Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa).

The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (FIS and FROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations.

A probabilistic Poisson-based model to detect PRRSV recirculation using sow production records.

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease associated with a decrease in the number of born alive piglets (NBA) and an increase in the number of lost piglets (NLP) per farrowing. Under practical conditions, it is critical to assess whether a farm is suffering PRRSV recirculation in the sow herd as soon as possible. The aim of this research work was to develop a new method to detect potential PRRSV recirculation in sow production farms. Sow reproductive performance records from one farm (farm T) were used to set up the method and records from ten additional farms (farms V1 to V10) were used for validation. A conditional Poisson model of NLP on NBA was proposed to fit the data. A three-step procedure was implemented to detect potential PRRSV recirculation: (i) computation of the maximum-likelihood estimates of the expected values of NBA and NLP in a PRRSV non-recirculating scenario; (ii) calculation, for each farrowing, of the p-value associated with the probability of jointly observing deviations towards decreased NBA and increased NLP. The detection of a potential PRRSV recirculation was based on (iii) the combined p-value resulting from weighing the p-values of the last N farrowings by the chi-square-inverse method. In order to gain specificity, a displacement on the expected non-recirculating NBA and NLP values was used for tuning purposes. With this approach, two PRRSV circulating periods were detected in farm T, which were confirmed with standard laboratorial diagnostic techniques. The method was subsequently validated in farms V1 to V10, where ten PRRSV-recirculating time episodes had been diagnosed. The method proposed here was able to detect the ten PRRSV recirculations using a relatively small set of contiguous farrowings, with only two mismatched weeks, one as a false negative, in farm V1, and one as a false positive, in farm V4. It is concluded that a conditional Poisson-based model of NLP on NBA can be a useful tool for routinely detecting PRRSV recirculation in sow herds.

Five genomic regions have a major impact on fat composition in Iberian pigs.

The adipogenic nature of the Iberian pig defines many quality attributes of its fresh meat and dry-cured products. The distinct varieties of Iberian pig exhibit great variability in the genetic parameters for fat deposition and composition in muscle. The aim of this work is to identify common and distinct genomic regions related to fatty acid composition in Retinto, Torbiscal, and Entrepelado Iberian varieties and their reciprocal crosses through a diallelic experiment. In this study, we performed GWAS using a high density SNP array on 382 pigs with the multimarker regression Bayes B method implemented in GenSel. A number of genomic regions showed strong associations with the percentage of saturated and unsaturated fatty acid in intramuscular fat. In particular, five regions with Bayes Factor >100 (SSC2 and SSC7) or >50 (SSC2 and SSC12) explained an important fraction of the genetic variance for miristic, palmitoleic, monounsaturated (>14%), oleic (>10%) and polyunsaturated (>5%) fatty acids. Six genes (RXRB, PSMB8, CHGA, ACACA, PLIN4, PLIN5) located in these regions have been investigated in relation to intramuscular composition variability in Iberian pigs, with two SNPs at the RXRB gene giving the most consistent results on oleic and monounsaturated fatty acid content.

TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Genetics and breeding for intramuscular fat and oleic acid content in pigs.

The intramuscular fat (IMF) and oleic acid (OL) content have been favorably related to pork quality and human health. This influences the purchasing behavior of consumers and, therefore, also shifts the attention of breeding companies toward whether these traits are included into the breeding goal of the lines producing for high-valued markets. Because IMF and OL are unfavorably associated with lean content, a key economic trait, the real challenge for the industry is not simply to increase IMF and OL, but rather to come up with the right trade-off between them and lean content. In this paper we review the efforts performed to genetically improve IMF and OL, with particular reference to the research we conducted in a Duroc line aimed at producing high quality fresh and dry-cured pork products. Based on this research, we conclude that there are selection strategies that lead to response scenarios where IMF, OL, and lean content can be simultaneously improved. Such scenarios involve regular recording of IMF and OL, so that developing a cost-efficient phenotyping system for these traits is paramount. With the economic benefits of genomic selection needing further assessment in pigs, selection on a combination of pedigree-connected phenotypes and genotypes from a panel of selected genetic markers is presented as a suitable alternative. Evidence is provided supporting that at least a polymorphism in the leptin receptor and another in the stearoyl-CoA desaturase genes should be in that panel. Selection for IMF and OL results in an opportunity cost on lean growth. The extent to which it is affordable relies on the consumers' willingness to pay for premium products and on the cost to benefit ratio of alternative management strategies, such as specific dietary manipulations. How the genotype can influence the effect of the diet on IMF and OL remains a topic for further research.

