SNP discovery and association study for growth, fatness and meat quality traits in Iberian crossbred pigs

Iberian pigs and its crosses are produced to obtain high-quality meat products. The objective of this work was to evaluate a wide panel of DNA markers, selected by biological and functional criteria, for association with traits related to muscle growth, fatness, meat quality and metabolism. We used 18 crossbred Iberian pigs with divergent postnatal growth patterns for whole genome sequencing and SNP discovery, with over 13 million variants being detected. We selected 1023 missense SNPs located on annotated genes and showing different allele frequencies between pigs with makerdly different growth patterns. We complemented this panel with 192 candidate SNPs obtained from literature mining and from muscle RNAseq data. The selected markers were genotyped in 480 Iberian × Duroc pigs from a commercial population, in which phenotypes were obtained, and an association study was performed for the 1005 successfully genotyped SNPs showing segregation. The results confirmed the effects of several known SNPs in candidate genes (such as LEPR, ACACA, FTO, LIPE or SCD on fatness, growth and fatty acid composition) and also disclosed interesting effects of new SNPs in less known genes such as LRIG3, DENND1B, SOWAHB, EPHX1 or NFE2L2 affecting body weight, average daily gain and adiposity at different ages, or KRT10, NLE1, KCNH2 or AHNAK affecting fatness and FA composition. The results provide a valuable basis for future implementation of marker-assisted selection strategies in swine and contribute to a better understanding of the genetic architecture of relevant traits.

Free-Range Feeding Alters Fatty Acid Composition at the sn-2 Position of Triglycerides and Subcutaneous Fat Physicochemical Properties in Heavy Pigs

Simple Summary

Fat content and the degree of fatty acid unsaturation in meat are two major concerns for consumers. Fat concentration and its molecular structure (fatty acid positional distribution) are related to the nutritional fat value and tissue rheological properties. Changes in fat concentration and/or fatty acid profile related to modifications of dietary treatments are well described in the literature. Nevertheless, studies aimed to control fatty acid positional distribution by dietary intervention in pigs are scarce, and studies have shown that the internal sn-2 position is highly regulated and resistant to dietary manipulation. However, this study demonstrated that heavy pigs fed on free-range with high levels of oleic acid can alter the fatty acid composition of the internal position of the triglyceride, thus affecting the nutritional value of their fat as well as their physicochemical properties.

Abstract

The nutritional value of fat consumption depends on both the fatty acid composition and the positional distribution of fatty acids within the triglyceride molecule. This research studies the effect of feeding with three different diets (4% lard-enriched; 11.5% high-oleic sunflower-enriched; and extensive feeding mainly with acorns) on the composition of fatty acids in the sn-2 position (and sn-1,3) of triglycerides and the textural properties of subcutaneous fat in heavy Iberian pigs (n = 210 castrated males). A moderate dietary enrichment with oleic acid in mixed diets did not alter the regulation of the sn-2 position of triglyceride (69.9% and 13.9% of palmitic and oleic acids, respectively), but the extremely high intake of oleic acid in pigs fed mainly on acorns changed the proportions of palmitic and oleic acids at the sn-2 position in the subcutaneous fat of pigs (55.0% and 27.2%, respectively). Hardness, adhesiveness, cohesiveness, gumminess, and chewiness showed the least values in EXT pigs, and the greatest values in LARD-fed barrows. SUN cohesiveness and gumminess did not differ from those fed LARD. In addition, Iberian pigs raised in free-range conditions had a more favorable nutritional lipid profile for human health compared to pigs fed conventional diets.

Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism

Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences, transcriptional regulation and genetic polymorphisms that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth. Morphometric measures and blood samples were obtained and samples from Biceps femoris muscle were employed for compositional and transcriptome analysis by RNA-Seq technology. Phenotypic differences were evident at this early age, including greater body size and weight in IBxDU and greater Biceps femoris intramuscular fat and plasma cholesterol content in IB newborns. We detected 149 differentially expressed genes between IB and IBxDU neonates (p < 0.01 and Fold-Change > 1. 5). Several were related to adipose and muscle tissues development (DLK1, FGF21 or UBC). The functional interpretation of the transcriptomic differences revealed enrichment of functions and pathways related to lipid metabolism in IB and to cellular and muscle growth in IBxDU pigs. Protein catabolism, cholesterol biosynthesis and immune system were functions enriched in both genotypes. We identified transcription factors potentially affecting the observed gene expression differences. Some of them have known functions on adipogenesis (CEBPA, EGRs), lipid metabolism (PPARGC1B) and myogenesis (FOXOs, MEF2D, MYOD1), which suggest a key role in the meat quality differences existing between IB and IBxDU hams. We also identified several polymorphisms showing differential segregation between IB and IBxDU pigs. Among them, non-synonymous variants were detected in several transcription factors as PPARGC1B and TRIM63 genes, which could be associated to altered gene function. Taken together, these results provide information about candidate genes, metabolic pathways and genetic polymorphisms potentially involved in phenotypic differences between IB and IBxDU pigs associated to meat quality and production traits.

