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[EN] 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 work was partially funded by the Center for Industrial Technological Development (CDTI) via grant IDI-20170304 and by grant CGL-2016-80155 from the Ministry of Economy, Industry and Competitiveness (MINECO), Spain.

[EN] The adipogenic nature of the Iberian pig defines many quality attributes of its fresh meat and dry-cured products. The distinct varieties of Iberian pig exhibit great variability in the genetic parameters for fat deposition and composition in muscle. The aim of this work is to identify common and distinct genomic regions related to fatty acid composition in Retinto, Torbiscal, and Entrepelado Iberian varieties and their reciprocal crosses through a diallelic experiment. In this study, we performed GWAS using a high density SNP array on 382 pigs with the multimarker regression Bayes B method implemented in GenSel. A number of genomic regions showed strong associations with the percentage of saturated and unsaturated fatty acid in intramuscular fat. In particular, five regions with Bayes Factor >100 (SSC2 and SSC7) or >50 (SSC2 and SSC12) explained an important fraction of the genetic variance for miristic, palmitoleic, monounsaturated (>14%), oleic (>10%) and polyunsaturated (>5%) fatty acids. Six genes (RXRB, PSMB8, CHGA, ACACA, PLIN4, PLIN5) located in these regions have been investigated in relation to intramuscular composition variability in Iberian pigs, with two SNPs at the RXRB gene giving the most consistent results on oleic and monounsaturated fatty acid content., The authors would like to acknowledge the help of Inga Food S.A. and their support staff in setting up the experiment (E. Magallon, M. Ramos, L. Munoz, and P. Diaz) and Dr L. Varona from University of Zaragoza for discussion. This study was funded by the INIA grant RTA 2012-0054-C02-01 and the Centre for the Development of Industrial Technology agreement IDI-20140447.

The aim of this study was to estimate the genetic and environmental parameters and crossbreeding effects on fatty acid and fat traits in the Iberian pig. Our final goal is to explore target selection traits and define crossbreeding strategies. The phenotypes were obtained under intensive management from 470 animals in a diallelic experiment involving Retinto, Torbiscal, and Entrepelado lines. The data set was composed of backfat thickness at the fourth rib (BFT), intramuscular fat (IMF) in the longissimus thoracis (LT), and the fatty acid profile for IMF and subcutaneous fat (SCF) traits. Data were analyzed through a Bayesian bivariate animal model by using a reparameterization of Dickerson's model. The results obtained showed an important genetic determinism for all traits analyzed with heritability ranging from 0.09 to 0.67. The common environment litter effect also had an important effect on IMF (0.34) and its fatty acid composition (0.06-0.53) at slaughter. The additive genetic correlation between BFT and IMF (additive genetic correlation [] = 0.31) suggested that it would be possible to improve lean growth independent of the IMF with an appropriate selection index. Furthermore, the high additive genetic correlation ( = 0.68) found between MUFA tissues would seem to indicate that either the LT or SCF could be used as the reference tissue for MUFA selection. The relevance of the crossbreeding parameters varied according to the traits analyzed. Backfat thickness at the fourth rib and the fatty acid profile of the IMF showed relevant differences between crosses, mostly due to line additive genetic effects associated with the Retinto line. On the contrary, those for IMF crosses were probably mainly attributable to heterosis effects. Particularly, heterosis effects were relevant for the Retinto and Entrepelado crosses (approximately 16% of the trait), which could be valuable for a crossbreeding system involving these lines.

[ES] La genética y la alimentación son dos de los principales factores que afectan a la producción del cerdo Ibérico, así como a la calidad de su carne y de sus productos cárnicos. El objetivo de este estudio fue evaluar el efecto de la línea genética y de la alimentación durante el cebo, así como su interacción, sobre los parámetros productivos del cerdo Ibérico. Para ello, se utilizaron un total de 96 cerdos Ibéricos machos y castrados, que fueron divididos en 12 lotes (n=8) siguiendo un diseño factorial 4×3 con dos líneas genéticas (Retinto, RR, y Torbiscal, TT) y sus cruces recíprocos (R×T and T×R). Los cerdos fueron cebados en intensivo con tres tipos de piensos enriquecidos con tres niveles de ácido oleico (bajo, L, medio, M y alto, H). Los resultados mostraron un menor (p

[EN] This study was aimed to evaluate the effect of different genetic lines, diets and their interaction on the weight, yield, intramuscular fat content (IMF) and colour of loin (m. Longissimus dorsi) of Iberian pig. Ninety-six castrated male Iberian pigs were allotted into twelve groups (n=8) following a 4×3 factorial design with two Iberian genetic lines (Retinto, RR, and Torbiscal, TT) and their reciprocal crosses (R×T and T×R) fed in intensive conditions with three different oleic acid enriched diets (low, L, medium, M and high, H levels). Regarding loin weight and yield a significant effect of genetic line was observed due to the higher (P

The adiponectin (ADIPOQ) locus is a positional and functional candidate gene for 2 porcine chromosome 13 (SSC13) QTL influencing cholesterol (CHOL) and low-density lipoprotein (LDL) concentrations in 190-d-old pigs. By sequencing 2.37 kb of the pig ADIPOQ cDNA, we have identified 1 c.*1512G>T 3' untranslated region polymorphism that has been genotyped in a Duroc pig commercial population with records for serum lipid levels at 45 and 190 d of age. Statistical analysis of the data have revealed significant associations between the ADIPOQ genotype and CHOL (P=0.0040) and LDL (P=0.0011) concentrations at 190 d but not at 45 d. In family 3, most of the SSC13 QTL effects on LDL levels at 190 d were explained by the ADIPOQ genotype. We also found an association with triglyceride levels at 45 d (P=0.0060) but not at 190 d. Measurement of allelic mRNA imbalance demonstrated that the G and T alleles are expressed at very similar levels in muscle and fat tissues, indicating that the c.*1512G>T polymorphism does not affect transcript abundance. As a whole, results obtained in the current work as well as previous data gathered in humans and pigs provide evidence that the magnitude of associations between blood lipid phenotypes and candidate loci genotypes may vary depending on the age of the individual, therefore suggesting the existence of dynamic genotype×environment interactions changing on a temporal scale.

