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Meat quality of Iberian pigs is defined by the combination of their genetic characteristics and the particular production system. To carry out a genetic analysis of the main meat quality traits, we estimated their heritabilities, genetic correlations and the association effects of 32 selected SNPs of 12 candidate genes. A total of ten traits were measured in longissimus dorsi samples from 1,199 Iberian pigs fattened in the traditional free-range system: water holding capacity (thawing, cooking and centrifuge force water losses), instrumental colour (lightness L*, redness a* and yellowness b*), myoglobin content, shear force on cooked meat, and shear force and maximum compression force on dry-cured loin. Estimated heritability values were low to moderate (0.01 to 0.43) being the lowest for L* and the highest for cooking loss. Strong genetic correlations between water holding capacity traits (0.93 to 0.96) and between myoglobin content and a* (0.94) were observed. The association analyses revealed 19 SNPs significantly associated with different traits. Consistent and strong effects were observed between PRKAG3 SNPs (rs319678464G > C and rs330427832C > T), MYH3_rs81437544T > C, CASP3_rs319658214G > T and CTSL_rs332171512A > G and water losses. Also for CAPN1_rs81358667G > A and CASP3_rs319658214G > T and shear force. The SNPs mapping on PRKAG3 showed the highest effects on Minolta colour traits. Genotyping of these SNPs could be useful for the selection of Iberian young boars with similar estimated breeding values for productive traits.

Background Previous studies on linkage disequilibrium have investigated second order linkage disequilibrium in animal and plant populations. The objective of this paper was to investigate the genome-wide levels of third order linkage disequilibrium in a composite line founded by admixture of four Iberian pig strains. A model for the generation of third order linkage disequilibrium by population admixture is proposed. A computer Expectation-Maximization algorithm is developed and applied to the estimation of third order linkage disequilibrium at inter- and intra-chromosomal level using 26,347 SNPs typed in 306 sows. The relationship of third order linkage disequilibrium with physical distance was investigated over 35 million triplets in SSC12. Basic and normalized estimates of inter and intra-chromosomal third order linkage disequilibrium are reported. Results Genome-wide analyses revealed that third order linkage disequilibrium is rather common among linked loci in this Iberian pig line. It is shown that population admixture of multiple populations may explain the observed levels of third order linkage disequilibrium although it could be generated by genetic drift. Third order linkage disequilibrium decreases rapidly up to 4 Mb and then declines slowly. The short distances between consecutive markers explain the maintenance of the observed third order linkage disequilibria levels when using a model incorporating the break-up of disequilibrium by recombination. Genome-wide testing also revealed that only 3.6% of the normalized estimates were different from 1, − 1, 0, or from a not well-defined situation in which there is only one possible value for the third order linkage disequilibrium parameter, given allele frequencies and pairwise linkage disequilibria parameters. Conclusions Third order linkage disequilibrium is common among linked markers in the analyzed pig line and may have been generated by population admixture of multiple populations or by genetic drift. As with second order linkage disequilibrium, the absolute value of the third order linkage disequilibrium decreases with physical distance. Normalization of third order linkage disequilibrium should be avoided for closely linked bi-allelic loci. Electronic supplementary material The online version of this article (10.1186/s12863-018-0661-4) contains supplementary material, which is available to authorized users.

Although the Torbiscal line of Iberian pigs has been largely studied, some aspects of its history are not well known. In this paper, we used pedigree-based methods on a complete genealogy of 4,077 entries in order to get a comprehensive analysis of its four founder strains and to evaluate the expected genetic contribution of each ancestral strain to the successive generations of the composite Torbiscal line. Between-strain differences and specific heterotic effects on piglet weight at 50 days of age were estimated from records of 9,052 piglets born in 1,571 litters of a complete diallel cross among the four strains. Moreover, we assessed the genetic singularity of the current Torbiscal pigs by other three studies, based on whole genome SNP genotypes, focused on the measure of its genetic diversity and differentiation with respect to other domestic and wild pig populations. The STRUCTURE algorithm detected two uppermost levels of the whole population structure, corresponding to European and Asian ancestries. These results confirmed the exclusive European origin of the Torbiscal and other Iberian pigs and the admixed origin of the Duroc breed. Finally, the comparison of Torbiscal with a representative pool of Iberian pigs showed a maximum genetic differentiation in regions of chromosomes three and seven, including some genes related to the regulation of muscle development.

Spanish legislation regulates the labelling of Iberian pig meat and dry-cured products, which are labelled as "Ibérico" or "100% Ibérico" when they come from Duroc x Iberian crossbred or Iberian purebred pigs. Although the analytical authentication of breed origin is not mandatory, a genetic diagnostic tool is demanded by producers and consumers. We have designed a 64 Single Nucleotide Variant genotyping panel displaying extreme allelic frequencies between Duroc and Iberian purebred samples. Average proportions of Iberian alleles of 0.99, 0.01, 0.77 and 0.48 were estimated by admixture clustering analysis of known origin samples, for Iberian and Duroc purebred, 75% Iberian and 50% Iberian classes, respectively. A supervised analysis with 1419 samples showed some overlapping between contiguous classes, but the calculated degrees of separability ranged from 0.800 to 0.996, exceeding the threshold value (0.70) for considering suitable for prediction. Therefore, this panel is a useful genetic tool to infer purebred or crossbred Iberian origin of live animals, meat and dry-cured products.

Data of 127,800 Iberian piglets were used to study genetic parameters of mortality at birth at the piglet level. These records proceed from three data sets 4,987 litter of 2,156 sows of a dam line, 2,768 litter of 817 sows of a complete diallel cross between four Iberian strains and 7,153 litter of 2,113 sows of the Torbiscal composite line. Perinatal mortality was considered as a binary trait, and Bayesian threshold animal models were fitted to separately analyse the three data sets. The posterior means of direct heritability were 0.010, 0.004 and 0.003, and those of maternal heritability were 0.034, 0.011 and 0.014 for dam line, diallel cross and Torbiscal line, respectively. Important effects of litter size and parity order were inferred in the three data sets, of within-breed cross-breeding parameters in the diallel cross and of sex and sow handling in the Torbiscal line Therefore, the inclusion of perinatal mortality in the objective of selection is questionable in this breed and strategies for reducing piglet mortality successful in other breeds should be considered. © 2017 Blackwell Verlag GmbH

Fatty acid composition and fat desaturation+ have profound effects on meat quality. One of the major enzymes participating in fatty acid metabolism is the stearoyl-CoA desaturase (SCD), which is the key enzyme involved in the fatty acid desaturation, in particular in the synthesis of C18:1 from C18:0 and C16:1 from C16:0. Previous studies have reported a likely causal SCD haplotype (g.2108C>T, g.2228T>C, g.2281A>G) determining desaturation potential in Duroc-based populations. In the current study we have evaluated the effects of SCD polymorphisms on fatty acid desaturation and SCD gene expression in muscle and subcutaneous fat in three experimental backcrosses and validated these effects in a Chinese-European hybrid pigs. In addition, we have evaluated the joint effects of SCD polymorphisms and major mutations (LEPR c.1987C>T, RYR1c.1843C>T, MC4Rc.1426A>G) previously reported to be involved in porcine fat deposition and fatty acids metabolism, in order to clarify SCD polymorphisms’ actual effects. The obtained results from association and gene expression analyses support the SCD haplotype effects on fatty acid desaturation, and moreover on fat atherogenic and thrombogenic indexes. It also reveals potential effects on intramuscular fat content, not previously reported, likely conditional on breed fatness status. Moreover, a new polymorphism, g.2520G>A, that could impact splicing and SCD translation and which appears in complete linkage disequilibrium with the causal SCD haplotype, has been here identified. In addition, the conducted joint analyses of SCD with LEPR, RYR1 and MC4R genetic variants show complex gene relations that could hamper the discrimination of specific gene effects and the success of selection strategies., This work was funded by Ministerio de Ciencia e Innovación (MICINN) (Spain) (Grant number AGL2014-56369-C2 and AGL2013-48121-C03-3).