Dietary vitamin A restriction affects adipocyte differentiation and fatty acid composition of intramuscular fat in Iberian pigs

The aim of this study was to investigate whether dietary vitamin A level is associated with differences in adipocyte differentiation or lipid accumulation in Iberian pigs at early growing (35.8kg live weight) and at finishing (158kg live weight). Iberian pigs of 16.3kg live weight were allocated to two feeding groups, one group received 10,000IU of vitamin A/kg diet (control); the other group received a diet with 0IU of vitamin A (var) for the whole experimental period. The dietary vitamin A level had no effect on growth performance and carcass traits. The early suppression of vitamin A increased the preadipocyte number in Longissimus thoracis (LT) muscle in the early growth period (P<0.001) and the neutral lipid content and composition (higher MUFA and lower SFA content) at the end of the finishing period (P<0.05). Vitamin A restriction in young pigs increases their lipogenic potential without affecting carcass traits.

Effect of micellized natural (D-α-tocopherol) vs. synthetic (DL-α-tocopheryl acetate) vitamin E supplementation given to turkeys on oxidative status and breast meat quality characteristics

This study evaluates the effect of vitamin E supplementation source (micellized natural vs. the synthetic form) and dosage (40, 80, or 120 mg/kg) on α-tocopherol concentration in plasma and muscle, antioxidant capacity, and breast meat quality in turkeys. Three hundred female turkeys were randomly selected at an average live weight 63.2 g±0.5 and distributed into 7 groups. One group (control) was fed a standard diet without vitamin E supplementation and the other 6 were given mixed diets supplemented with the natural (d-α-tocopherol) or synthetic (dl-α-tocopheryl acetate) form of vitamin E in 3 dosages (40, 80, or 120 mg/kg). Following 11 wk feeding, results showed that performance parameters were not modified either by source or dosage of vitamin E supplementation to the turkeys. Plasma and muscle α-tocopherol at d 9 of refrigerated storage were higher when turkeys were supplemented with the natural form at higher doses. Losses in the concentration of α-tocopherol in meat between the beginning and the end of the 9 d refrigerated storage were greater in the groups supplemented with the synthetic form of vitamin E compared to those receiving the natural supplementation. The relationship between plasma α-tocopherol and the Trolox equivalent antioxidant capacity followed a different trend depending on the vitamin E source. Intramuscular fat was not significantly affected by the vitamin E source supplementation; however the slope of the linear regression equation was lower for the natural form than for the synthetic form. Turkeys given the natural form had higher C18:1n-9 but lower C15:1, C17:1, C20:5n-3, and C22:6n-3 in breast muscle. Meat samples from turkeys supplemented with natural vitamin E had higher deoxymyoglobin at d 3, 6, and 9 and lower metmyoglobin at d 9 of refrigerated storage than those receiving the synthetic form. Dietary supplementation with medium doses (80 mg/kg) micellized d-α-tocopherol is an interesting feeding strategy for ensuring antioxidant status and improving meat quality.

Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics

BACKGROUND

The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in piglets of both genetic types, in order to identify genes, pathways and regulatory factors responsible for their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DU×IB) were generated. Piglets (14 from each genetic type) were slaughtered at weaning (28 days) and longissimus dorsi was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays.