[EN] An experiment of a 2 x 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 (similar to 340 days and similar to 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., The authors acknowledge the technicians of the IRTA (M.J. Garcia-Santana) and of the INGAFOOD Company (Manuel Ramos, Lourdes Munoz and Pilar Diaz) for cooperating in the experimental protocol and their technical support. The work was partially funded by the Center for Industrial Technological Development (CDTI) grant IDI-20100447 and by the grant RTA2012-00054-C02-01 from the Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Spain.

The aim of this study was to estimate the genetic and environmental parameters and crossbreeding effects on fatty acid and fat traits in the Iberian pig. Our final goal is to explore target selection traits and define crossbreeding strategies. The phenotypes were obtained under intensive management from 470 animals in a diallelic experiment involving Retinto, Torbiscal, and Entrepelado lines. The data set was composed of backfat thickness at the fourth rib (BFT), intramuscular fat (IMF) in the longissimus thoracis (LT), and the fatty acid profile for IMF and subcutaneous fat (SCF) traits. Data were analyzed through a Bayesian bivariate animal model by using a reparameterization of Dickerson's model. The results obtained showed an important genetic determinism for all traits analyzed with heritability ranging from 0.09 to 0.67. The common environment litter effect also had an important effect on IMF (0.34) and its fatty acid composition (0.06-0.53) at slaughter. The additive genetic correlation between BFT and IMF (additive genetic correlation [] = 0.31) suggested that it would be possible to improve lean growth independent of the IMF with an appropriate selection index. Furthermore, the high additive genetic correlation ( = 0.68) found between MUFA tissues would seem to indicate that either the LT or SCF could be used as the reference tissue for MUFA selection. The relevance of the crossbreeding parameters varied according to the traits analyzed. Backfat thickness at the fourth rib and the fatty acid profile of the IMF showed relevant differences between crosses, mostly due to line additive genetic effects associated with the Retinto line. On the contrary, those for IMF crosses were probably mainly attributable to heterosis effects. Particularly, heterosis effects were relevant for the Retinto and Entrepelado crosses (approximately 16% of the trait), which could be valuable for a crossbreeding system involving these lines.

Genetic evaluations using purebred data alone and combined purebred and crossbred information were performed for lean meat percentage in a pig breeding scheme. One purebred (PB) model and 2 crossbred models (CCPS1 and CCPS2) were used in the analyses. Data were obtained from the Seleccion Batalle S.A. Company (Riudarenes, Spain) and spanned a period of 4 yr (2006 to 2009). The data corresponded to 3 nuclei of purebred populations, Landrace (LD), Duroc (DU), and Pietrain (PI); 1 multiplying farm with animals from a 2-way cross (TB1; DU × LD); and commercial farms with animals from a 3-way cross (TB2; TB1 × PI). Genetic parameters were similar across the models, with the exception of purebred PI. The DU and LD purebreds presented large heritabilities (0.5 to 0.6) for lean meat percentage, whereas the PI purebred showed a lower heritability (approximately 0.1) for the PB model and moderate heritability for the CCPS1 and CCPS2 models (0.2 to 0.3). The mean reliability of the predicted purebred breeding values was clearly increased when the CCPS1 and CCPS2 models were used. Moreover, a reranking of the animals with important changes in the selection decisions was observed in the PI purebred. In a simulation study, the CCPS1 model achieved a greater response to selection than the PB model for the PI purebred. On another hand, between the CCPS1 and CCPS2 models, CCPS1 was slightly superior in terms of predictive ability, exhibiting a greater robustness. These results illustrate the usefulness of using crossbred models to evaluate lean meat percentage in this pig breeding scheme.

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.

We developed and implemented change-point recursive models and compared them with a linear recursive model and a standard mixed model (SMM), in the scope of the relationship between litter size (LS) and number of stillborns (NSB) in pigs. The proposed approach allows us to estimate the point of change in multiple-segment modeling of a nonlinear relationship between phenotypes. We applied the procedure to a data set provided by a commercial Large White selection nucleus. The data file consisted of LS and NSB records of 4,462 parities. The results of the analysis clearly identified the location of the change points between different structural regression coefficients. The magnitude of these coefficients increased with LS, indicating an increasing incidence of LS on the NSB ratio. However, posterior distributions of correlations were similar across subpopulations (defined by the change points on LS), except for those between residuals. The heritability estimates of NSB did not present differences between recursive models. Nevertheless, these heritabilities were greater than those obtained for SMM (0.05) with a posterior probability of 85%. These results suggest a nonlinear relationship between LS and NSB, which supports the adequacy of a change-point recursive model for its analysis. Furthermore, the results from model comparisons support the use of recursive models. However, the adequacy of the different recursive models depended on the criteria used: the linear recursive model was preferred on account of its smallest deviance value, whereas nonlinear recursive models provided a better fit and predictive ability based on the cross-validation approach.

The primary goal of this study was to detect and confirm QTL on SSC6 for growth and fatness traits in 2 experimental F 2 intercrosses: Iberian x Landrace (IB x LR) and Iberian x Meishan (IB x MS), which were used in this study for the first time in a QTL analysis related to productive traits. For this purpose, single- and joint-population analyses with single and bivariate trait models of both populations were performed. The presence of the SSC6 QTL for backfat thickness previously identified in the IB x LR cross was detected in this population with additional molecular information, but also was confirmed in the IB x MS cross. In addition, a QTL affecting BW was detected in both crosses in a similar position to the QTL detected for backfat thickness. This is the first study in which a QTL affecting BW is detected on SSC6 in the IB x LR cross, as well as in the IB x MS resource population. Furthermore, we analyzed a previously described nonsynonymous leptin receptor (LEPR) SNP located in exon 14 (c.2002C > T) for causality with respect to this QTL within both F 2 populations. Our results supported the previously reported association between LEPR alleles and backfat thickness in the IB x LR cross, and this association was also confirmed within the IB x MS cross. An association not reported before between LEPR alleles and BW was identified in both populations.