A trial was performed to compare the effects of different dietary sources of MUFA on the fat- ty acid (FA) composition, lipid metabolism, and gene transcription in different tissues of Iberian pigs. Twenty- seven Iberian male pigs of 28 kg live weight (LW) were divided in 2 groups and fed with 1 of 2 isocaloric diets: a standard diet with carbohydrates as energy source (CH) and a diet enriched with high-oleic sunflower oil (HO). Ham adipose tissue was sampled by biopsy at 44 and 70 kg LW. At 110 kg LW pigs were slaughtered and backfat, loin, and liver tissues were sampled. Ani- mals of the HO group showed higher MUFA content and lower SFA in all the analyzed tissues (P < 0.001). These main effects were established early during the treatment and increased only slightly along time. Small diet effects were also detected on PUFA, which showed differences according to sampling time, tissue, and lipid fraction. Effects of diet on gene expression were explored with a combined approach analyzing adipose tissue transcriptome and quantifying the expression of a panel of key genes implicated in lipogenesis and lip- id metabolism processes in backfat, muscle, and liver. Backfat transcriptome showed small effects of diet on gene expression, in number and magnitude. According to the posterior probabilities (PP) of the probe-specific expression differences between dietary groups (PP < 0.01), 37 genes were considered differentially expressed (DE). Gene ontology allowed relating them with sev- eral biological functions including lipid metabolic pro- cesses. Quantitative PCR confirmed several DE genes in adipose tissue (RXRG, LEP, and ME1; P < 0.0001, P < 0.05, and P < 0.0001, respectively), but no DE gene was found in loin or liver tissues. Joint results agree with a metabolic adjustment of adipose tissue FA levels by the subtle effect of the diet on the regulation of several lipid metabolism pathways, mainly FA oxidation and pros- tanoid synthesis, with LEP, RXRG, and PTGS2 genes playing mayor roles.

Coat colour gene variants, such as MC1R and KIT alleles, are successfully used to characterize livestock breeds and populations.

Diet influences animal body and tissue composition due to direct deposition and to the nutrients effects on metabolism. The influence of specific nutrients on the molecular regulation of lipogenesis is not well characterized and is known to be influenced by many factors including timing and physiological status. A trial was performed to study the effects of different dietary energy sources on lipogenic genes transcription in ham adipose tissue of Iberian pigs, at different growth periods and on feeding/fasting situations. A total of 27 Iberian male pigs of 28 kg BW were allocated to two separate groups and fed with different isocaloric feeding regimens Standard diet with carbohydrates as energy source (CH) or diet enriched with high oleic sunflower oil (HO). Ham subcutaneous adipose tissue was sampled by biopsy at growing (44 kg mean BW) and finishing (100 kg mean BW) periods. The first sampling was performed on fasted animals, while the last sampling was performed twice, with animals fasted overnight and 3 h after refeeding. Effects of diet, growth period and feeding/fasting status on gene expression were explored quantifying the expression of a panel of key genes implicated in lipogenesis and lipid metabolism processes. Quantitative PCR revealed several differentially expressed genes according to diet, with similar results at both timings RXRG, LEP and FABP5 genes were upregulated in HO group while ME1, FASN, ACACA and ELOVL6 were upregulated in CH. The diet effect on ME1 gene expression was conditional on feeding/fasting status, with the higher ME1 gene expression in CH than HO groups, observed only in fasting samples. Results are compatible with a higher de novo endogenous synthesis of fatty acids (FA) in the carbohydrate-supplemented group and a higher FA transport in the oleic acid-supplemented group. Growth period significantly affected the expression of most of the studied genes, with all but PPARG showing higher expression in finishing pigs according to a pattern dissimilar from the usual in cosmopolitan pig breeds. Feeding/fasting status only influenced PPARG gene transcription. The lack of effects of feeding/fasting status on lipogenic gene expression and the higher ME1 response to diet in fasting samples than in postprandial sampling, suggest the persistence of de novo lipogenesis during fasting. Overall results improve the understanding of the influence of different factors on lipid metabolism regulation in Iberian pigs. © The Animal Consortium 2016.

The complete pedigree of two closed Iberian pig lines (Gamito and Torbiscal), with 798 and 4077 reproducers, has been used to measure the evolution of coancestry (f) and inbreeding (F) for autosomal and X-linked genes along 16 and 28 respective equivalent discrete generations. At the last generation, the mean values of each line were f = 0.41 and 0.22, F = 0.35 and 0.18, fX = 0.46 and 0.22 and FX = 0.47 and 0.19, respectively. Other calculated parameters were the effective number of founders (final values, 6.8 and 35.2) and non-founders (1.5 and 2.4), founder genome equivalents (1.2 and 2.3) and effective population size (16.0 and 57.7). Measures of Torbiscal effective size based on rates of coancestry (66.1), inbreeding (65.0) and linkage disequilibrium (71.0) were estimated from whole-genome SNP genotyping data. Values of new and old inbreeding and their respective rates by generation were computed to detect purging effects of natural selection. The analysis of 6854 Torbiscal litters showed significant negative impacts of new and fast inbreeding on litter size, as expected from the purging hypothesis -0.20 born piglets per litter by a 10% of new inbreeding, and -0.03 and -0.02 piglets by 1% of total and new inbreeding rates, respectively. The analysis performed on 1274 litters of the Gamito line failed to show purging effects. The only significant results were reductions in -0.91 and -0.17 piglets by a 10% of old and X-linked genes inbreeding, respectively. These results may be useful for some practical issues in conservation programs of farm or captive wild animals. © 2016 Blackwell Verlag GmbH.

The leptin receptor (LEPR) is a key gene in the control of food intake and energy homeostasis. The sequence variant LEPR{NM-001024587.1}c.1987C>T has been associated with growth, fatness, and body composition in several pig populations. The purpose of this work was to confirm the phenotypic effects of this SNP in two new experimental backcrosses involving Iberian, Landrace, and Duroc breeds, and to evaluate the quantitative effects of the SNP on the hypothalamic expression of LEPR and two other downstream genes. Results indicate significant additive effects of the SNP on body weight, back fat thickness, and hypothalamic LEPR gene expression in both populations. Allele T fixed in the Iberian breed is systematically associated with a higher growth and fat deposition and leads to an intense reduction of LEPR hypothalamic expression, providing new functional evidence that supports the causality of the analyzed SNP with respect to previously reported and newly observed phenotypic effects. Also, some effects of the LEPR genotype on neuropeptide Y (NPY) and cocaine- and amphetamine-regulated transcript (CART) genes are detected, although they are conditioned by the breed. Finally, a change in mRNA structure and an increase in free energy is predicted for allele T, agreeing with a cis-acting functional effect on mRNA stability, which also supports the causality hypothesis. The lower expression of the LEPR gene in Iberian pigs fits with obesity by leptin resistance observed in this breed. A reduction in leptin signaling could thus be considered one of the determinants of the obese phenotype characteristic of Iberian breed. © 2010 Springer Science+Business Media, LLC.

