosome and mitochondrial haplotypes were found in a few Nicaraguan pigs. The existence of Spanish and Portuguese commercial routes linking Asia with America might have favored the introduction of Far Eastern breeds into this continent.

Two single nucleotide polymorphisms in the myostatin (GDF8) gene have significant association with muscle depth of commercial Charollais sheep.

To assess whether the same mutation(s) were responsible for similar phenotypes attributed to ovine chromosome 2 (OAR2) quantitative trait loci (QTL) in different sheep breeds, Suffolk, Texel and Charollais rams from British commercial flocks were genotyped for two single nucleotide polymorphisms (SNPs) located in the myostatin (GDF8) region of OAR2, previously detected in progeny of Belgian Texel rams exhibiting muscular hypertrophy. The first SNP (g.-2449G>C) was located upstream from the transcription start site and the second SNP (g.+6723G>A) in the 3' UTR of GDF8. The g.-2449C and g.+6723A alleles were absent in the Suffolk sires sampled, almost fixed in the Texel and segregating in the Charollais sires. Mixed model association analyses using SNP data on 338 Charollais lambs from 17 paternal half-sib families and phenotype and pedigree data on 56 500 lambs revealed that both SNPs had a significant association with muscle depth (P < 0.001). The SNPs were segregating at intermediate frequencies (p = 0.3) and exhibited strong linkage disequilibrium (r(2) = 0.90). Animals with the g.+6723AA genotype had significantly greater muscle depth than those with either the g.+6723GG or the g.+6723AG genotypes (P < 0.002), with the g.+6723A allele, the likely causative mutation, having an additive effect of 1.20 (+/-0.30) mm and a dominance effect of -0.73 (+/-0.36) mm. Based on estimated allelic effects and sample allele frequencies, the g.+6723G>A SNP explained 14% of the additive genetic variance of muscle depth. The maximum genetic variance for the trait (38%) attributed to the SNP would be attained at a g.+6723A allele frequency of 0.7. Our findings indicate that marker-assisted selection using these two GDF8 SNPs would be beneficial for the Charollais breed.

Proteomic analysis of ovine muscle hypertrophy.

Two-dimensional electrophoresis was used to investigate the effects of a QTL for muscle hypertrophy on sarcoplasmic protein expression in ovine muscles. In the Belgian Texel breed, the QTL for muscle hypertrophy is localized in the myostatin-encoding gene. Based on microsatellite markers flanking the myostatin gene, we compared the hypertrophied genotype with the normal genotype. The average age of the sheep was 3 mo. Among the 4 muscles studied, in the hypertrophied genotype only the vastus medialis was normal, whereas the semimembranosus, tensor fasciae latae, and LM were hypertrophied. In the hypertrophied genotype, these muscles showed upregulation of enzymes involved in glycolytic metabolism together with oxidative metabolism in LM. Certain chaperone proteins, including glutathione S-transferase-Pi, heat shock protein-27, and heat shock cognate-70, were also more highly expressed, probably due to increased use of energetic pathways. Expression of the iron transport protein transferrin was increased. Alpha-1-antitrypsin was the only protein showing a similar pattern of expression (i.e., less expressed) in all 4 muscles of the hypertrophied genotype. It is suggested that transferrin and alpha-1-antitrypsin may interact to reinforce myogenic proliferative signaling.

Polymorphic microRNA-target interactions: a novel source of phenotypic variation.

Studying the muscular hypertrophy of Texel sheep by forward genetics, we have identified an A-to-G transition in the 3'UTR of the GDF8 gene that reveals an illegitimate target site for microRNAs miR-1 and miR-206 that are highly expressed in skeletal muscle. This causes the down-regulation of this muscle-specific chalone and hence contributes to the muscular hypertrophy of Texel sheep. We demonstrate that polymorphisms which alter the content of putative miRNA target sites are common in human and mice, and provide evidence that both conserved and nonconserved target sites are selectively constrained. We speculate that these polymorphisms might be important mediators of phenotypic variation including disease. To facilitate studies along those lines, we have constructed a database (www.patrocles.org) listing putative polymorphic microRNA-target interactions.

The value of prior information for detection of QTL affecting longitudinal traits: an example using Von Bertalanffy growth function.

A Bayesian procedure is presented for detecting quantitative trait loci (QTL) affecting longitudinal traits. The statistical model assumes a QTL affecting the prior distribution of the parameters of a given production function, under a hierarchical Bayesian scheme. Marginal posterior distributions for the effects associated with the QTL are calculated using Markov chain Monte Carlo methods. Furthermore, the Bayesian analysis allows the use of some available relevant information that can improve the detection of the QTL substantially. To illustrate the procedure, an example of QTL detection using the Von Bertalanffy growth function is presented with a F2 pig population bred from Iberian boars and Landrace sows. Animals of the F2 population were genotyped for seven markers in chromosome 2 (SSC2). Two prior distributions for the mean effect of the parameters related with birth and adult weight were compared. On the one hand, vague prior distributions were used, and, on the other, there were assumed univariate Gaussian distributions that ensure biologically meaningful adult and birth weights on the posterior growth curves. Results from the second prior distribution supported the presence of QTL, by showing that individuals with both alleles of Iberian origin had lower rates of maturation. On the contrary, when vague priors were used, the procedure was not able to detect QTL.