A Bayesian threshold model was fitted to analyze the genetic parameters for farrowing mortality at the piglet level in Large White, Landrace, and Pietrain populations. Field data were collected between 1999 and 2006. They were provided by 3 pig selection nucleus farms of a commercial breeding company registered in the Spanish Pig Data Bank (BDporc). Analyses were performed on 3 data sets of Large White (60,535 piglets born from 4,551 litters), Landrace (57,987 piglets from 5,008 litters), and Pietrain (42,707 piglets from 4,328 litters) populations. In the analysis, farrowing mortality was considered as a binary trait at the piglet level and scored as 1 (alive piglet) or 0 (dead piglet) at farrowing or within the first 12 h of life. Each breed was analyzed separately, and operational models included systematic effects (year-season, sex, litter size, and order of parity), direct and maternal additive genetic effects, and common litter effects. Analyses were performed by Bayesian methods using Gibbs sampling. The posterior means of direct heritability were 0.02, 0.06, and 0.10, and the posterior means of maternal heritability were 0.05, 0.13, and 0.06 for Large White, Landrace, and Pietrain populations, respectively. The posterior means of genetic correlation between the direct and maternal genetic effects for Landrace and Pietrain populations were -0.56 and -0.53, and the highest posterior intervals at 95% did not include zero. In contrast, the posterior mean of the genetic correlation between direct and maternal effects was 0.15 in the Large White population, with the null correlation included in the highest posterior interval at 95%. These results suggest that the genetic model of evaluation for the Landrace and Pietrain populations should include direct and maternal genetic effects, whereas farrowing mortality could be considered as a sow trait in the Large White population.

The vascular cell adhesion molecule 1 (VCAM1) has a strong influence on embryonic development and on the formation of the umbilical cord and placenta. These developmental processes are crucial to ensure the success of pregnancy. In this work, we have identified two T306A and C558T single nucleotide polymorphisms (SNP) at exons 2 and 3 of the pig VCAM1 locus, respectively. The T306A substitution involves a non conservative Asn to Lys replacement at amino acid position 102, whereas the C558T polymorphism is synonymous. An in silico prediction of the consequences of the Asn₁₀₂[rightward arrow]Lys₁₀₂ mutation with the PolyPhen software revealed that it is not deleterious. The T306A SNP segregated in the Iberian, Pietrain, Duroc, Large White and Landrace breeds as well as in European wild boars. The C558T SNP also segregated and most of commercial standard breeds. The genotyping of the C558T SNP in an Iberian x Meishan intercross allowed to find a suggestive association (Bonferroni threshold, p < 0.004) between C558T genotype and time the newborn piglet needs to reach the udder (p = 0.013) as well as a significant one with time to make the first ingestion of colostrum (p = 0.003). The biological basis of these associations remains unclear and they should be interpreted with caution.

The aim of this study was to investigate chromosomal regions affecting gestation length in sows. An experimental F2 cross between Iberian and Meishan pig breeds was used for this purpose and we genotyped 119 markers covering the 18 porcine autosomal chromosomes. Within this context, we have developed a new empirical Bayes factor (BF) approach to compare between nested models, with and without the quantitative trait loci (QTL) effect, and after including the location of the QTL as an unknown parameter in the model. This empirical BF can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null QTL effects. Linkage analyses were performed in each chromosome using an animal model to account for infinitesimal genetic effects. Initially, three QTL were detected at chromosomes 6, 8 and 11 although, after correcting for multiple testing, only the additive QTL located in cM 110 of chromosome 8 remained. For this QTL, the allelic effect of substitution of the Iberian allele increased gestation length in 0.521 days, with a highest posterior density region at 95% ranged between 0.121 and 0.972 days. Although future studies are necessary to confirm if detected QTL is relevant and segregating in commercial pig populations, a hot-spot on the genetic regulation of gestation length in pigs seems to be located in chromosome 8. © 2008 The Animal Consortium.

We identified 22 polymorphisms in the adipocyte fatty-acid binding protein (FABP4) gene, a strong positional candidate gene for the FAT1 locus in porcine chromosome 4. The most informative polymorphism, an insertion/deletion in intron 1, together with a single nucleotide polymorphism in intron 3, was genotyped in a cross between Iberian and Landrace pigs. After performing QTL, single marker, and haplotype analyses, we showed that there were at least 2 quantitative trait genes in the FAT1 region and that the FABP4 polymorphism was tightly associated to fatness. A comparison of allelic frequencies in a panel of pig breeds suggested that the Del2634C polymorphism was under indirect selection. We also showed that FABP4 is tightly associated to fatness but not growth. Furthermore, a haplotype analysis suggests that there is genetic heterogeneity at the FAT1 locus within the Landrace breed.

Malic enzyme 1 (ME1) is a part of the tricarboxylate shuttle that provides NADPH and acetyl-CoA required in fatty acid biosynthesis. The pig ME1 locus maps on the proximal end of chromosome 1, where a quantitative trait loci (QTL) affecting fat deposition has been previously described. We amplified fragments of 1457 and 1459 bp that corresponded to the complete coding region and the 3'-untranslated region (UTR), respectively, of the pig ME1 gene. The sequences of these two fragments in pigs from three breeds (Landrace, Large White and Piétrain) contained five single nucleotide polymorphisms (SNP) in the 3'-UTR: C1706T, G1762T, A1807C, C1857A and T1880A. Three haplotypes were found in two generations of a selected Landrace population: H1 (C1706 G1762 A1807 C1857 A1880), H2 (C1706 G1762 A1807 C1857 T1880) and H3 (T1706 T1762 C1807 A1857 T1880). Using Bayesian association analyses, significant associations (highest posterior density at 95%) between ME1 genotype and backfat (BF) thickness at 171 days and muscular pH were found in a Landrace population.

The IGF2-intron3-G3072A substitution has been recently described as the causal factor of the imprinted QTL for fat deposition and muscle growth detected within the porcine IGF2 region. The objective of this study was to investigate the IGF2 substitution effect in a Large White outbred population and in an Iberian x Landrace F 2 cross. The results showed that the substitution has significant effects on fatness, growth, and shape traits with estimated effects in the expected direction. These results agree with those obtained in the F 2 cross, where the IGF2-intron3-G3072A substitution is segregating only in a small family. In addition, a QTL scan has been performed in the F 2 population for the traits used in the IGF2 substitution effect validation. Results of this study demonstrated that there are QTL segregating in swine chromosome 2 other than the IGF2 substitution for carcass weight, LM area, and pH measured at 24 h after slaughter. The results confirm the relevance of the IGF2 substitution, but they also show that there are still valuable mutations to be revealed in this chromosome.

