J. L. Noguera

A comparison of carcass, meat quality and histochemical characteristics of Iberian (Guadyerbas line) and Landrace pigs

Carcass, meat quality and histochemical traits were studied in 20 Landrace (LR) pigs from a maternal line and 12 Iberian pigs (IB) from the Guadyerbas line, including boars and gilts. The animals were reared under commercial intensive management and fed ad libitum from 27 kg liveweight (12 weeks of age) to 100 kg for LR, while IB pigs were 6 weeks older in order to reach the tentative 100 kg slaughter weight at the same time. Actual LR and IB slaughter weights were 105±10 and 118±11 kg, respectively. Iberian pigs had higher killing out percentage (78.6 vs. 72.4, P<0.001) and backfat depth (48.1 vs. 20.7 mm, P<0.001) than LR pigs. Higher pH 24 h post-mortem were observed in m. longissimus lumborum and m. semimembranosus muscles of IB than of LR breeds. Also, IB breed had higher haem pigment contents than LR. Iberian pigs showed higher intramuscular fat percentage (3.91 vs. 0.66 in longissimus, P<0.001), more saturated and monounsaturated backfat and lower concentrations of C18:2 and C18:3 than LR pigs. Muscle showed a more oxidative metabolism in IB than in LR pigs. The proportion of type I fibres was higher (12.09 vs. 9.09%, P<0.001) and their diameter was larger (44.37 vs. 40.83 μm, P<0.05) in IB than in LR pigs, whereas the opposite occurred for type 2B fibres proportion and diameter. The percentage of intramuscular fat in IB pigs was positively correlated (P<0.05) with the proportion of type I fibres.

Fine mapping of porcine chromosome 6 QTL and LEPR effects on body composition in multiple generations of an Iberian by Landrace intercross.

The leptin receptor gene (LEPR) is a candidate for traits related to growth and body composition, and is located on SSC6 in a region where fatness and meat composition quantitative trait loci (QTL) have previously been detected in several F2 experimental designs. The aims of this work were: (i) to fine map these QTL on a larger sample of animals and generations (F3 and backcross) of an Iberian x Landrace intercross and (ii) to examine the effects of LEPR alleles on body composition traits. Eleven single nucleotide polymorphisms (SNPs) were detected by sequencing LEPR coding regions in Iberian and Landrace pig samples. Three missense polymorphisms were genotyped by pyrosequencing in 33 F0, 70 F1, 418 F2, 86 F3 and 128 individuals coming from the backcross of four F2 males with 24 Landrace females. Thirteen microsatellites and one SNP were also genotyped. Traits analysed were: backfat thickness at different locations (BF(T)), intramuscular fat percentage (IMF(P)), eye muscle area (EM(A)), loin depth (LO(D)), weight of shoulder (SH(W)), weight of ribs (RIB(W)) and weight of belly bacon (BB(W)). Different statistical models were applied in order to evaluate the number and effects of QTL on chromosome 6 and the possible causality of the LEPR gene variants with respect to the QTL. The results support the presence of two QTL on SSC6. One, at position 60-100 cM, affects BF(T) and RIB(W). The other and more significant maps in a narrow region (130-132 cM) and affects BF(T), IMF(P), EM(A), LO(D), SH(W), RIB(W) and BB(W). Results also support the association between LEPR alleles and BF(T) traits. The possible functional implications of the analysed polymorphisms are considered.

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

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

Single- and joint-population analyses of two experimental pig crosses to confirm quantitative trait loci on Sus scrofa chromosome 6 and leptin receptor effects on fatness and growth traits.

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.

Genome-wide association study for intramuscular fatty acid composition in an Iberian × Landrace cross

The lipid content and fatty acid (FA) profile have an important impact in human health as well as in the technological transformation and nutritional and organoleptic quality of meat. A genome-wide association study (GWAS) on 144 backcross pigs (25% Iberian × 75% Landrace) was performed for 32 traits associated with intramuscular FA composition and indices of FA metabolism. The GWAS was carried out using Qxpak 5.0 and the genotyping information obtained from the Porcine SNP60K BeadChip (Illumina Inc., San Diego, CA). Signals of significant association considering a false- discovery rate (q-value < 0.05) were observed in 15 of the 32 analyzed traits, and a total of 813 trait-associated SNP (TAS), distributed in 43 chromosomal intervals on almost all autosomes, were annotated. According to the clustering analysis based on functional classification, several of the annotated genes are related to FA composition and lipid metabolism. Some interesting positional concordances among TAS and previously reported QTL for FA compositions and/or other lipid traits were also found. These common genomic regions for different traits suggest pleiotropic effects for FA composition and were found primarily on SSC4, SSC8, and SSC16. These results contribute to our understanding of the complex genetic basis of FA composition and FA metabolism.

Estrogen receptor polymorphism in Landrace pigs and its association with litter size performance

Polymorphism at the estrogen receptor locus (ESR) and its association with reproductive performance in Landrace pig is reported. A total of 124 sows from a control line, and 163 sows from a line selected for litter size were genotyped. The traits studied were number born alive (NBA) and total number born (TNB). Prolificacy in first, second and third or later parities were considered as three different traits. A mixed model considering the ESR genotype as a fixed effect and polygenic background as a random effect, was carried out using Bayesian inference, implemented via the Gibbs sampling procedure. Two alternative statistical models, with and without ESR genotype by line interaction, were considered. Association of an additive ESR effect with NBA and TNB was not detected. Moreover, in third and further parities, a line by ESR genotype interaction was observed for both NBA and TNB. For third and further parities, allele B was associated with increasing litter size in selected animals, whereas the opposite was observed in control animals. These results suggest that a background genotype by ESR interaction exists, although a spurious association due to sampling or the possibility of different linkage phases between the ESR polymorphism and a putative QTL close by cannot be ruled out.

A study of heterogeneity of environmental variance for slaughter weight in pigs

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

A quantitative trait locus genome scan for porcine muscle fiber traits reveals overdominance and epistasis

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.

Estimates of genetic parameters for litter size at different parities in pigs

Abstract Different genetic models for litter size in pigs were compared. (Co)variance components at different parities were estimated by REML in two Landrace populations. Maternal genetic effects were also assessed. Data consisted of 34417 and 16750 litters records collected on each population. Different analyses for the number of pigs born in total and alive using an animal model were performed: univariate analyses with direct and maternal genetic effects (using a repeatability animal model when more than one parity was involved) and series of bivariate and multivariate analyses with each of first five parities treated as a different trait (without maternal genetic effects). The estimates of direct heritability obtained by a repeatability animal model ranged from 0.05 to 0.07. Maternal genetic effects were not significant in any populations, neither in the first parity nor in all parities. The estimates of direct heritability in each of the first five parities using series of bivariate or multivariate analyses were not different from each other within population. Nor were these estimates different from the heritability estimates obtained by a repeatability model. Estimates of genetic correlations between parities were not significantly different from unity, except for the estimate between the first and the third parity in one population ( r g = 0.5). These results confirmed the adequacy of a simple repeatability model without maternal effects in the selection for litter size in the populations analysed.

Bayes factor analyses of heritability for serum and muscle lipid traits in Duroc pigs.

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 BF >1. 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.