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.

Summary Refinement of previous QTL on porcine chromosome 12 for fatty-acid composition and a candidate gene association analysis were conducted using an Iberian × Landrace cross. The concentrations of ten fatty acids were assayed in backfat tissue from which four metabolic ratios were calculated for 403 F2 animals. Linkage analysis identified two significant QTL. The first QTL was associated with the average chain length ratio and the percentages of myristic, palmitic and gadoleic acids. The second QTL was associated with percentages of palmitoleic, stearic and vaccenic acids. Based upon its position on SSC12, fatty acid synthase was tested as a candidate gene for the first QTL and no significant effects were found. Similarly, gastric inhibitory polypeptide (GIP) and acetyl-coenzyme A carboxylase alpha (ACACA) were tested as candidate genes for the second QTL using three SNPs in GIP and 15 synonymous SNPs in ACACA cDNA sequences. Two missense SNPs in GIP showed significant effects with palmitoleic and stearic fatty-acid concentration. Highly significant associations were found for two SNPs in ACACA with stearic, palmitoleic and vaccenic fatty-acid concentrations. These associations could be due to linkage disequilibrium with the causal mutations.

The effect of two diets, respectively enriched with SFA (. S) and PUFA (. P), on FA tissue composition and gene expression was studied in fattened Iberian pigs. The FA composition of adipose, muscular and liver tissues was affected by dietary treatment. S group showed higher MUFA and MUFA/SFA ratio and lower PUFA and n-. 6/. n-. 3 ratio than P group in all analyzed tissues. In muscle and liver the extracted lipids were separated into neutral lipids and polar lipid fractions which showed significantly different responses to the dietary treatment, especially in liver where no significant effect of diet was observed in NL fraction. The expression of six candidate genes related to lipogenesis and FA oxidation was analyzed by qPCR. In liver, stearoyl CoA desaturase (SCD), acetyl CoA carboxylase alpha (ACACA) and malic enzyme 1 (. ME1) genes showed higher expression in S group. SCD, ACACA, ME1, and fatty acid synthase (FASN) gene expression levels showed a wide variation across the tested tissues, with much higher expression levels observed in adipose tissue than other tissues. Tissue FA profile and gene expression results support the deposition of dietary FA, the lipogenic effect of dietary saturated fat in liver and the employment of saturated dietary fat for endogenous synthesis of MUFA in all the analyzed tissues. © 2014 Elsevier Ltd.

Background The increasing availability of DNA markers provides new metrics of inbreeding based on single nucleotide polymorphisms (SNPs), i.e. molecular inbreeding or the proportion of runs of homozygosity (ROH), as alternatives to traditional pedigree-based inbreeding coefficients. However, none of these metrics incorporate the length of ROH as an indicator of recent inbreeding. Novel inbreeding coefficients that incorporate length of ROH as a random variable with an associated density are investigated. Methods New inbreeding metrics based on the distribution of the length of ROH are proposed: (1) the Kolmolgorov–Smirnov test, (2) a function of the quantiles of the cumulative distribution function of an individual versus the population, and (3) fitting of an exponential distribution to ROH lengths (mean, variance, and the probability of drawing at random a ROH larger than a given threshold). The new inbreeding and pedigree-based metrics were compared using 217 sows of an Iberian line that belong to three groups: C1 (conservation), C2 (conservation derived from C1), and S (selected and derived from C1), with complete pedigrees and genotyped for 35,023 SNPs. Results Correlations between pedigree-based and the new genomic inbreeding coefficients ranged from 0.22 to 0.72 but most ranged from 0.60 to 0.70. The correlation between quantile chromosomal inbreeding coefficients (using molecular information of just one chromosome at the time) and chromosomal length was 0.84 (SE = 0.14), supporting the hypothesis that these coefficients incorporate information on ROH length as an indication of recent inbreeding. Kolmogorov–Smirnov and exponential chromosomal inbreeding coefficients were also correlated with chromosomal length (0.57). Chromosome 1 had the largest quantile ROH inbreeding coefficient (largest ROH sizes), whereas chromosome 10 had the lowest (shortest ROH sizes). Selection for lean growth increased ROH-based inbreeding coefficients for group S when compared to unselected groups C1 and C2. At the chromosomal level, this comparison showed that the level of autozygosity and the length of ROH for most of the autosomes increased in the selection line. Conclusions Quantile and exponential probability inbreeding coefficients using ROH length as a random variable provide additional information about recent inbreeding compared to existing inbreeding coefficients such as molecular, pedigree-based or total ROH content inbreeding coefficients. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0153-1) contains supplementary material, which is available to authorized users.

The analysis of structural genetic variability in candidate genes can make it possible to analyse the selection footprint and deepen the understanding of the genetic basis of complex traits. The leptin (LEP) and its receptor (LEPR) porcine genes are involved in food intake and energy homeostasis, and polymorphisms associated to growth and fatness traits have been detected in both genes. The main objective of this study was to explore the genetic variability of the most polymorphic regions of both genes in a variety of pig populations and wild boars from diverse European and Asian origins. In total, 54 animals were included in the analyses, with a remarkable sampling of Spanish wild boars and Iberian pigs. The sequencing allowed the identification of 69 and 26 polymorphisms in LEP and LEPR genes, respectively. Neighbour-joining trees built for the 69 haplotypes identified in the LEP and the 24 haplotypes detected in the LEPR showed the known genetic divergence between European and Asian pig breeds. A high variability of the LEP was detected in the different analysed populations providing new data for the existence of two domestication centres in Asia. In comparison to the LEP gene, the LEPR showed a lower variability, especially in the Iberian breed that showed no variability. Moreover, results of the Hudson-Kreitman-Aguadé neutrality test support a possible selection event of the LEPR gene region in this breed, potentially related with its leptin resistance pattern and good adaptation to a traditional extensive production system with strong seasonal changes of feeding resources. © 2015, Institute of Plant Genetics, Polish Academy of Sciences, Poznan.

The usefulness of molecular genetic markers as a tool for the conservation, characterisation and differentiation of domestic animal populations are shown in the following text, that summarises diverse applications to Iberian pigs.

Nucleotide sequences of mitochondrial DNA (mtDNA) cytochrome B gene (1140 bp) and control region (707 bp) were used to determine the phylogenetic relationships among 51 pig samples representing ancient and current varieties of Iberian pigs (26), Spanish wild boars (seven) and other domestic pigs (18) of cosmopolitan (Duroc, Large White, Landrace, Pietrain and Meishan) and local (Spotted Black Jabugo, Basque and Mangalitza) breeds. A neighbour-joining tree constructed from pairwise distances provide evidence of the European origin of both Iberian pigs and Spanish wild boars. The introgression of Asian mtDNA haplotypes in the genetic pool of the Iberian breed seems unlikely. Four estimates of sequence divergence between European and Asian clades were calculated from the two main domains of the D-loop region and the synonymous and nonsynonymous nucleotide substitutions in the cytochrome B gene. The time since the divergence of pig ancestors was estimated at about 600,000 years before present.