RESULTS

Loin muscle chemical composition showed significant differences between genetic types in intramuscular fat content (6.1% vs. 4.3% in IB and DUxIB animals, respectively, P = 0.009) and in saturated (P = 0.019) and monounsaturated fatty acid proportions (P = 0.044). The statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR < 0.10), 102 upregulated in IB and 154 upregulated in DU×IB. Transcript differences were validated for a subset of DE genes by qPCR. We observed alteration in biological functions related to extracellular matrix function and organization, cellular adhesion, muscle growth, lipid metabolism and proteolysis. Candidate genes with known effects on muscle growth were found among the DE genes upregulated in DU×IB. Genes related to lipid metabolism and proteolysis were found among those upregulated in IB. Regulatory factors (RF) potentially involved in the expression differences were identified by calculating the regulatory impact factors. Twenty-nine RF were found, some of them with known relationship with tissue development (MSTN, SIX4, IRX3), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these RF and DE genes show relevant differences between genetic types.

CONCLUSION

These results provide valuable information about genetic mechanisms determining the phenotypic differences on growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. Transcription factors and regulatory mechanisms are proposed for these altered biological functions.

Alpha-tocopherol stereoisomer analysis as discriminant method for distinguishing Iberian pig feed intake during the fattening phase

The use of stereoisomers of α-tocopherol to correctly classify Iberian pig fat samples according to their feeding system was investigated. Samples were obtained over two different seasons in controlled farms from the four categories of pigs described in the Industry Quality Policy (FREE-RANGE: pigs fed exclusively under free-range conditions; FREE-FEED: pigs fed free-range and supplemented with feed; FEED-OUT: pigs fed outdoors with access to grass and a mixed diet; and FEED: pigs fed exclusively a mixed diet). A higher presence of RRR-stereoisomer indicated a greater consumption of the natural form of tocopherol provided by acorns or grass, whereas a higher proportion of S forms were related to a higher mixed diet intake. Validation results showed 90% success in fat sample classification. Analysis of the RRR-stereoisomer together with γ- and α-tocopherol determination can be considered as a potent tool for distinguishing fat from pigs fed under free-range conditions or exclusively with acorns and grass from those receiving a supplemented diet at any time of their fattening phase.

Short- and long-term effect of oral administration of micellized natural vitamin E (D-α-tocopherol) on oxidative status in race horses under intense training

This study tested the effect of micellized vitamin E (D-α-tocopherol; 1,400 IU/d) administered 12 and 1 h orally before training for 1 d (ST-VitE) or 8 d (LT-VitE) compared with an unsupplemented control (CONTROL) on plasma α-tocopherol, thiobarbithuric acid-reactive substances (TBARS), total glutathione (GSHt), and trolox equivalent antioxidant capacity (TEAC) in 10 race horses. Different sampling times [immediately before training (BEF) and after intense training (END) or 8 h after recovery (+8h)] were investigated. Plasma α-tocopherol concentration was greater in the ST-VitE group than the CONTROL group at +8h (P < 0.05). Natural vitamin E supplementation increased plasma α-tocopherol (P < 0.001) in the LT-VitE group by approximately 1.6-fold at BEF, END, and +8h. In all groups, TBARS tended to be slightly greater (P = 0.087) immediately after training when compared with values BEF or +8h and the lowest TBARS values were observed at +8h in LT-VitE. Vitamin E supplementation did not affect the GSHt concentrations at BEF, END, or +8h. The TEAC values were modified by the vitamin E administration (P = 0.010). The greatest TEAC was found in the LT-VitE group at all sampling times and similar concentrations were reached in the ST-VitE group at +8h. The CONTROL group was not able to maintain TEAC after training (P < 0.001), indicating consumption of antioxidants (mainly vitamin E) and consequently oxidative stress because of the antioxidant system being overwhelmed by a reduced antioxidant supply. In conclusion, micellized natural vitamin E at 1,400 IU/d for 8 d efficiently increased plasma α-tocopherol concentration of race horses undergoing intense training conditions and maintained the general oxidative status.

Effect of diet saturation on growth performance, carcass characteristics and fat quality of heavy pigs