Carotenoid intake and SCD genotype exert complementary effects over fat content and fatty acid composition in Duroc pigs.

Nutritional and genetic strategies are needed to enhance intramuscular fat (IMF) and MUFA content without altering carcass leanness. Dietary vitamin A restriction has been suggested to specifically promote IMF, whereas a polymorphism of the () gene has shown to specifically increase MUFA. The purpose of this study was to investigate the combined effects of provitamin A (PVA) carotenoid intake and genotype (>) on hepatic retinoid content and on the liver, muscle (LM and gluteus medius [GM]), and subcutaneous fat (SF) content and fatty acid composition. Following a split-plot design, 32 castrated Duroc pigs, half of each of the 2 homozygous genotypes (CC and TT), were subjected from 165 to 195 d of age to 2 finishing diets differing in the PVA carotenoid content (an enriched-carotene diet [C+] and a control diet [C-]). Both diets were identical except for the corn line used in the feed. The C+ was formulated with 20% of a carotenoid-fortified corn (M37W-Ph3) whereas the C- instead used 20% of its near isogenic M37W line, which did not contain PVA carotenoids. No vitamin A was added to the diets. The C- was estimated to provide, at most, 1,300 IU of vitamin A/kg and the C+ to supply an extra amount of at least 800 IU vitamin A/kg. Compared with the pigs fed the C-, pigs fed with C+ had 3-fold more retinoic acid ( < 0.01) and 4-fold more gene expression in the liver ( = 0.06). The diet did not affect performance traits and backfat thickness, but pigs fed the C+ had less fat (4.0 vs. 5.0%; = 0.07) and MUFA (18.3 vs. 22.5%; = 0.01) in the liver, less IMF (5.4 vs. 8.3%; = 0.04) in the GM, and more fat content (90.4 vs. 87.9%; = 0.09) and MUFA (48.0 vs. 46.6%; = 0.04) in SF. The TT genotype at the gene increased MUFA ( < 0.05) in all tissues (21.4 vs. 19.5% in the liver, 55.0 vs. 53.1% in the LM, 53.9 vs. 51.7% in the GM, and 48.0 vs. 46.7% in SF for TT and CC genotypes, respectively). Liver fat and MUFA content nonlinearly declined with liver all- retinoic acid, indicating a saturation point at relatively low all- retinoic acid content. The results obtained provide evidence for a complementary role between dietary PVA and genotype, in the sense that the TT pigs fed with a low-PVA diet are expected to show higher and more monounsaturated IMF without increasing total fat content.

The effect of SCD and LEPR genetic polymorphisms on fat content and composition is maintained throughout fattening in Duroc pigs.

The effects of the stearoyl-CoA desaturase (SCD; AY487830:g.2228T>C) and leptin receptor (LEPR; NM_001024587:g.1987C>T) polymorphisms on fat content and fatty acid (FA) composition were investigated throughout fattening. Samples of Longissimus thoracis (LT) and subcutaneous fat (SF) from 214 Duroc barrows were collected from 160days to slaughter age (220days) using a longitudinal design. Results indicated that the positive effect of the T allele at the SCD gene on monounsaturated FA and of the T allele at the LEPR gene on saturated FA are maintained throughout the growing-finishing period, both in LT and SF. In LEPR, however, compositional changes, particularly in SF, are a result of increased fatness. There is very limited evidence of genotype by age interaction, and thus it is concluded that the combined selection for the SCD T and LEPR C alleles is a good strategy to increase the MUFA/SFA ratio regardless of the age at slaughter.

Relationship between perilipin genes polymorphisms and growth, carcass and meat quality traits in pigs.

The perilipins (PLIN) belong to a family of structural proteins that play a role regulating intracellular lipid storage and mobilization. Here, PLIN1 and PLIN2 have been evaluated as candidate genes for growth, carcass and meat quality traits in pigs. A sample of 607 Duroc pigs were genotyped for two single-nucleotide polymorphisms, one in intron 2 of the PLIN1 gene (JN860199:g.173G>A) and the other at the 3' untranslated region of the PLIN2 gene (GU461317:g.98G>A). Using a Bayesian approach, we have been able to find evidence of additive, dominant and epistatic associations of the PLIN1 and PLIN2 polymorphisms with early growth rate and carcass length. However, the major effects were produced by the dominant A allele at the PLIN2 polymorphism, which also affected the carcass lean weight. Thus, pigs carrying an additional copy of the A allele at the g.98G>A PLIN2 polymorphism had a probability of at least 98% of producing carcasses with heavier lean weight (+0.41 kg) and ham weight (+0.10 kg). The results obtained indicate that the PLIN2 polymorphism could be a useful marker for lean growth. In particular, it may help to reduce the undesired negative correlated response in lean weight to selection for increased intramuscular fat content, a common scenario in some Duroc lines involved in the production of high quality pork products.