The genetic basis of the main components of boar taint was investigated in intact male pigs in a commercial population. We analyzed fat androsten-one and skatole concentrations from 217 males of an outbred Landrace population. Records were normalized using a logarithm transformation and tested for normality using a Wilk-Shapiro test. Bayesian analysis was then used to map QTL in 10 candidate regions previously selected on chromosomes 1, 2, 3, 4, 6, 7, 8, 9, 10, and 13. The criterion for QTL detection was the Bayes factor (BF) between polygenic models with and without QTL effects. Both traits had considerable genetic determination, with posterior means of total heritabilities ranging from 0.59 to 0.73 for androstenone and from 0.74 to 0.89 for skatole. Positive evidence for a fat skatole QTL was detected on SSC6 (BF = 5.16); however, no QTL for androstenone were found in any of the 10 chromosomal regions analyzed. With the detection of a QTL for the fat skatole concentration segregating in this population, marker-assisted selection or even gene-assisted selection could be used once the causal mutation of the QTL was identified.

The Bayes factor (BF) procedure was applied to examine the additive genetic component of several physiological and vitality variables for newborn pigs. Nine variables were studied: heart rate, arterial oxygen saturation, rectal temperature (all at birth and 60 min later), birth weight, interval between birth and first teats contact, and interval between birth and first colostrum intake. The available numbers of data ranged from 288 (heart rate at 60 min) to 839 records (birth weight) from F(2) Iberian x Meishan newborn pigs. We compared a model with zero heritability (nonheritable) with the one where the additive genetic background was included. The BF was used to discriminate between both candidate models. Very strong evidence of genetic background was detected for heart rate 60 min after birth (BF = 48.90), and strong evidence was detected for rectal temperature at birth (BF = 13.82). Posterior modes (means) of heritabilities were 0.29 (0.32) and 0.40 (0.39), respectively. In addition, substantial evidence of absence of genetic background was detected for arterial oxygen saturation at birth.

A simulation study has been performed to evaluate the power and the rate of false positives for the detection of causal mutations under two different models of analysis. We used an F2 design generated from an F0 population of five sires of line 1 and 40 dams of line 2 to produce an F1 population of 10 sires and 80 dams. Two different locations of the causal mutation and several frequencies of the mutations in the parental populations were considered. The first model included only the genetic configuration of the mutation, while the second model also included the probability of line origin given the neutral markers. Both models performed well when the mutation at the candidate gene was the causal mutation, although a greater power was obtained using the first model, because of its relative simplicity compared to the second one. However, when the candidate gene mutation was a neutral mutation, the second model presented a lower rate of false positives than the first. Moreover, in some cases the second model allowed distinction between the neutral and the causal mutation. The F2 design has a great power to detect quantitative trait loci provided by linkage disequilibrium, but also makes it difficult to discriminate between causal and neutral mutations. Therefore a high percentage of false positives can be expected. The limitations of F2 designs for discriminating between neutral and causal mutations are discussed.

Eight physiological and vitality variables related to the first minutes of the life of Iberian x Meishan F2 piglets were analyzed. Variables included rectal temperature, arterial oxygen saturation, heart rate (all were monitored at birth and 60 min later), time to reach the udder, and time to the first colostrum intake. Litter effect within boar, a random source of variation, influenced all variables, whereas the random boar effect was not significant for heart rate and arterial oxygen saturation at birth and the time to reach the udder. Birth weight influenced rectal temperature at birth (P < 0.01) and 60 min later (P < 0.001), arterial oxygen saturation 1 h after birth (P < 0.05), heart rate 1 h after birth (P < 0.001), time to reach the udder (P < 0.05), and time to the first suckle (P < 0.01), whereas viability score influenced rectal temperatures (at birth and 60 min later; P < 0.001), and time to reach the udder (P < 0.001) and to suckle (P < 0.001). Finally, the order of birth showed significant effects for rectal temperature 1 h after birth (P < 0.001) and time to first colostrum intake (P < 0.001). Correlation coefficients between physiological variables were generally low, with the exception of the ones for rectal temperature 1 h after birth and arterial oxygen saturation 1 h after birth (0.38; P < 0.001), and for rectal temperature at birth and rectal temperature 1 h after birth (0.34; P < 0.001). Times to reach the udder and to suckle were highly correlated (0.67; P < 0.001) and also were moderately and negatively correlated with rectal temperature 1 h after birth (-0.36 and -0.38 respectively; P < 0.001). Heart rates at birth and 1 h later, as well as arterial oxygen saturation at birth and 1 h later, were not correlated, showing that the values at birth do not necessarily provide information about the physiological status of the pig 1 h after birth. The recording of physiological variables, birth weight, and viability score may be useful to identify weak piglets quickly and to establish palliative measures.

Iberian x Meishan F2 piglet's preweaning survivability was analyzed using categorical data regression procedures within the proportional hazards assumption. A frailty sire model was assumed with the litter effect treated as an additional random source of variation. Moreover, the relative birth weight within litter and the litter effect were considered time-dependent covariates that changed their values in the second day of life due to cross fostering carried out to standardize litters. Six variables had a significant effect on survivability: birth weight (P < 0.01), relative birth weight within litter (P < 0.001), rectal temperature 60 min after birth (P < 0.01), type of presentation at birth (P < 0.05), presence of stillbirths (P < 0.001), and presence of mummified fetuses (P < 0.001). Small piglets (

Summary We have characterized the near complete coding sequence of the pig pyruvate carboxylase (PC) gene in six individuals belonging to the Iberian, Large White and Pietrain breeds. The pig PC nucleotide sequence was 3.517 bp long and encoded one 1.171 amino acid protein displaying a remarkable level of amino acid identity (75–92%) with other vertebrate pyruvate carboxylase sequences. The pig PC mRNA was expressed in several tissues such as liver, backfat, abdominal fat, ovary, uterus and testicle. Sequence aligment allowed to identify one silent (C/T)837 polymorphism at exon 6 that was typed in a number of Pietrain, Landrace and Large White pigs by using a primer extension-based approach. Allelic frequencies were 0.23 (Pietrain), 0.64 (Landrace) and 0.47 (Large White) for the C allele. Radiation hybrid mapping of the pig PC locus revealed that this gene maps to 2p17, near the SW2623 and the SW256 genetic markers. Zusammenfassung Strukturelle Charakterisierung des porcinen Pyruvat-Carboxylasegens (PC) Wir haben annahernd die komplette kodierende Sequenz des Pyruvat-Carboxylasegens (PC)-Gens beim Schwein anhand von sechs Individuen der Rassen Iberisches Schwein, Large White and Pietrain charakterisiert. Die Nukleotidsequenz des porcinen PC-Gens ist 3517 Basenpaare lang und kodiert fur ein 1171 Aminosauren langes Protein, das eine bemerkenswerte Homologie von 75-92% zur Aminosaurensequenz von anderen Vertebraten aufweist. Die porcine PC-mRNA wurde in einigen Geweben z. B. Leber, Ruckenfett, Bauchfett, Ovarien, Uterus und den Hoden exprimiert. Ein Alignment der Sequenzen ermoglichte die Identifizierung eines stillen C/T837 Polymorphismus im Exon 6, der in Pietrain, Landrasse und Large White Tieren mit Hilfe einer auf Primer Extension beruhenden Methode typisiert wurde. Die Allelfrequenzen fur das C-Allel wurden bei Pietrain auf 0,23, bei Large White auf 0,47 und bei der Landrasse auf 0,64 geschatzt. Eine Radiation Hybrid Kartierung des porcinen PC-Locus zeigte, dass dieses Gen auf 2p17 in der Nahe der genetischen Marker SW2623 und SW256 liegt.