Twenty-four castrated male (Duroc × Large Withe × Landrace) with an average weight of 69.4 kg were randomly distributed and located in individual cages and given the experimental diets. Diets were provided ad libitum and were formulated containing three levels of palm oil and hydropalm (hydrogenated palm stearine): 4% and 0% (low saturation), 2% and 2% (moderate saturation) and 0% and 4% (high saturation). Pigs were slaughtered at a local slaughterhouse with an average weight of 129.1 kg. The dietary treatment had no significant influence on growth performances and carcass characteristics. The diet saturation led to an increase of C18:0 and ΣSFA (saturated fatty acids) proportions and to a reduction of C18:1 n-9, C18:2 n-6 and ΣPUFA (polyunsaturated fatty acids) proportions and in subcutaneous backfat outer and inner layers. The dietary treatment affected significantly the melting point of subcutaneous backfat outer layer but had no significant influence on the melting point of the subcutaneous backfat inner layer. However, a linear effect of C18:0 proportion of subcutaneous backfat outer and inner layers on the melting point was observed. Dietary treatment had no significant effect on the main fatty acids pattern of intramuscular neutral and polar lipids from Longissimus dorsi muscle. In neutral lipids of liver a dietary influence (p < 0.05), but not a clear dose--response relationship, was observed for C16:0, C18:1 n-9, ΣSFA and ΣPUFA fatty acids, whereas in polar lipids the dietary treatment had no significant effect on the main fatty acids proportions. No effect of diet saturation was found on rheological properties of fat except for the hardness. The hardness was higher in the pigs that received the diet with 0% of palm oil and 4% hydropalm than in those given the diet with 4% of palm oil and 0% hydropalm.

Dietary vitamin A concentration alters fatty acid composition in pigs

This experiment was conducted to study the effect of vitamin A concentration in the diet on fatty acid composition in pigs. One-hundred and twenty eight Duroc × (Large White × Landrace) castrated male pigs were used. Pigs were randomly distributed and located in cages of four pigs each to the following treatment: vitamin A-enriched diet (100,000IU/kg) (n=16) and control diet with a basal level (7500IU/kg) (n=16). The pigs were slaughtered at an average weight of 125.9kg. No effect of diet vitamin A level on performance, carcass traits and intramuscular fat percentage was observed. The retinol concentration in subcutaneous backfat and retinol and retinol palmitate contents in liver were higher in the pigs that were given the vitamin A enriched diet than in those receiving the control diet. However the vitamin A supplementation did not increase the retinol content in the muscle. Pigs receiving the vitamin A enriched diet showed a higher C16:0 and ∑SFA proportions in the outer layer and C18:0 and ∑SFA proportions in the inner layer. Moreover, the diet rich in vitamin A led to a reduction of C18:1 n-9 and ∑MUFA proportions in subcutaneous backfat inner layer. Dietary vitamin A concentration had not influence on main fatty acids composition of intramuscular lipids. Dietary vitamin A enrichment lead to a higher C16:0, ∑SFA concentration in liver lipids.

Feeding level in the period previous to the late fattening phase influences fat composition at slaughter in free-ranged Iberian pigs

A group of 11 pigs was fed with 70 g feed per kg of metabolic weight (H pigs) and another group of 11 pigs was fed with 50g feed per kg of metabolic weight (L pigs). In both experimental groups (H and L pigs), it was observed that the higher initial proportion of C16:0, C18:0 and C18:2 (n-6) in backfat at the beginning of the free-range feeding period, the greater decrease rate of these fatty acid proportions regarding weight gain during the free-range fattening period took place. On the other hand, the greater initial proportion of C18:1 (n-9), the smaller increase rate in the concentration of this fatty acid was observed. The intramuscular neutral lipids from L pigs had higher C18:3 (n-3) and lower proportions of monounsaturated fatty acids (MUFA) than those from H pigs, while intramuscular polar lipids from L pigs had significantly higher proportions of C18:0, PUFA, C18:3 (n-3) and (n-3) and significantly lower MUFA and C18:1 (n-9) proportions than those from H pigs. The alpha-tocopherol concentration found in Longissimus dorsi from L pigs was significantly higher (p < 0.012) than those from H pigs.

Effect of dietary copper and vitamin E supplementation, and extensive feeding with acorn and grass on longissimus muscle composition and susceptibility to oxidation in Iberian pigs

The objective of this study was to assess the effect of dietary copper and/or vitamin E supplementation on composition and oxidation of M. longissimus in Iberian pigs and to compare it with meat samples from pigs produced extensively and fed with acorn and grass. Grass had the highest alpha-tocopherol content (> 150 mg/kg DM), while acorns had the highest copper concentration (78.1 mg/kg DM). Dietary treatment did not affect copper composition in muscle and no interactions were detected between copper and alpha-tocopherol. The alpha-tocopherol content in muscle from pigs fed diets supplemented with alpha-tocopheryl acetate (100 mg/kg feed) was 1.5 times greater (p < 0.0001) than those from pigs receiving a basel diet. M. longisssimus dorsi from pigs fed extensively had a higher concentration of alpha-tocopherol than those fed in confinement with the basel level of alpha-tocopheryl acetate, but lower values than pigs fed supplemented levels. Total n-3 fatty acids (p < 0.02) and hematin (p < 0.0001) concentrations were significantly higher in muscle from pigs fed extensively than when fed in confinement. Muscle homogenates from Iberian pigs fed in extensive conditions showed significantly (p < 0.02) higher susceptibility to oxidation than those from pigs fed mixed diets. Dietary alpha-tocopheryl acetate supplementation (100 mg/kg feed) significantly (p < 0.05) reduced lipid oxidation of muscle, while dietary copper concentration did not modify susceptibility to lipid oxidation.