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.

Bayesian techniques allow to analyze performance data from growth functions taking into account all the information recorded from each animal, its relatives and the individuals whose data are located in the same systematic effects. This procedure was used to estimate crossbreeding parameters for growth performance up to 95 kg using two data sets from a complete diallel cross among four strains of Iberian pigs (i) 14 037 weight records from 1274 pigs with restricted feeding; and (ii) 3280 records from 450 pigs hand-fed to appetite. The intercept (a) and the slope (b) of the linear growth function were analyzed with a bivariate animal model including as covariables the crossbreeding parameters. The means of posterior distributions of heritabilities and genetic correlation were ha2 = 0.48 and 0.58, hb2 = 0.32 and 0.55, rG =0.81 and 0.99, for the two data sets, respectively. Expressed as percentage of parental strains, the values of the mean heterosis were 14.1 and 12.1 for the intercept and 14.6 and 10.9 for the slope. © 2002 Elsevier Science B.V. All rights reserved.

Genetic markers provide a useful tool toestimate pairwise coancestry betweenindividuals in the absence of a known pedigree. Inthe present work 62 pigs from two relatedstrains of Iberian breed, Guadyerbas andTorbiscal, belonging to a conservationprogramme with completely known pedigrees since1945, have been genotyped for 49microsatellites. Four coefficients thatsummarise molecular resemblance betweenindividuals together with eightestimators of coancestry have been calculatedfrom this information. Their values werecompared with the genealogical coancestry,calculated from the complete or partialpedigree. The eight estimations obtained usingmolecular information substantiallyunderestimate the coancestry calculated usingthe genealogical analysis. The correlationbetween the estimates and the genealogicalvalues was also calculated. This correlationwas high, between 0.78 and 0.93 for differentestimators, when all pairwise comparisons amongthe 62 animals were considered. However, thecorrelation decreases remarkably to 0.49–0.69and 0.37–0.47 for the Guadyerbas and Torbiscalpopulations respectively, when they wereanalysed separately. All the correlations weresimilar to those obtained when using simplecoefficients of molecular resemblance such asmolecular coancestry or similarity indexes.Finally, simulations were carried out tofurther explore the results obtained. It isconcluded that lack of information on theallele frequencies in the base population mayexplain the bias of these estimators inpopulations with complex pedigrees.

Summary The time since the divergence of European and East Asian domestic pigs and wild boars has been estimated in several phylogenetic analyses, generally based on partial mitochondrial sequences or on a small number of complete mtDNA sequences. In the present study, we obtained a refined estimate of this divergence time based on a set of 32 near-complete mtDNA sequences from wild and domestic pigs of European and Asian types, including 14 new and 18 previously published sequences. A weighted average for different functional mtDNA components resulted in an estimate of 746 000 YBP for the divergence of Asian-type from European-type pigs. In addition, our data allowed us to estimate a divergence time between wild and domestic European pigs of 8500 YBP. However, it must be considered cautiously, as most of the estimated values of this sequence divergence were not different from zero, and isolation between wild and domestic pigs has never been complete.

Genotype by environment interaction (G×E) is a potential source of reduced efficiency in genetic improvement programs in livestock. The objective of the current work consisted of checking the existence of G×E interaction in carcass traits and in intramuscular fat content (IMF) in Iberian pigs fattened in two free-range systems. Genetic component and estimated breeding values (EBV) of the percentage of hams, shoulders and loins and IMF in loin were obtained from records of 4,348 and 1,818 pigs fattened in campo (C) and montanera (M) systems, respectively. A multitrait model where the performances of each system are considered as different traits was implemented. Three selection indexes were built with different treatments about the quality trait, two of them based in the optimal trait theory. The Pearson correlation between EBV and indexes and the Spearman correlation between the rankings of progenies of 21 boars fattened in both systems were calculated. Heritability results were different in both systems (h2 range from 0.43 to 0.66 and from 0.24 to 0.33 in C and M system, respectively) and genetic correlation of same traits expressed in the two systems also pointed out to a weak G×E interaction (0.64, 0.67 and 0.66 in hams, shoulders and IMF, respectively). Pearson and Spearman correlations were always significantly different to 1. The obtained results advised to consider this G×E interaction in the analysis model of a breeding program focused on free range production system and to include IMF in the index selection assuming an optimum range for this quality trait, in order to avoid negative effects of selection for carcass performances.

[Background]: Linkage maps are essential tools for the study of several topics in genome biology. High density linkage maps for the porcine autosomes have been constructed exploiting the high density data provided by the PorcineSNP60 BeadChip. However, a high density SSCX linkage map has not been reported up to date. The aim of the current study was to build an accurate linkage map of SSCX to provide precise estimates of recombination rates along this chromosome and creating a new tool for QTL fine mapping., [Results]: A female-specific high density linkage map was built for SSCX using Sscrofa10.2 annotation. The total length of this chromosome was 84.61 cM; although the average recombination rate was 0.60 cM/Mb, both cold and hot recombination regions were identified. A Bayesian probabilistic to genetic groups and revealed that the animals used in the current study for linkage map construction were likely to be carriers of X chromosomes of European origin. Finally, the newly generated linkage map was used to fine-map a QTL at 16 cM for intramuscular fat content (IMF) measured on longissimus dorsi. The sulfatase isozyme S gene constitutes a functional and positional candidate gene underlying the QTL effect., [Conclusions]: The current study presents for the first time a high density linkage map for SSCX and supports the presence of cold and hot recombination intervals along this chromosome. The large cold recombination region in the central segment of the chromosome is not likely to be due to structural differences between X chromosomes of European and Asian origin. In addition, the newly generated linkage map has allowed us to fine-map a QTL on SSCX for fat deposition., This work was funded by MICINN projects AGL2008-04818-C03/GAN, AGL2011-29821-C02 and CSD2007-00036.

A Bayesian procedure coupled with Gibbs sampling was implemented to obtain inferences about genetic parameters and breeding values for height and diameter of 7-year-old Eucalyptus globulus Labill. is described. The data set consisted of 21 708 trees from 260 open-pollinated families taken from 10 different Australian provenances, from one Spanish population, and from two clones. The trees are distributed over eight sites in the south of Spain, with 20 blocks per site. Data were corrected for heterogeneity of phenotypic variances between blocks. In the analysis, a self-pollination rate of 30% for the open-pollinated families is assumed in the relationship matrix. The posterior means (and standard deviations) of the heritabilities of height and diameter and the genetic and phenotypic correlation were 0.217 (0.014), 0.128 (0.084), 0.768 (0.028), and 0.799 (0.003). Results from the standard restricted maximum likelihood method were 0.173, 0.113, 0.759, and 0.798, respectively. Most of the discrepancy in heritability estimates from both methods can be attributed to the adjustement of residual maximum likelihood estimates to the assumed self-pollination rate, which ignores the presence of clones in the trial. The effect of the method of prediction of breeding values (best linear unbiased prediction or Bayesian techniques) on the genetic superiority of the selected trees was not important. Differences in breeding value among provenances and among families were evidenced for both traits.

