R. N. Pena

Acetyl-CoA carboxylase and stearoyl-CoA desaturase protein expression in subcutaneous adipose tissue is reduced in pigs selected for decreased backfat thickness at constant intramuscular fat content.

The objectives of this study were 1) to determine whether selection toward less subcutaneous fat thickness at constant intramuscular fat content in pigs is related to tissue-specific changes in the expression of lipogenic enzymes acetyl-CoA carboxylase (ACC), stearoyl-CoA desaturase (SCD), and Delta(6)-desaturase (Delta6d); and 2) to investigate tissue specific distribution of the porcine ACC, SCD, and Delta6d. The study was conducted on 20 purebred Duroc barrows. Ten animals were from a group selected for decreased subcutaneous fat thickness at constant intramuscular fat content (experimental group). The other 10 animals were from the unselected (control) group. Distribution of ACC, SCD, and Delta6d was investigated in semimembranosus muscle (SM), subcutaneous adipose tissue (SA), liver (L), kidney (K), heart (H), diaphragm (D), rectus capitis muscle (RCM), and abdominal fat (AF). The enzyme expression was studied in 10 animals in the case of SM and SA and in 4 animals in the case of other tissues. The following expression pattern was established for ACC: SM <or= H = K <or= D < RCM < L < AF = SA, whereas the expression patterns for SCD and Delta6d proteins were SM < H < RCM < D < L < K < AF = SA and RCM = SM = D < L <or= H < SA < K < AF, respectively. Expression of ACC and SCD proteins was less in subcutaneous adipose tissue of the experimental animals when compared with the control group (P < 0.001). However, no difference (P > 0.1) in ACC and SCD protein expression between the control and experimental groups was observed in SM. Expression of Delta6d protein did not differ between the control and experimental groups for SA (P = 0.47) or SM (P = 0.31). There was a positive relationship between muscle SCD protein expression and intramuscular fat content (r = 0.48, P < 0.05). Intramuscular fat content did not correlate with ACC or Delta6d protein expression (P = 0.23 and P = 0.80, respectively). We conclude that SCD might be an effective potential biomarker for intramuscular fat deposition.

Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects.

Intramuscular fat (IMF) storage is a biological process with a strong impact on nutritional and technological properties of meat and also with relevant consequences on human health. The genetic architecture of IMF content and composition phenotypes has been thoroughly studied in pigs through the identification of QTL and the estimation of genetic parameters. A question that has not been elucidated yet is if the genetic determinants of IMF-related phenotypes are muscle specific or, conversely, have broad effects on the whole skeletal muscle compartment. We have addressed this question by generating lipid QTL maps for 2 muscles with a high commercial value, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), in a Duroc commercial population (n = 350). Our data support a lack of concordance between the GM and LTL QTL maps, suggesting that the effects of polymorphisms influencing IMF, cholesterol, and fatty acid contents are modulated to some extent by complex spatial factors related to muscle location, metabolism, and function. These results have important implications on the implementation of genomic selection schemes aimed to improve the lipid profile of swine meat.

Polymorphism of the pig acetyl-coenzyme A carboxylase α gene is associated with fatty acid composition in a Duroc commercial line

Acetyl-coenzyme A carboxylase alpha (ACACA) catalyses the first committed step in the biosynthesis of long-chain fatty acids (FA) by converting acetyl-CoA into malonyl-CoA. In pigs, the ACACA gene maps to a chromosome 12 QTL with important effects on FA composition. In the present study, we have sequenced the coding region of the pig ACACA gene in 15 pigs, identifying 21 polymorphic sites that were either synonymous or non-coding. Ten of these SNPs segregated in a Duroc commercial population (n = 350) for which lipid metabolism and meat and carcass quality trait records were available. Significant associations were found between two linked single nucleotide polymorphisms (c.4899G>A and c.5196T>C) and percentages of carcass lean, intramuscular fat, monounsaturated, saturated (myristic, palmitic and stearic) and polyunsaturated (linoleic) FAs in the longissimus thoracis et lumborum muscle, along with serum HDL-cholesterol concentration. The most important allele substitution effects were observed for the polyunsaturated/saturated FA ratio (13-21% of the phenotypic mean) as well as for the percentages of omega-6 and polyunsaturated FAs, especially linoleic acid (7-16% of the phenotypic mean). These results suggest the existence of a causal mutation, mapping to the chromosomal region containing the pig ACACA gene, with marked effects on FA composition of meat.