Derivation of a Bayes factor to distinguish between linked or pleiotropic quantitative trait loci.

A simple procedure to calculate the Bayes factor between linked and pleiotropic QTL models is presented. The Bayes factor is calculated from the marginal prior and posterior densities of the locations of the QTL under a linkage and a pleiotropy model. The procedure is computed with a Gibbs sampler, and it can be easily applied to any model including the location of the QTL as a variable. The procedure was compared with a multivariate least-squares method. The proposed procedure showed better results in terms of power of detection of linkage when low information is available. As information increases, the performance of both procedures becomes similar. An example using data provided by an Iberian by Landrace pig intercross is presented. The results showed that three different QTL segregate in SSC6: a pleiotropic QTL affects myristic, palmitic, and eicosadienoic fatty acids; another pleiotropic QTL affects palmitoleic, stearic, and vaccenic fatty acids; and a third QTL affects the percentage of linoleic acid. In the example, the Bayes factor approach was more powerful than the multivariate least-squares approach.

Quantitative trait locus mapping for meat quality traits in an Iberian x Landrace F2 pig population.

An experimental F2 cross between Iberian and Landrace pig strains was performed to map quantitative trait loci (QTL) for diverse productive traits. Here we report results for meat quality traits from 369 F2 animals with records for pH 24 h postmortem (pH 24 h), muscle color Minolta measurements L* (lightness), a* (redness), and b* (yellowness), H* (hue angle), C* (chroma), intramuscular fat (IMF) and haematin pigment content measured in the longissimus thoracis. Pigs were genotyped for 92 markers covering the 18 porcine autosomes (SSC). Results of the genome scan show evidence for QTL for IMF (SSC6; F = 27.16), pH 24 h (SSC3; F = 7.73), haematin pigments (SSC4 and SSC7; F = 8.68 and 9.47 respectively) and Minolta color measurements L* (SSC4 and SSC7; F =16.42 and 7.17 respectively), and a* (SSC4 and SSC8; F = 8.05 and 7.36 respectively). No QTL were observed for the color measurements b*, H*, and C*. Alternative models fitting epistasis between QTL were also tested, but detected epistatic interactions were not significant at a genome-wise level. In this work we identify genomic regions related with meat quality traits. Improvement by traditional selection methods is complicated, and finer mapping would be required for their application in introgression programs.

QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects.

Results from a QTL experiment on growth and carcass traits in an experimental F2 cross between Iberian and Landrace pigs are reported. Phenotypic data for growth, length of carcass and muscle mass, fat deposition and carcass composition traits from 321 individuals corresponding to 58 families were recorded. Animals were genotyped for 92 markers covering the 18 porcine autosomes (SSC). The results from the genomic scan show genomewide significant QTL in SSC2 (longissimus muscle area and backfat thickness), SSC4 (length of carcass, backfat thickness, loin, shoulder and belly bacon weights) and SSC6 (longissimus muscle area, backfat thickness, loin, shoulder and belly bacon weights). Suggestive QTL were also found on SSC1, SSC5, SSC7, SSC8, SSC9, SSC13, SCC14, SSC16 and SSC17. A bidimensional genomic scan every 10 cM was performed to detect interaction between QTL. The joint action of two suggestive QTL in SSC2 and SSC17 led to a genome-wide significant effect in live weight. The results of the bidimensional genomic scan showed that the genetic architecture was mainly additive or the experimental set-up did not have enough power to detect epistatic interactions.

A QTL on pig chromosome 4 affects fatty acid metabolism: evidence from an Iberian by Landrace intercross.

Three Iberian boars were bred to 31 Landrace sows to produce 79 F1 pigs. Six F1 boars were mated to 73 F1 sows. The F2 progeny from 33 full-sib families (250 individuals) were genotyped for seven microsatellites spanning the length of chromosome 4. Least squares procedures for interval mapping were used to detect quantitative trait loci (QTL). A permutation test was used to establish nominal significance levels associated with QTL effects, and resulting probability levels were corrected to a genomewide basis. Observed QTL effects were (genomewide significance, position of maximum significance in centimorgans): percentage of linoleic acid in subcutaneous adipose tissue (< 0.01, 81); backfat thickness (< 0.01, 83); backfat weight (< 0.01, 80); longissimus muscle area (0.02, 83); live weight (0.19, 88); and percentage of oleic acid in subcutaneous adipose tissue (0.25, 81). Gene action was primarily additive. The Iberian genotypes were fatter, slower growing, and had lower linoleic and higher oleic acid contents than Landrace genotypes. The interval from 80 to 83 cM contains the FAT1 and A-FABP loci that have been shown previously to affect fat deposition in pigs. This is the first report of a QTL affecting fatty acid composition of subcutaneous adipose tissue in pigs and provides a guide for the metabolic pathways affected by candidate genes described in this region of chromosome 4.