A previous study allowed the identification of two QTL regions at positions 11–34 cM (QTL1) and 68–76 cM (QTL2) on porcine chromosome SSC12 affecting several backfat fatty acids in an Iberian x Landrace F2 intercross. In the current study, different approaches were performed in order to better delimit the quoted QTL regions and analyze candidate genes. A new chromosome scan, using 81 SNPs selected from the Porcine 60KBeadChip and six previously genotyped microsatellites have refined the QTL positions. Three new functional candidate genes (ACOX1, ACLY, and SREBF1) have been characterized. Moreover, two putative promoters of porcine ACACA gene have also been investigated. New isoforms and 24 SNPs were detected in the four candidate genes, 19 of which were genotyped in the population. ACOX1 and ACLY SNPs failed to explain the effects of QTL1 on palmitic and gadoleic fatty acids. QTL2, affecting palmitoleic, stearic, and vaccenic fatty acids, maps close to the ACACA gene location. The most significant associations have been detected between one intronic (g.53840T > C) and one synonymous (c.5634T > C) ACACA SNPs and these fatty acids. Complementary analyses including ACACA gene expression quantification and association studies in other porcine genetic types do not support the expected causal effect of ACACA SNPs., This work was funded by MICINN projects AGL2008-04818-C03/GAN and CSD2007-00036. María Muñoz was funded by a FPI Ph.D. grant from the INIA Institution.

[Background]: In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besides, Iberian pigs exhibit high meat quality as well as appetite and propensity to obesity. Here we provide a genome wide analysis of nucleotide and structural diversity in a reduced representation library from a pool (n=9 sows) and shotgun genomic sequence from a single sow of the highly inbred Guadyerbas strain. In the pool, we applied newly developed tools to account for the peculiarities of these data., [Results]: A total of 254,106 SNPs in the pool (79.6 Mb covered) and 643,783 in the Guadyerbas sow (1.47 Gb covered) were called. The nucleotide diversity (1.31x10-3 per bp in autosomes) is very similar to that reported in wild boar. A much lower than expected diversity in the X chromosome was confirmed (1.79x10-4 per bp in the individual and 5.83x10-4 per bp in the pool). A strong (0.70) correlation between recombination and variability was observed, but not with gene density or GC content. Multicopy regions affected about 4% of annotated pig genes in their entirety, and 2% of the genes partially. Genes within the lowest variability windows comprised interferon genes and, in chromosome X, genes involved in behavior like HTR2C or MCEP2. A modified Hudson-Kreitman-Aguadé test for pools also indicated an accelerated evolution in genes involved in behavior, as well as in spermatogenesis and in lipid metabolism., [Conclusions]: This work illustrates the strength of current sequencing technologies to picture a comprehensive landscape of variability in livestock species, and to pinpoint regions containing genes potentially under selection. Among those genes, we report genes involved in behavior, including feeding behavior, and lipid metabolism. The pig X chromosome is an outlier in terms of nucleotide diversity, which suggests selective constraints. Our data further confirm the importance of structural variation in the species, including Iberian pigs, and allowed us to identify new paralogs for known gene families., AE is funded by the Spanish Ministry of Research PhD studentship program (FPI). Work funded by grants AGL2010-14822 to MPE, CGL2009-09346 (MICINN, Spain) to SERO , by a Consolider grant from Spanish Ministry of Research, CSD2007-00036 “Centre for Research in Agrigenomics”, and by the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013) / ERC Grant agreement n° 249894 (SelSweep project) to MAMG.

Multilocus homozygosity, measured as the proportion of the autosomal genome in homozygous genotypes or in runs of homozygosity, was compared with the respective pedigree inbreeding coefficients in 64 Iberian pigs genotyped using the Porcine SNP60 Beadchip. Pigs were sampled from a set of experimental animals with a large inbreeding variation born in a closed strain with a completely recorded multi-generation genealogy. Individual inbreeding coefficients calculated from pedigree were strongly correlated with the different SNP-derived metrics of homozygosity (r = 0.814-0.919). However, unequal correlations between molecular and pedigree inbreeding were observed at chromosomal level being mainly dependent on the number of SNPs and on the correlation between heterozygosities measured across different loci. A panel of 192 SNPs of intermediate frequencies was selected for genotyping 322 piglets to test inbreeding depression on postweaning growth performance (daily gain and weight at 90 days). The negative effects on these traits of homozygosities calculated from the genotypes of 168 quality-checked SNPs were similar to those of inbreeding coefficients. The results support that few hundreds of SNPs may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding. © 2013 Blackwell Verlag GmbH.

Data from 4150 Landrace pigs tested during the period 1989-94 for backfat thickness and age at 100 kg in an open selection nucleus were analysed with the standard restricted maximum likelihood/best linear unbiased prediction method and with a Bayesian approach based on the marginal posterior distributions of parameters of interest achieved via Gibbs sampling. Breeding values and fixed effects were sampled from normal distributions and (co)variance components from inverted Wishart distributions. The Bayesian analysis indicated that the selection was effective for both traits. Assuming flat priors for the (co)variance components, the posterior means of the annual rates of response to selection for both traits were −0·473 days and −0·212 mm. The influence of informative priors constructed from (co)variances estimated in the French Landrace breed on inferences about genetic and common environmental parameters, genetic group effects and total and annual responses was also examined.

Studies of the variation in recombination rate across the genome provide a better understanding of evolutionary genomics and are also an important step towards mapping and dissecting complex traits in domestic animals. With the recent completion of the porcine genome sequence and the availability of a high-density porcine single nucleotide polymorphism (SNP) array, it is now possible to construct a high-density porcine linkage map and estimate recombination rate across the genome. A total of 416 animals were genotyped with the Porcine SNP60BeadChip, and high-density chromosome linkage maps were constructed using CRI-MAP, assuming the physical order of the Sscrofa10 assembly. The total linkage map length was 2018.79 cM, using 658 meioses and 14 503 SNPs. The estimated average recombination rate across the porcine autosomes was 0.86 cM/Mb. However, a large variation in recombination rate was observed among chromosomes. The estimated average recombination rates (cM/Mb) per chromosome ranged from 0.48 in SSC1 to 1.48 in SSC10, displaying a significant negative correlation with the chromosome sizes. In addition, the analysis of the variation in the recombination rates taking 1-Mb sliding windows has allowed us to demonstrate the variation in recombination rates within chromosomes. In general, a larger recombination rate was observed in the extremes than in the centre of the chromosome. Finally, the ratio between female and male recombination rates was also inferred, obtaining a value of 1.38, with the heterogametic sex having the least recombination., This work was funded by MICINN projects AGL2008-04818-C03/GAN and CSD2007-00036. María Muñoz was funded by an FPI PhD grant from the INIA institution. Yuliaxis Ramayo-Caldas was funded by an FPU PhD grant from Spanish Ministerio de Educación.

BackgroundThe traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP) and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses.ResultsThree generations (F3, Backcross 1 and Backcross 2) of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes.ConclusionsThe use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine genome annotation., This work was funded by MICINN projects AGL2008-04818-C03/GAN and CSD2007-00036. DPM was funded by a FPI Ph.D grant from the Spanish Ministerio de Educación (BES-2009-025417). YR was funded by a FPU Ph.D grant from the Spanish Ministerio de Educación (AP2008-01450).