Functional and association studies on the pig HMGCR gene, a cholesterol-synthesis limiting enzyme

The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) is the rate-limiting enzyme in the biosynthesis of cholesterol. We have studied the role of the HMGCR gene in pig lipid metabolism by means of expression and structural analysis. We describe here the complete coding region of this gene in pigs and report two synonymous single nucleotide polymorphisms in the coding region. We have, additionally, studied the association of one of these polymorphisms (HMGCR:c.807A>C) with several lipid deposition- and cholesterol-related traits in a half-sib population generated from a commercial Duroc line, showing in some families a positive relationship of HMGCR:c.807A allele with serum low-density lipoprotein (LDL)-bound cholesterol and triglyceride levels, and also with intramuscular fat (IMF) content of gluteus medius muscle. We have also assessed the expression levels in muscle and in liver from 68 Duroc individuals corresponding to the most extreme animals for the analysed traits. Liver HMGCR expression correlated negatively with the serum high-density lipoprotein (HDL) levels, carcass lean percentage and stearic acid content, while muscle expression correlated also negatively with the carcass lean percentage, stearic and linoleic acids content, but showed a positive correlation with the serum lipid cholesterol (HDL, LDL and total cholesterol), IMF and muscle oleic and palmitic fatty acid content. With this information, we have performed an association analysis of expression data with lipid metabolism phenotypic levels and the HMGCR genotype. The results indicate that HMGCR expression levels in muscle are different in the two groups of pigs with extreme values for fat deposition and total cholesterol levels, and also between animals with the different HMGCR genotypes.

Quantitative trait loci analysis of a Duroc commercial population highlights differences in the genetic determination of meat quality traits at two different muscles

We performed a whole-genome scan with 110 informative microsatellites in a commercial Duroc population for which growth, fatness, carcass and meat quality phenotypes were available. Importantly, meat quality traits were recorded in two different muscles, that is, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), to find out whether these traits are determined by muscle-specific genetic factors. At the whole-population level, three genome-wide QTL were identified for carcass weight (SSC7, 60 cM), meat redness (SSC13, 84 cM) and yellowness (SSC15, 108 cM). Within-family analyses allowed us to detect genome-wide significant QTL for muscle loin depth between the 3rd and 4th ribs (SSC15, 54 cM), backfat thickness (BFT) in vivo (SSC10, 58 cM), ham weight (SSC9, 69 cM), carcass weight (SSC7, 60 cM; SSC9, 68 cM), BFT on the last rib (SSC11, 48 cM) and GM redness (SSC8, 85 cM; SSC13, 84 cM). Interestingly, there was low positional concordance between meat quality QTL maps obtained for GM and LTL. As a matter of fact, the three genome-wide significant QTL for colour traits (SSC8, SSC13 and SSC15) that we detected in our study were all GM specific. This result suggests that QTL effects might be modulated to a certain extent by genetic and environmental factors linked to muscle function and anatomical location.

Application of the microarray technology to the transcriptional analysis of muscle phenotypes in pigs

The transcriptome refers to the collection of all transcripts present in a cell. Gene expression has a very dynamic nature; it acts as a bridge between epigenetic marks, DNA sequence and proteins and changes to accommodate the requirements of the cell at each given time. Recent technological advances have created new opportunities to study complex phenotypes from a global point of view. From an animal production perspective, muscle transcriptomics has been investigated in relation to muscle growth, carcass fattening and meat quality traits. In this review, we discuss the impact of nutritional, anatomical and genetic factors on muscle gene expression and meat quality of pigs assessed by microarray technologies. Altogether, several common themes have been revealed by the in-depth analysis of the current body of knowledge, for instance, the involvement of genes related to energy balance and substrate turnover in the oxidative/glycolytic phenotype of red/white muscle fibre types and in the storage of intramuscular fat. The review also covers recent advances in the discovery of expression QTL and regulatory RNAs in porcine breeds as well as technical developments in the field of deep-sequencing technologies that are expected to substantially increase our knowledge about the genetic architecture of meat quality and production traits.

Genomic architecture of heritability and genetic correlations for intramuscular and back fat contents in Duroc pigs.