The present study investigated differences in the allocation patterns of body stores in lactating female mice from a line selected for high litter size at birth (S-line, average litter size of 20) and dams from a nonselected control line (C-line, average litter size of 10). Body weight, litter size, litter weight, and absolute and relative lipid and protein mass were measured at peak lactation (2 wk in lactation) and at weaning (3 wk in lactation). Body size in S-line females has been increased as a correlated effect of selection for high litter size at birth, allowing for larger litters and higher absolute milk production. However, these dams produce larger litters relative to their own body weight. At peak lactation, lipid and protein percentage did not differ between lines. At weaning, S-line females had a higher protein percentage (P < 0.001) and lower lipid percentage (P < 0.05) than C-line females. Apparently, S-line females produce more offspring but at a greater cost to their own metabolism. This process was insufficient to supply the offspring with adequate resources, resulting in reduced (P < 0.0001) pup development and increased (P < 0.0001) preweaning mortality rates.

Summary The importance of using fixed or random contemporary groups in the genetic evaluation of litter size in pigs was analysed by using farm and simulated data. Farm data were from four Spanish pig breeding populations, two Landrace (13 084 and 13 619 records) and two Large White (2762 and 8455 records). A simulated population (200 sows and 10 boars) selected for litter size, in which litter size was simulated using a repeatability animal model with random herd–year–season (HYS), was used to obtain simulated data. With farm data, the goodness-of-fit and the predictive ability of a repeatability animal model were calculated under several definitions of the HYS effect. A residual maximum likelihood estimator of the HYS variance in each population was obtained as well. In this sense, HYS was considered as either fixed or random with different number of individuals per level. Results from farm data showed that HYS variance was small in relation to the total variance (ranging from 0.01 to 0.04). The treatment of HYS effect as fixed, reduced the residual variance but the size of HYS levels does not explain by itself the goodness-of-fit of the model. The results obtained by simulation showed that the predictive ability of the model is better for random than for fixed HYS models. However, the improvement of predictive ability does not lead to a significant increase of the genetic response. Finally, results showed that random HYS models biased the estimates of genetic response when there is an environmental trend.

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.

The adiponectin (ADIPOQ) locus is a positional and functional candidate gene for 2 porcine chromosome 13 (SSC13) QTL influencing cholesterol (CHOL) and low-density lipoprotein (LDL) concentrations in 190-d-old pigs. By sequencing 2.37 kb of the pig ADIPOQ cDNA, we have identified 1 c.*1512GT 3' untranslated region polymorphism that has been genotyped in a Duroc pig commercial population with records for serum lipid levels at 45 and 190 d of age. Statistical analysis of the data have revealed significant associations between the ADIPOQ genotype and CHOL (P=0.0040) and LDL (P=0.0011) concentrations at 190 d but not at 45 d. In family 3, most of the SSC13 QTL effects on LDL levels at 190 d were explained by the ADIPOQ genotype. We also found an association with triglyceride levels at 45 d (P=0.0060) but not at 190 d. Measurement of allelic mRNA imbalance demonstrated that the G and T alleles are expressed at very similar levels in muscle and fat tissues, indicating that the c.*1512GT polymorphism does not affect transcript abundance. As a whole, results obtained in the current work as well as previous data gathered in humans and pigs provide evidence that the magnitude of associations between blood lipid phenotypes and candidate loci genotypes may vary depending on the age of the individual, therefore suggesting the existence of dynamic genotype×environment interactions changing on a temporal scale.

Data on 187 DNA-tested purebred Landrace pigs were used to compare heterozygous RYR1 genotypes (Nn) and normal homozygotes (NN) in performance (growth, fat deposition rate and feeding behaviour patterns), and carcass, meat and fat quality traits. From 75 to 165 days of age, live body weight (BW), ultrasonic midback (UMB) and loin (ULB) backfat measurements were recorded periodically on the same animal. Individual voluntary feed intake (DFI), number of visits (NVD) and feeding time (FTD) were measured on a daily basis using an automatic feeding system. Polynomial models with random regression coefficients were used to describe BW, UMB, ULB, DFI, NVD and FTD as a function of age. Carcass, meat and fat quality traits were analysed using a mixed model with the RYR1 genotype as a fixed effect. No significant (p

Fertility is a discrete trait with two categories (1, successful mating, 0, unsuccessful mating). A Bayesian analysis with a binary threshold animal model has been performed with 18 695 AI mating records from 1987 to 1997, concerning 4085 sows and 187 boars. The pedigree included all individuals genetically linked with data. The binary response was modeled under a probit approach. The model for liability includes paternal and maternal genetic and permanent environmental effects, 54 herd-year–season and seven order of parity effects. Posterior mean (and standard deviation) for paternal heritability was 0.028 (0.014), for maternal heritability 0.038 (0.014), and 0.028 (0.009) and 0.072 (0.017) for ratios of paternal and maternal permanent environmental effects. Posterior mean (and standard deviation) of genetic correlation between paternal and maternal genetic effects was −0.513 (0.264). Differences between parities suggest that fertility is bigger in second parity than in the first one, and decrease in subsequent parities.