Leptin signalling plays a fundamental role in growth, fatness and body composition. The aim of this study was to investigate the porcine LEP gene sequence in an Iberian × Landrace experimental cross to identify polymorphisms associated with productivity and quality traits. Because of the documented effects on these traits of the LEPR c.1987C>T polymorphism, the LEP and LEPR c.1987C>T polymorphisms and their interactions have been jointly investigated. The LEP gene sequencing has allowed the identification of 39 polymorphisms, eight of which are novel. Three intronic SNPs, LEP g.1382C>T, LEP g.1387C>T and LEP g.1723A>G, have been genotyped, and association analyses have been carried out. Analyses of LEP g.1387C>T, fully linked to LEP g.1382C>T, have revealed additive effects on live and carcass weights and dominant effects on several backfat thickness measurements. Novel effects of both LEP and LEPR polymorphisms on fatty acid composition in subcutaneous fat have been detected, probably mediated through the effects on fatness. The results reported here suggest that the T alleles of both LEP g.1387C>T and LEPR c.1987C>T, which are fixed in the Iberian pigs, would lead to an increase in growth, fatness and saturated fatty acid content in fat, which could be explained by an increased feed intake., This work was funded by MICINN project AGL2008-04818-C03/GAN. Dafne Pérez-Montarelo was funded by an FPI PhD grant from the Spanish Ministerio de Educación (BES-2009-025417).

Polymorphisms MC4R c.1426A>G (p.Asp298Asn) and LEPR c.2002C>T (p.Leu663Phe) have been associated in pigs with feed intake, growth and fatness. Our aims were to analyze how these polymorphisms influence production and quality traits in Duroc × Iberian crossbred pigs, and moreover evaluate how the effects of gender and Duroc line were affecting these traits. Significant effects of gender, Duroc sire line and LEPR c.2002C>T mutation, were detected on the main traits. LEPR c.2002T allele increased body weight (2.5 ± 0.7. kg), backfat thickness (1.5 ± 0.4. mm), loin intramuscular fat (0.7 ± 0.2 %), and lightness (1.0 ± 0.3); however it was decreasing premium cuts yield (-0.9 ± 0.2%). Allele c.2002T increased SFA (0.60 ± 0.12 %), and decreased MUFA (-0.35 ± 0.12%) and PUFA (-0.25 ± 0.06%). No significant effects of MC4R c.1426A>G SNP were identified. A genetic test based on the LEPR c.2002C>T SNP may be useful to select Duroc sires to reduce undesirable heterogeneity of carcasses and premium cuts of crossbred animals. © 2010 The American Meat Science Association., This study was financed by the FIT-2006-060000 grant.

Background The aim of this work was to study the effects on litter size of variants of the porcine genes RBP4, ESR1 and IGF2, currently used in genetic tests for different purposes. Moreover, we investigated a possible effect of the interaction between RBP4-MspI and ESR1-PvuII polymorphisms. The IGF2-intron3-G3072A polymorphism is actually used to select lean growth, but other possible effects of this polymorphism on reproductive traits need to be evaluated. Methods Detection of polymorphisms in the genomic and cDNA sequences of RBP4 gene was carried out. RBP4-MspI and IGF2-intron3-G3072A were genotyped in a hyperprolific Chinese-European line (Tai-Zumu) and three new RBP4 polymorphisms were genotyped in different pig breeds. A bivariate animal model was implemented in association analyses considering the number of piglets born alive at early (NBA12) and later parities (NBA3+ ) as different traits. A joint analysis of RBP4-MspI and ESR1-PvuII was performed to test their possible interaction. In the IGF2 analysis, paternal or maternal imprinting effects were also considered. Results Four different RBP4 haplotypes were detected (TGAC, GGAG, GAAG and GATG) in different pig breeds and wild boars. A significant interaction effect between RBP4-MspI and ESR1-PvuII polymorphisms of 0.61 ± 0.29 piglets was detected on NBA3+. The IGF2 analysis revealed a significant increase on NBA3+ of 0.74 ± 0.37 piglets for the paternally inherited allele A. Conclusions All the analyzed pig and wild boar populations shared one of the four detected RBP4 haplotypes. This suggests an ancestral origin of the quoted haplotype. The joint use of RBP4-MspI and ESR1-PvuII polymorphisms could be implemented to select for higher prolificacy in the Tai-Zumu line. In this population, the paternal allele IGF2-intron3-3072A increased litter size from the third parity. The non-additive effects on litter size reported here should be tested before implementation in other pig breeding schemes.

Iberian pigs and wild boars are the source of highly priced meat and dry-cured products. Iberian maternal origin is mandatory for labeled Iberian products, making necessary the authentication of their maternal breed origin. Discrimination between wild and domestic pig maternal origin may be useful to distinguish labeled wild boar meat obtained from hunting or farming. In order to detect useful polymorphisms to trace Iberian, Duroc and wild boar maternal lineages, we herein investigated the complete porcine mitochondrial DNA (mtDNA) using three complementary approaches. Near-complete mtDNA sequences (16989 bp), excluding the minisatellite present in the displacement loop region (D-loop), were successfully determined in six Iberian pigs, two Duroc and six European wild boars. To complete the mtDNA analysis, the D-loop minisatellite region was also analyzed in the same set of samples by amplification and capillary electrophoresis detection. Finally, the frequencies of Asian and European Cytochrome B (Cyt B) haplotypes were estimated in Iberian (n = 96) and Duroc (n = 125) breeds. Comparison of near-complete mtDNA sequences revealed a total of 57 substitutions and two Indels. Out of them, 32 polymorphisms were potential Iberian markers, 10 potential Duroc markers and 16 potential wild boar markers. Fourteen potential markers (five Iberian and nine Duroc), were selected to be genotyped in 96 Iberian and 91 Duroc samples. Five wild boar potential markers were selected and tested in samples of wild boars (73) and domestic pigs including 96 Iberian, 16 Duroc, 16 Large White and 16 Landrace. Genotyping results showed three linked markers (m.7998C>T, m.9111T>C, m.14719A>G) absent in Duroc and present in Iberian pigs with a frequency 0.72. Six markers (m.8158C>T, m.8297T>C, m.9230G>A, m.11859A>G, m.13955T>C, m.16933T>C), three of them linked, were absent in Iberian pigs and present in Duroc with a joint frequency of almost 0.50. Finally three linked markers (m.7188G>A, m.9224T>C, m.15823A>G) were solely detected in wild boars with a frequency 0.22. The D-loop minisatellite results showed overlapping ranges of fragment sizes and suggested heteroplasmy, a result that nullify the use of this region for the development of breed diagnostic markers. The Cyt B haplotype results showed the presence of European haplotypes in Iberian while one of the Asian haplotypes was detected in Duroc with a frequency 0.22, linked to the Duroc marker m.9230G>A. Our results are valuable to resolve the problems of Iberian and wild boar maternal origin determination but additional markers are required to achieve totally useful genetic tests. © The Animal Consortium 2009.