Genetic parameters such as heritability and correlations of fat traits in a Duroc population were dissected using molecular markers. The heritabilities of intramuscular fat in 2 muscles, the gluteus medius and LM, and back fat were 0.54, 0.48, and 0.23, respectively. The genetic correlations were well estimated with standardized SNP effects, being 0.65 between intramuscular fat traits and ∼0.37 between any intramuscular fat trait and back fat. Genetic correlations were overestimated when ignoring molecular information. Twelve chromosomes showed additive genetic variance for intramuscular fat compared with 8 for back fat. Population structure was accommodated using 4 different models. The number of significant, P < 5 × 10(-5) (suggestive, P < 2 × 10(-3)), SNP varied across models and ranged from 0 to 4 (2 to 261) for intramuscular fat in the gluteus medius, from 0 to 57 (9 to 564) for intramuscular fat in the LM, and from 3 to 4 (22 to 168) for back fat. Several SNP showed significant deviations from an additive mode of action. Only 2 SNP significantly affected 2 traits simultaneously.

Nucleotide Sequence and Association Analysis of Pig Apolipoprotein-B and LDL-Receptor Genes

Three genes are the major determinants of heritable hypercholesterolemia diseases in humans: APOB, LDLR and LDLRAP1, which encode for proteins that physically interact to promote cholesterol uptake in the cell. We have carried out association analyses of these variants with serum cholesterol and triglycerides concentrations in a half-sib Duroc pig population. Given the structure of the population (six paternal half-sib families), we have used a statistical model that considers separately the allele transmission through dams (at population level) and through sires (within-families from heterozygous sire). Only polymorphisms showing a relevant substitution effect for both male- and female-transmitted alleles are likely to be causal mutations. Thus, although we have found statistical association between genotypes for LDLR and APOB polymorphisms and serum lipid levels (mean allele substitution effects ranging from 15 to 40% of the standard deviation of these traits), none of them seem to be the causal mutation but probably represent closely linked polymorphisms. We have shown here that these three genes also contribute to genetic variability in pigs, with the description of new polymorphisms in their coding regions. Moreover, we have demonstrated that variants on two of these three genes are segregating in a number of commercial breeds. Finally, we report here the coding region for the porcine LDLRAP1 gene and describe a polymorphism in the last exon of this gene.

Appearance, flavor, and texture attributes of pig dry-cured hams have a complex polygenic genomic architecture.

The influence that the genetics of species used as food sources has on the human perception of sensory attributes has been rarely addressed in previous studies. Dry-cured hams are high-quality highly appreciated pork products obtained by salting, curing, drying, and aging processes. We performed a QTL scan for 17 sensory attributes (including appearance, taste, flavor, and texture) and the overall liking evaluated by a panel of trained tasters in both semimembranosus (SM) and biceps femoris (BF) muscles of dry-cured hams from pigs raised in identical nutrition and management conditions. The QTL scan yielded a large array of chromosome- and genomewide QTL, reflecting the complex polygenic architecture of these traits. Among them, 6 QTL affecting SM flavor attributes (aged, matured, sweetness, and umami), 7 QTL associated to SM texture defects (adhesiveness and pastiness), and a single QTL for appearance (BF color intensity) reached the genomewide significant threshold. Discrepancies were observed between the BF and SM QTL maps, probably due to the differential drying and ripening rates determined by the external (SM) vs. internal (BF) location of each muscle. Within muscle, a certain degree of pleiotropy is supported by QTL co-localization for flavor (aged, matured, and sweet) or texture (such as pastiness and adhesiveness defects caused by excessive proteolysis) attributes. On the whole, QTL for overall sensory liking tended to co-localize with aged and matured QTL. Several functional candidate genes involved in the biochemical processes that shape flavor and texture attributes, such as ANPEP, LIPE, LIPA, MEP1B, and MMP28, co-localized with QTL hotspots. These results demonstrate that genetic factors of the pig influence the perception of the sensory attributes generated during dry-cured ham processing and represent a first contribution to elucidate which genetic factors may modulate the sensory properties of dry-cured hams.

Genetics of serum and muscle lipids in pigs

Pork meat is one of the most important sources of animal protein in the human diet. Its nutritional properties are partly determined by intramuscular fat content and composition, with existing general consensus about the detrimental effects of cholesterol and saturated fat on cardiovascular health in humans. Because of their physiological resemblance, pigs can be also used as a valuable animal model to study the genetics of human diseases such as atherosclerosis, obesity and dyslipidaemias. Heritability estimates and QTL maps of porcine muscle and serum lipid traits evidence that a considerable amount of genetic variance determining these phenotypes exists, but its molecular basis remains mostly unknown. The recent advent of high-throughput genotyping and sequencing technologies has revolutionised the field of animal genomics. With these powerful tools, finding needles in the genomic haystack has become increasingly feasible. However, these methodological advances should not be deemed as magic bullets. The goal of identifying the many polymorphisms that shape the variability of lipid phenotypes is so challenging that success can be achieved only under the scope of large international consortia.