Irritable bowel syndrome is the most frequently diagnosed disorder in gastroenterology. It has been demonstrated with specialized motility studies that these patients compared to healthy subjects show changes in rectoanal electrical and mechanical activity and in rectoanal sensitivity. However, until now no report has been published on morphological alterations in the rectum or the internal anal sphincter. Twenty-five consecutive patients with irritable bowel syndrome (mean age 32, range 17-47 years; 24 females) were evaluated prospectively by transrectal ultrasonography, rectal sensitivity studies, and recordings of both electrical and mechanical activity of the distal rectum and internal anal sphincter during a 2-h inter-digestive period. Ten healthy volunteers (mean age 34.5, range 19-50 years) served as a control group. Paired and non-paired Student's two-tailed t test and linear regression analysis were used. It was shown that muscle thickness of the rectum during rest (4.7 +/- 0.1 mm) was correlated neither with its rectal spike amplitude (0.73 +/- 0.1 mV) nor with rectal spike frequency (17.06 +/- 3.6 spike/2 h). In addition, the diameter of the internal anal sphincter (1.2 +/- 0.1 mm) was correlated neither with its resting pressure, nor with frequency (17.1 +/- 3.2/2 h), duration (14.9 +/- 1.5 s), or amplitude (14.1 +/- 1.9 mmHg), of inhibition of the spontaneous rectoanal inhibitory reflex. No correlation was found between ultrasonographic parameters and rectal distension variables (r = 0.03). This study demonstrates for the first time morphological anorectal changes in patients with irritable bowel syndrome compared to healthy subjects, in addition to showing that morphological changes are independent of physiological ones. Therefore both transrectal ultrasonography to determine anorectal morphology and electromanometry to assess anorectal function are important measures in the evaluation of patients with irritable bowel syndrome.

Predictions of two models were compared. The models relate ovulation rate (OR) and prenatal survival (PS) to litter size (LS): the uterine capacity model (UCM), where maximum LS is limited by uterine capacity (UC), and the threshold model (TM) whereby PS is modelled as a binary threshold trait. Records were simulated according to both models using statistics from Trench Large White gilts. Both models were able to reproduce closely the observed curvilinear relationship between OR and LS, with LS reaching a plateau at high OR. Several genetic correlations (ρg) fulfilling the conditions h20R= 0·34 and h2LS= 0·12 (the residual maximum likelihood estimates in the population) were studied by means of stochastic computer simulation. The genetic correlation between OR and LS was very sensitive to changes in h2uc, whereas ρgLS,PSwas always positive, and ρgOR,PSwas always negative. The correlation between PS and UC was larger than 0·90, except for very small h2UCThis suggests that genes affecting PS have a strong influence on UC and that PS can be a good indirect criterion to select for UC. Both models predicted that the advantage of an index combining OR and LS with respect to direct selection on LS diminishes in successive generations of selection and that the size of the experiment needed to detect significant differences is very large. Records were also simulated by halving the mean and variance of UC, so as to mimic unilateral hysterectomy-ovariectomy (UHO). If the UHO treatment results in halving UC, LS of UHO females should behave very much as half the UC of intact females.

[EN] 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 F-2 Iberian x 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, Financial support was provided by Spain's Ministerio de Ciencia y Tecnologia (AGL2000-1229-C03), Ministerio de Educacion Ciencia (AGL2004-08368-C03) and Ministerio de Ciencia e Innovacion (AGL2008-04818-C03). The authors are indebted to the staff of Nova Genetica (Solsona, Spain) for cooperating in the experimental protocol, in particular to F. Marquez, I. Riart, R. Male, F. Rovira, M. Gonzalez and E. Ramells, to M. Arque (IRTA-Lleida, Lleida, Spain) for her active and friendly collaboration during data collection and to the staff of the Escorxador Frigorific d'Osona SA (ESFOSA) for facilitating tissue sample collection at slaughter. The authors gratefully acknowledge the contributions of the INRA (France) and the SIA El Deheson del Encinar (Spain) for providing the purebred Meishan sows and Iberian boars, respectively. The research contract of J. Casellas was partially financed by Spain's Ministerio de Ciencia e Innovacion (programs Juan de la Cierva, Jose Castillejo and Ramon y Cajal). M. Martinez-Giner was funded by a fellowship from the Spain's Ministerio de Educacion y Ciencia.

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.

A considerable number of fatness QTL have been identified in growing pigs, but there is a lack of knowledge about the genetic architecture of this trait in gilts and sows. We have performed a genome scan, in 255 Iberian × Meishan F(2) sows, for backfat thickness (BF) at 150 (BF(150) ) and 210 (BF(210)) days of age, 30 days after conception (BF(30)) and 7-10 days before farrowing (BF(bf)). We have found one BF150 QTL in SSC6 (120 cM) that was highly significant (P0.001) at the chromosome-wide level and suggestive at the genome-wide level (P0.1). Ten additional chromosome-wide significant QTL were found for sow BF(150) (SSC1, SSC13), BF(210) (SSC6, SSC8, SSC15), BF(30) (SSC5, SSC6) and BF(bf) (SSC1, SSC6, SSC13). The location of several of the BF QTL varied depending on the growing and reproductive status of the sow, suggesting that part of these genetic effects may have a temporal pattern of phenotypic expression.

Genetic evaluations using purebred data alone and combined purebred and crossbred information were performed for lean meat percentage in a pig breeding scheme. One purebred (PB) model and 2 crossbred models (CCPS1 and CCPS2) were used in the analyses. Data were obtained from the Selección Batallé S.A. Company (Riudarenes, Spain) and spanned a period of 4 yr (2006 to 2009). The data corresponded to 3 nuclei of purebred populations, Landrace (LD), Duroc (DU), and Pietrain (PI); 1 multiplying farm with animals from a 2-way cross (TB1; DU × LD); and commercial farms with animals from a 3-way cross (TB2; TB1 × PI). Genetic parameters were similar across the models, with the exception of purebred PI. The DU and LD purebreds presented large heritabilities (0.5 to 0.6) for lean meat percentage, whereas the PI purebred showed a lower heritability (approximately 0.1) for the PB model and moderate heritability for the CCPS1 and CCPS2 models (0.2 to 0.3). The mean reliability of the predicted purebred breeding values was clearly increased when the CCPS1 and CCPS2 models were used. Moreover, a reranking of the animals with important changes in the selection decisions was observed in the PI purebred. In a simulation study, the CCPS1 model achieved a greater response to selection than the PB model for the PI purebred. On another hand, between the CCPS1 and CCPS2 models, CCPS1 was slightly superior in terms of predictive ability, exhibiting a greater robustness. These results illustrate the usefulness of using crossbred models to evaluate lean meat percentage in this pig breeding scheme.