The objective of this work was to analyse the porcine Fatty acid binding protein 2, intestinal (FABP2) gene as a candidate gene for a fatty acid composition quantitative trait loci (QTL) previously described on porcine chromosome 8 in an Iberian by Landrace F2 cross (IBMAP). Re-sequencing of the porcine FABP2 gene in three Iberian and eight Landrace parental animals resulted in the identification of three single-nucleotide polymorphisms, all of them localized in intron 1. The polymorphism FABP2:g.412T>C, localized in intron 1, and two additional microsatellites were genotyped in the IBMAP population in order to perform an association test of the FABP2 gene and to better define the QTL position previously described. Association analyses of the FABP2:g.412T>C with the fatty acid composition traits were not significant in simple association and marker-assisted association tests, suggesting that the FABP2 region sequenced is not responsible for the QTL. However, the addition of three new markers to the pedigree allowed us to define the S0144–SW61 marker interval as the most likely QTL position, facilitating the future study of other candidate genes for this QTL., Work funded by grants from INIA (Acción especial CPE03-010-C3) and MCYT (AGF99-0284-CO2-02). We are indebted to NOVA GENETICA (Lleida, Spain) and SIA ‘Dehesón del Encinar’ (Oropesa, Spain) and their staff for providing the experimental pigs. J. Estellé is recipient of a FPU fellowship from the Spanish Ministerio de Educación y Ciencia. R.N. Pena holds a contractual grant from INIA.

Simulation results of closed MOET schemes have evidenced several problems issuing from selection in small populations using family information and diverse modifications of the original schemes have been proposed. Mate selection, based on linear programming techniques, includes most of the desirable properties of other methods and offers additional advantages. Some applications of this technique to improve the results of dairy cattle MOET schemes with hierarchical and factorial mating systems have been analysed in this note by computer simulation. Other applications of the method are also discussed. © 1991, British Society of Animal Science. All rights reserved.

Genetic progress for reproductive performance in pigs is limited by mothering ability. It is a critical aspect for dam lines, in which litter weight at weaning could be included with litter size in the selection goal. Our objective was to investigate in Iberian pigs the genetic basis of the number of alive born piglets (NBA) and the litter weight at 21days (LW21) over the successive parities (t). Records for NBA were available from 6,775 litters born from 1,893 sows of the Torbiscal line, and LW21 records proceeded from 1,431 sows and 2,963 litters without crossfostering. Genetic parameters were estimated using an animal model with repeatability, a multi-trait animal model, and a random regression model. Estimated values of heritabilities for NBA and genetic correlations between parities confirm a partially different genetic control of prolificacy at parity 1 and at later parities. Results for LW21 indicate that this trait may be partially controlled by different genes at the first two parities and at the later ones. Estimated genetic parameters for NBA (t = 1), NBA (t >/= 2), LW21 (t /= 3) were: heritability, hE2 = 0.15, 0.12, 0.22 and 0.15, respectively, and coefficient of permanent environmental effects, pE2 = 0.05, 0.02 and 0.24, respectively for the three last traits. The values of genetic correlations ranged from 0.44 to 0.84. A multitrait approach would be useful to estimate accurate genetic parameters, and to improve the low persistency of reproductive performance in the later parities of Iberian sows. La mejora genética de la eficiencia reproductiva en cerdos está limitada por su aptitud maternal. Es éste un aspecto crítico en las líneas maternas, en las que el peso de la camada al destete podría ser incluido junto al tamaño de camada en el objetivo de selección. El objetivo del trabajo fue investigar en cerdos Ibéricos la base genética del número de lechones nacidos vivos (NBA) y el peso de camada a 21 días (LW21) a lo largo de los sucesivos partos (t). Se dispuso de registros de NBA de 6.775 camadas nacidas de 1.893 cerdas, y registros de LW21 procedentes de 1.431 cerdas y 2.963 camadas sin adopciones. Se estimaron parámetros genéticos mediante tres modelos: con repetibilidad, multicarácter y de regresión aleatoria. Los valores de las heredabilidades y las correlaciones genéticas entre NBA en diferentes partos confirman su control genético, parcialmente distinto en el parto primero y posteriores. Los resultados para LW21 indican que este carácter puede estar parcialmente controlado por diferentes genes en los dos primeros partos y en los sucesivos. Los parámetros genéticos estimados para NBA (t = 1), NBA (t >/= 2), LW21 (t /= 3) fueron: heredabilidad, hE2 = 0,15, 0,12, 0,22 y 0,15, respectivamente, y coeficiente de efectos de ambiente permanente, pE2 = 0,05, 0,02 y 0,24, respectivamente para los tres últimos caracteres. El rango de las correlaciones genéticas fue de 0,44 a 0,84. Un enfoque genético multicarácter sería útil para estimar parámetros genéticos precisos y mejorar la escasa persistencia del rendimiento reproductivo en los últimos partos.

[EN] Genetic diversity measures support the conservation decisions aiming to maintain the genetic flexibility of animal populations and breeds. Many of these measures utilize neutral genetic markers and are based on classical concepts as coancestry and expected heterozygosity. As a component of genetic diversity, allelic richness is also important in conservation genetics. Its measurement requires that variations of sample size be taken into account using either the rarefaction and extrapolation techniques. Methods to estimate genetic diversity and allelic richness were compared in this study. DNA samples from 68 wild boars and 234 domestic pigs of the Duroc and Iberian breeds, including 63 animals of the Torbiscal and Guadyerbas Iberian lines, were genotyped for 18 microsatellites (one per autosome). As the results outline, the rank of these pig populations according to their contributions to the diversity will be different depending on the criteria utilized, because genetic diversity and private allelic richness do not exactly address the same type of diversity. Rarefaction and extrapolation-based techniques also produce partially discrepant results. The desirable integration of allelic richness into the diversity theory poses at the moment some unsolved difficulties., [ES] Diversas medidas de diversidad genética sustentan las tácticas conservacionistas que procuran mantener la flexibilidad genética de poblaciones animales y razas domésticas. Muchas de estas medidas utilizan marcadores genéticos neutrales y se basan en conceptos clásicos como el parentesco y la heterocigosidad esperada. Como componente de la diversidad genética, la riqueza alélica tiene asimismo importancia en la genética de la conservación. Su medida requiere tener en cuenta las variaciones de tamaño muestral mediante técnicas de rarefacción o extrapolación. En este estudio se han comparado métodos de análisis de diversidad genética y riqueza alélica. Se genotiparon para 18 microsatélites (uno por autosoma) muestras de ADN de 68 jabalíes y 234 cerdos domésticos de las razas Duroc e Ibérico, incluyendo 63 animales de las líneas de cerdo Ibérico Torbiscal y Guadyerbas. Los resultados indican que la ordenación de estas poblaciones de acuerdo a sus contribuciones a la diversidad total se modifica en función de los criterios empleados, ya que diversidad genética y riqueza de alelos privados no contemplan el mismo tipo de diversidad. Asimismo, las técnicas empleadas de rarefacción o extrapolación dan lugar a resultados parcialmente discrepantes. La deseable integración de la riqueza alélica en la teoría de la diversidad genética plantea algunas dificultades no resueltas por el momento., This research was funded by INIA RZ03-010 grant.

The effects of physical activity on performance, carcass traits, Psoas major lysosomal and exoprotease acitivies and meat quality were studied in 24 castrated male Iberian pigs during the last fattening period (from 111.1 ± SD 5.2 kg). Pigs were randomly distributed in three groups. Two groups receiving the same diet were reared in confinement, one housed in individual pens of 8 m2 (sedentary group) and the other was housed outdoor with daily (up to 2 km) forced walking (exercise group).;one group was reared under the traditional production system walking daily several km and fed mostly with acorn from Quercus ilex and Quercus rotundifolia and grass (free-range group). No differences were found in performance and carcass traits. In exercised pigs a lower activity of cathepsin B + L and total cathepsins (P < 0.05) was observed. Exercise induced the inhibition of dipeptidyl peptidases II and III and arginyl aminopeptidase and the activation of dipeptidyl peptidases IV and leucyl aminopeptidase (P < 0.05). Although no effects on total free amino acids in Psoas major muscle were observed the concentration of branched chain amino acids decreased in the free-range pig group probably related to an increase in physical activity. Exercise had no effects in Psoas major postmortem tenderness and water holding capacity. © 2007.