Effect of dietary oils and alpha-tocopheryl acetate supplementation on lipid (TBARS) and cholesterol oxidation in cooked pork

The effect of n-3 fatty acid-enriched diets (in the form of 0.5% linseed oil with either 1.5% sunflower oil or 1.5% olive oil) and alpha-tocopheryl acetate supplementation (200 mg/kg feed) on lipid oxidation (thiobarbituric acid-reactive substances, TBARS) and cholesterol oxide products (COPS) in cooked pork was investigated. Longissimus muscle was studied. Meat from pigs fed 0.5% linseed oil-enriched diets had a higher proportion of n-3 fatty acid than meat from pigs in other dietary groups in neutral (P < 0.0001) and polar lipids (P < 0.0001), and a 20% reduction in the n-6:n-3 ratio was observed. Alpha-tocopheryl acetate supplementation increased (P < 0.05) monounsaturated fatty acids in polar lipids and increased (P = 0.0001) alpha-tocopherol levels in muscle. Alpha-tocopherol concentration in muscle was affected by dietary fat (P < 0.05). Groups receiving diets enriched with sunflower oil had significantly higher alpha-tocopherol levels (P < 0.05) in muscle than those groups receiving olive oil-enriched diets. Numbers of TBARS were significantly (P < 0.05) lower in the group fed supplemental olive oil than in those fed sunflower oil. Dietary linseed oil increased (P < 0.05) lipid oxidation principally at the initial period of storage in cooked pork. Overall, dietary alpha-tocopheryl acetate supplementation significantly increased (P < 0.001) lipid stability and decreased (P < 0.05) total COP production across the dietary groups. Alpha-tocopherol was a more effective antioxidant for decreasing TBARS values in cooked meat when adding sunflower oil to the diets instead of olive oil.

Dietary polyunsaturated fatty acids and plasma butyrylcholinesterase activity in piglets

Diets containing different ratios of n-3:n-6 polyunsaturated fatty acids, were fed to piglets for a period of 10 days. Diets with n-3:n-6 ratios of 0.2 and 0.3 decreased the group mean activity of plasma butyrylcholinesterase when compared with a diet with a ratio of 0.1.

Dietary vegetable oils and alpha-tocopherol reduce lipid oxidation in rabbit muscle

This experiment was conducted to study the effect of dietary vegetable oil on lipid oxidation in rabbit muscle. A control diet with no added fat and two diets with olive or sunflower oil (30 g/kg) were used. Within each treatment, one group was fed a low level of alpha-tocopheryl acetate (10 mg/kg diet), and the other a supplemental level (200 mg/kg). Rabbits were fed experimental diets from weaning (20 d) to slaughter (69 d). The supplemental level of dietary alpha-tocopheryl acetate produced higher alpha-tocopherol concentration in muscle (P < 0.006) and lower lipid oxidation (P < 0.004). Rabbits that received sunflower oil had higher concentrations of thiobarbituric acid reactive substances than rabbits that consumed olive oil (P < 0.05). Moreover, a significant effect due to fat inclusion in the diet was found. Muscles from rabbits fed diets not enriched with fat had higher susceptibility to lipid oxidation (P < 0.005) and higher concentration of (n-3) fatty acids in polar lipids (P < 0.04) than those from rabbits fed fat-enriched diets. A second experiment was conducted and confirmed the higher lipid oxidation in the muscle of rabbits fed diets not enriched with fat than in that of rabbits fed diets containing sunflower oil (28 g/kg) (P < 0.003) as well as in diets with identical digestible energy. In this experiment, alpha-tocopheryl acetate was at the lower level (10 mg/kg feed). Inclusion of oils rich in oleic (olive oil) or linoleic acid (sunflower oil) in rabbit diets reduces lipid oxidation in muscles.