Intramuscular fat (IMF) storage is a biological process with a strong impact on nutritional and technological properties of meat and also with relevant consequences on human health. The genetic architecture of IMF content and composition phenotypes has been thoroughly studied in pigs through the identification of QTL and the estimation of genetic parameters. 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 addressed 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 polymorphisms influencing IMF, cholesterol, and fatty acid contents are modulated to some extent by complex spatial 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.

We developed and implemented change-point recursive models and compared them with a linear recursive model and a standard mixed model (SMM), in the scope of the relationship between litter size (LS) and number of stillborns (NSB) in pigs. The proposed approach allows us to estimate the point of change in multiple-segment modeling of a nonlinear relationship between phenotypes. We applied the procedure to a data set provided by a commercial Large White selection nucleus. The data file consisted of LS and NSB records of 4,462 parities. The results of the analysis clearly identified the location of the change points between different structural regression coefficients. The magnitude of these coefficients increased with LS, indicating an increasing incidence of LS on the NSB ratio. However, posterior distributions of correlations were similar across subpopulations (defined by the change points on LS), except for those between residuals. The heritability estimates of NSB did not present differences between recursive models. Nevertheless, these heritabilities were greater than those obtained for SMM (0.05) with a posterior probability of 85%. These results suggest a nonlinear relationship between LS and NSB, which supports the adequacy of a change-point recursive model for its analysis. Furthermore, the results from model comparisons support the use of recursive models. However, the adequacy of the different recursive models depended on the criteria used: the linear recursive model was preferred on account of its smallest deviance value, whereas nonlinear recursive models provided a better fit and predictive ability based on the cross-validation approach.

Concern about pork quality has increased during last decades. Given the influence of fat content and composition on sensorial, nutritional, and technological variables of pork meat, an accurate knowledge about genetic control of pig lipid metabolism is required. This study focused on providing a broad characterization for serum and meat lipid trait heritability estimates in pigs. Analyses were performed on a population of 370 Duroc barrows and measured the additive polygenic background for the serum concentrations of cholesterol, triglyceride, and low- and high-density lipoproteins at 45 and 190 d of age (at slaughter), as well as intramuscular fat, cholesterol content, and C:12 to C:22 fatty acid content in longissimus thoracis et lumborum and gluteus medius muscles at slaughter. These traits were analyzed under Bayesian univariate animal linear models, and the statistical relevance of heritability estimates was evaluated through Bayes factor (BF); the model with polygenic additive effects was favored when BF1. All serum lipid traits showed relevant genetic determinism, but the BF reached greater values at 190 d of age. Serum lipid traits displayed moderate modal estimates for heritability that ranged from 0.18 to 0.30. On the other hand, the genetic determinism for meat quality traits showed a heterogeneous behavior with large and less-than-1 BF. In general, longissimus thoracis et lumborum and gluteus medius muscles showed a similar pattern, with strong evidence of polygenic additive effects for intramuscular fat and palmitic, stearic, and cis-vaccenic fatty acids content, whereas oleic and muscle cholesterol content showed moderate to weak BF with moderate heritabilities. Similarly, results regarding linoleic, arachidonic, n-3, and n-6 fatty acids suggested a moderate genetic determinism, but only in gluteus medius muscle. For the remaining traits (myristic and palmitoleic fatty acids in both muscles, along with linoleic, arachidonic, n-3, and n-6 fatty acids in the longissimus thoracis et lumborum muscle), no statistical evidence for genetic control was observed in this study. As a whole, these results confirm the complexity of lipid metabolism in pigs.

The previous results from a genome scan for total number of piglets born and number of piglets born alive in a F2 Iberian by Meishan intercross showed several single and epistatic QTL. One of the most interesting results was obtained for SSC12, where two QTL affecting both traits showed epistatic interaction. In this study, we proposed two genes (SLC9A3R1 and NOS2) as biological and potentially positional candidates underlying these QTL. Both cDNAs were characterized and 23 polymorphisms were detected. A chromosome scan was conducted with 12 markers, plus one SNP in SLC9A3R1 and one in NOS2, covering 110 cM of SSC12. The epistatic QTL (QTL1 at 15 cM and QTL2 at 97 cM) were confirmed, and SLC9A3R1 and NOS2 were mapped around the QTL1 and QTL2 regions respectively. Several SNPs in both genes were tested with standard animal model and marker assisted association tests. The most significant results were obtained with the NOS2 haplotype defined by one missense SNP c.2192C > T (Val to Ala) and a 15 bp duplication at the 3′UTR. This duplication seems to include AU-rich elements, and could be a target site for miRNA, therefore there are statistical and biological indications to consider this haplotype as the potential causal mutation underlying QTL2. SLC9A3R1 results were not conclusive. Although the interaction between the SNPs was not significant, we cannot reject the possibility of interaction of the NOS2 haplotype with other polymorphisms closely linked to the SL9A3R1 SNPs analysed. © 2009 Stichting International Foundation for Animal Genetics.

Despite the economic interest of the fatty acid profile in pigs, no gene has been convincingly associated with this trait so far. Here, the porcine microsomal triglyceride transfer protein (MTTP) gene, which plays a crucial role in the assembly of nascent lipoproteins, has been analysed as a positional candidate gene for a QTL affecting the fatty acid composition that was previously identified on chromosome 8 in an Iberian by Landrace F(2) cross. By resequencing a panel of different breeds, a non-synonymous polymorphism in a conserved residue of the lipid transfer domain of MTTP was identified. Association analyses with this polymorphism showed a strong association with the fatty acid composition of porcine fat, much stronger than the QTL effect, in the F(2) cross and in a synthetic Sino-European line. In addition, in vitro activity assays in liver protein extracts have shown that this mutation is also associated with the lipid transfer activity of the MTTP protein (P0.1). These results suggest that the detected polymorphism is a potential causal factor of the fatty acid composition QTL. There appears to be an interaction between the porcine MTTP genotype and the type of fat source in the pig diet, which would agree with the previous results on the biology of MTTP biology.