The objective of this study was to search for polymorphisms in the coding region of the estrogen receptors 1 and 2 (ESR1 and ESR2 )and to analyze the effects of these variants and the well known intronic ESR1 Pvu II polymorphism on litter size in a Chinese-European pig line. We identified five silent single nucleotide polymorphisms (SNP) in the ESR1 cDNA: c.669T > C (exon 3), c.1227C > T (exon 5), c.1452C > T (exon 7), c.1665T > C and c.1755A > G (exon 8). One pair of these SNP (c.1665T > C and c.1755A > G) co-segregated in the analyzed line, and the SNP c.669T > C showed the same segregation pattern as the Pvu II polymorphism. These polymorphisms were tested in this study, although the c.1452C > T SNP within exon 7 was not analyzed due to its low informativeness. In the ESR2 cDNA, one missense SNP was found within exon 5, which caused an amino acid substitution in the coded protein: "c.949G > A (p.Val317Met)" and was tested on sow litter size. Information on 1622 litter records from 408 genotyped sows was analyzed to determine whether these SNP influenced the total number of piglets born (TNB) or the number of born alive (NBA). The polymorphisms ESR1: [Pvu II; c.669T > C], ESR1: [c.1665T > C; c.1755A > G] and ESR2: c.949G > A showed no statistically significant association with litter size. However, the ESR1: c.1227T allele was significantly associated with TNB. The additive substitution effect was estimated to be 0.40 piglets born per litter (P < 0.03), and no dominance effects were observed. This SNP could be useful in assisted selection for litter size in some pig lines, as a new genetic marker in linkage disequilibrium with the causative mutation.

The melanocortin receptor 4 (MC4R) gene is implicated in the regulation of feeding behaviour and body weight in humans and mice. A missense mutation (Asp298Asn) located in a highly conserved region of this gene has clearly been associated with backfat depth, feed intake and growth rate in different porcine lines. In this work the complete coding region of the gene was sequenced in samples from six pigs of a commercial hybrid line and two polymorphisms were detected at positions 709 (C/T) and 1426 (G/A). The last one corresponds to the missense mutation, and has been genotyped in 333 animals with phenotypic records and 68 out of their 81 parents. An association study of these genotypes with several performance and quality traits was performed within the statistical animal model framework. The results confirmed the effect of the missense mutation on growth and fat deposition traits (live weight at 140d and backfat depth), and supported new effects on carcass composition (loin and shoulder weights) and traits related to fat and meat quality (profile of fatty acids; muscle Minolta L*, a* and Ho colour parameters). A transmission-disequilibrium test provided no evidence of spurious association due to population stratification. © 2005 Elsevier Ltd. All rights reserved.

Within the area of sex allocation, one of the topics that has attracted a lot of attention is the sex ratio problem. Fisher (1930) proposed that equal numbers of males and females have been promoted by natural selection and it has an adaptive significance. But the empirical success of Fisher's theory remains doubtful because a sex ratio of 0.50 is also expected from the chromosomal mechanism of sex determination. Another way of approaching the subject is to consider that Fisher's argument relies on the underlying assumption that offspring inherit their parent's tendency in biased sex ratio and therefore that genetic variance for this trait exists. Here, we analyzed sex ratio data of 56,807 piglets coming from 550 boars and 1893 dams. In addition to classical analysis of heterogeneity we performed analyses fitting linear and threshold animal models in a Bayesian framework using Gibbs sampling techniques. The marginal posterior mean of heritability was 2.63 × 10−4 under the sire linear model and 9.17 × 10−4 under the sire threshold model. The probability of the hypothesis p(h2 = 0) fitting the last model was 0.996. Also, we did not detect any trend in sex ratio related to maternal age. From an evolutionary point of view, the chromosomal sex determination acts as a constraint that precludes control of offspring sex ratio in vertebrates and it should be included in the general theory of sex allocation. From a practical view that means that the sex ratio in domestic species is hardly susceptible to modification by artificial selection.

Although the function of the OCA2 gene product has not been totally clarified, variation in OCA2 has been associated with skin and hair pigmentation in human and mouse. However, its contribution to skin colour in domestic species has not been reported. In this study, cDNA and intron 9 sequences of the porcine OCA2 gene have been characterized in several pig populations. The cDNA sequence alignment of 20 animals from eight porcine populations allowed the identification of 10 single nucleotide polymorphisms (SNPs); five of the 10 SNPs were non-synonymous. The intron 9 sequence alignment of 12 animals belonging to four pig populations revealed four additional SNPs. Skin colour variation was analysed in a red strain of Iberian pigs with segregation of three SNPs forming two OCA2 intragenic haplotypes. Results from this study provide evidence of a suggestive dominant effect of haplotypes on colour intensity and indicate an important contribution of additive polygenic effects (h2 = 0.56 ± 0.21) to the variance of this trait. © 2005 International Society for Animal Genetics.

The census and structure of Iberian pig breed have experienced important changes along the last decades. Bayesian methods based on multilocus genotypes have been applied for ascertaining the actual breed structure and for identifying genetically distinctive populations. DNA samples from 170 Iberian pigs previously assigned to the strains or varieties Torbiscal, Guadyerbas, Retinto, Entrepelado and Lampiño and 64 Duroc pigs were genotyped for 36 microsatellites. A best partition of only five clusters was estimated in the clustering analysis at group level, when the previous assignation to populations was taken into account. But the individual-based assessment of population structure, ignoring the previous assignation of animals to populations, showed a more complex partition of ten clusters. Results of admixture analyses for artitioning individuals into the inferred clusters showed an important proportion of admixed individuals pre-assigned to the Retinto, Entrepelado and Lampiño varieties. The frequencies of private alleles of the MC1R gene also evidenced an important genetic flow between these varieties. The future definition of conservation units in the Iberian breed should consider these results. El censo y la estructura de la raza porcina Ibérica han experimentado cambios importantes durante las últimas décadas. Se han utilizado métodos bayesianos basados en genotipos multigénicos para discernir la actual estructura de la raza e identificar en ella poblaciones genéticamente singulares. Con este objetivo, se genotiparon 36 microsatélites en muestras de ADN procedentes de 170 cerdos Ibéricos asignados previamente a las estirpes o variedades Torbiscal, Guadyerbas, Retinto, Entrepelado y Lampiño además de 64 cerdos Duroc. Cuando se tuvo en cuenta esta asignación previa en el análisis, se obtuvo una partición óptima de sólo cinco clases, una de las cuales agrupaba las variedades Retinto y Entrepelado. El análisis individual, ignorando la asignación previa de los animales a las razas o variedades, permitió inferir una partición más compleja de diez clases. Los resultados de los análisis con modelos de mestizaje mostraron una importante proporción de animales mestizos preasignados a las variedades Retinto, Entrepelado y Lampiño. Las frecuencias de los alelos específicos del gen MC1R confirmaron el importante flujo genético producido entre estas variedades. Una futura definición de unidades de conservación en la raza Ibérica debería considerar estos resultados.