[EN] Inbreeding is a biological phenomenon of special relevance in domestic species in which its influence has been typically associated with reductions in animal fitness. Nevertheless, recent research suggests substantial founder-specific variability in terms of inbreeding depression on some productive traits. although this centred on a very reduced number of founders. This research focuses on the modelling of founder-specific inbreeding depression (FSID) effects from a more general point of view, characterizing the expected distribution of FSID effects on sow longevity. Under a change-point Weibull proportional hazards model solved through Bayesian inference, a skew-normal a priori distribution for the FSID effects of 19 founders was assumed. In terms of the deviance information criterion, this model was clearly preferred to other prior distributions for FSID effects as well as to a standard analysis of the overall inbreeding depression effect, although all models were consistent with an overall negative genetic effect of inbreeding on sow longevity. The joint posterior distribution of FSID effects showed a skewed pattern with substantial right-tail overexpression, in which the mean (0.036). mode (0.034), S.D. (0.032) and asymmetry parameter (0.045) reported a higher incidence of positive estimates (85.2%) with an unfavourable effect on sow longevity. The founder with the worst inbreeding depression effect reduced sow longevity by 32 days for 1% or 167 days for 10% partial inbreeding. As a whole, our analyses highlighted substantial variability in FSID effects, with unfavourable, neutral and even favourable influences on sow longevity. This heterogeneity could be related to an uneven distribution of the recessive deleterious genetic load among founder genomes, and also with the different selection pressures applied to each founder line. The implementation of skew-normal priors also proved an appealing way to bypass the strict scenario imposed by the standard symmetric-Gaussian distribution, allowing right- and left-tail overexpression as well as non-zero modal estimates., The research contract of J. Casellas was partially financed by the Spanish Ministry of Education and Science (the Juan de la Cierva programme) within the framework of the project AGL2004-08368-CO3. Financial support was provided by the IRTA (grant number IRTA21022). We are indebted to the staff of Nova Genética and COPAGA SCCL and, in particular, to E. Ramells, F. Marquez, R. Male¿ and F. Rovira, for their technical support. We are also indebted to two anonymous referees for their helpful comments on the manuscript.

The primary goal of this study was to detect and confirm QTL on SSC6 for growth and fatness traits in 2 experimental F(2) intercrosses: Iberian x Landrace (IB x LR) and Iberian x Meishan (IB x MS), which were used in this study for the first time in a QTL analysis related to productive traits. For this purpose, single- and joint-population analyses with single and bivariate trait models of both populations were performed. The presence of the SSC6 QTL for backfat thickness previously identified in the IB x LR cross was detected in this population with additional molecular information, but also was confirmed in the IB x MS cross. In addition, a QTL affecting BW was detected in both crosses in a similar position to the QTL detected for backfat thickness. This is the first study in which a QTL affecting BW is detected on SSC6 in the IB x LR cross, as well as in the IB x MS resource population. Furthermore, we analyzed a previously described nonsynonymous leptin receptor (LEPR) SNP located in exon 14 (c.2002CT) for causality with respect to this QTL within both F(2) populations. Our results supported the previously reported association between LEPR alleles and backfat thickness in the IB x LR cross, and this association was also confirmed within the IB x MS cross. An association not reported before between LEPR alleles and BW was identified in both populations.

A Bayesian threshold model was fitted to analyze the genetic parameters for farrowing mortality at the piglet level in Large White, Landrace, and Pietrain populations. Field data were collected between 1999 and 2006. They were provided by 3 pig selection nucleus farms of a commercial breeding company registered in the Spanish Pig Data Bank (BDporc). Analyses were performed on 3 data sets of Large White (60,535 piglets born from 4,551 litters), Landrace (57,987 piglets from 5,008 litters), and Pietrain (42,707 piglets from 4,328 litters) populations. In the analysis, farrowing mortality was considered as a binary trait at the piglet level and scored as 1 (alive piglet) or 0 (dead piglet) at farrowing or within the first 12 h of life. Each breed was analyzed separately, and operational models included systematic effects (year-season, sex, litter size, and order of parity), direct and maternal additive genetic effects, and common litter effects. Analyses were performed by Bayesian methods using Gibbs sampling. The posterior means of direct heritability were 0.02, 0.06, and 0.10, and the posterior means of maternal heritability were 0.05, 0.13, and 0.06 for Large White, Landrace, and Pietrain populations, respectively. The posterior means of genetic correlation between the direct and maternal genetic effects for Landrace and Pietrain populations were -0.56 and -0.53, and the highest posterior intervals at 95% did not include zero. In contrast, the posterior mean of the genetic correlation between direct and maternal effects was 0.15 in the Large White population, with the null correlation included in the highest posterior interval at 95%. These results suggest that the genetic model of evaluation for the Landrace and Pietrain populations should include direct and maternal genetic effects, whereas farrowing mortality could be considered as a sow trait in the Large White population.

Muscle histochemical characteristics are decisive determinants of meat quality. The relative percentage and diameters of the different muscular fiber types influence crucial aspects of meat such as color, tenderness, and ultimate pH. Despite its relevance, however, the information on muscle fiber genetic architecture is scant, because histochemical muscle characterization is a laborious task. Here we report a complete QTL scan of muscle fiber traits in 160 animals from a F(2) cross between Iberian and Landrace pigs using 139 markers. We identified 20 genome regions distributed along 15 porcine chromosomes (SSC1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, and X) with direct and(or) epistatic effects. Epistasis was frequent and some interactions were highly significant. Chromosomes 10 and 11 seemed to behave as hubs; they harbored 2 individual QTL, but also 6 epistatic regions. Numerous individual QTL effects had cryptic alleles, with opposite effects to phenotypic pure breed differences. Many of the QTL identified here coincided with previous reports for these traits in the literature, and there was overlapping with potential candidate genes and previously reported meat quality QTL.

SummaryStatistical models for genetic evaluation often make use of Gaussian distributions. However, some new statistical developments allow the use of an asymmetric distribution for the residuals. Within this context, we analysed three different patterns for the residual term on a data set consisting of 63 208 litter-size records, belonging to 19 255 sows, with a pedigree including 27 911 individuals. The three different residual distributions were: (1) Gaussian distribution, (2) asymmetric Gaussian distribution and (3) asymmetric Gaussian distribution with a hierarchical scheme for the asymmetry parameter. The operational model always included order of parity and herd-year-season as systematic effects, and the permanent environmental and infinitesimal genetic effect of each sow as random effects. The most suitable model using the deviance information criterion (DIC) and posterior predictive checking was model 3. This implies systematic, additive genetic and permanent environmental control of both litter size and the asymmetry parameter of the residual distribution. The asymmetry parameter can be understood as a measure of sensitivity to negative (or positive) environmental influences on phenotypes. The posterior mean (standard deviation) of the additive genetic variance was 0·28 (0·06) for litter size and 0·07 (0·01) for the asymmetry parameter. The posterior mean (standard deviation) of the additive genetic correlation between litter size and the asymmetry parameter was 0·21 (0·07).