[THE GENETIC DIVERSITY OF PIG BREEDS ON TEN PRODUCTION QUANTITATIVE TRAITS LOCI].

Genetic structure of 11 pig breeds and lines of different origins and production specialization for 10 quantitative traits loci: RYR1, GH, IGF2, CTSL, CTSS, CTSB, CTSK, MC4R, ESR1 & PRLR was analyzed. The results allow us to suppose that the uniqueness of genetic structure of each breed is largely determined by features of the allelic structure of a number of loci. Breeds of different production specialization differ significantly for such QTL, as RYR1, MC4R, ESR1 and IGF2. However, we have found that the loci CTSB, CTSL, CTSK, CTSS and PRLR in most of investigated breeds showed similar distribution of alleles, significant genetic differentiation between breeds and within breeds for these loci is missing. The exception is the Large Black breed for the CTSB locus and Ukrainian steppe spotted breed for the CTSL locus. Also, it can be assumed that allelic structure of some of investigated loci are more connected with the origins of pig breeds than to the selection on production traits. This refers, for example, to the growth hormone gene, the using of which in marker assisted selection could be effective only in some populations. The genetic distance between breeds and lines was defined and the dendrogram of the genetic relationship was built. Breeds are grouped in connection with the production specialization, as well as by their origins.

Expression profiling of the GBP1 gene as a candidate gene for porcine reproductive and respiratory syndrome resistance.

A genomic region in pig chromosome 4 has been previously associated with higher viraemia levels and lower weight gain following porcine reproduction and respiratory syndrome virus (PRRSV) infection. The region includes the marker WUR1000125, a G>A polymorphism next to a putative polyadenylation site in the 3'-untranslated region (3'-UTR) of the guanylate-binding protein 1, interferon-induced (GBP1) gene. The protein encoded by GBP1 is a negative regulator of T-cell responses. We show here that GBP1 expression is lower in liver and tonsils of pigs carrying the WUR1000125-G allele due to differential allele expression (allele A expression is 1.9-fold higher than for allele G). We also show that the GBP1 gene has two active polyadenylation signals 421 bp apart and that polyadenylation usage is dependent on the WUR1000125 genotype. The distal site is the most prevalently used in all samples, but the presence of the A allele favours the generation of shorter transcripts from the proximal site. This is confirmed by a differential allele expression study in AG genotype liver and tonsil samples. The interaction between WUR1000125 and other mutations identified in the 5'- and 3'-UTR regions of this gene needs to be studied. In conclusion, our study indicates that the WUR1000125 mutation is associated with changes in the expression of the negative T-cell regulator GBP1 gene. However, the chromosome 4 locus for PRRSV viraemia levels and weight gain contains a cluster of four other GBP genes that remain to be studied as candidate genes for this QTL.

A polymorphism in the stearoyl-CoA desaturase gene promoter increases monounsaturated fatty acid content in dry-cured ham.

Data on 125 dry-cured hams from purebred Duroc pigs were used to examine whether the favorable effect of the T allele in the promoter region of the stearoyl-CoA desaturase gene (AY487830:g.2228T>C) on monounsaturated fatty acid (MUFA) content in green ham is maintained after the curing process. It is shown that pigs carrying the T allele produced dry-cured hams with increased C16:1, C18:1n-9, C18:1n-7, and MUFA and decreased C18:0 and saturated fatty acid (SFA) content. The TT pigs had 1.39% more MUFA and 1.62% less SFA than the CC animals, while gilts had 0.74% more MUFA and 0.34% less SFA than barrows. The correlation between MUFA in green and dry-cured hams (n=53) was high (r=0.88), with TT pigs being more effective in retaining increased MUFA in green hams until the end of the curing period. It is concluded that increasing the presence of the T allele could have more impact than gender to produce hams with a high level of MUFA.

Investigating reference genes for quantitative real-time PCR analysis across four chicken tissues.

Accurate normalization of data is required to correct for different efficiencies and errors during the processing of samples in reverse transcription PCR analysis. The chicken is one of the main livestock species and its genome was one of the first reported and used in large scale transcriptomic analysis. Despite this, the chicken has not been investigated regarding the identification of reference genes suitable for the quantitative PCR analysis of growth and fattening genes. In this study, five candidate reference genes (B2M, RPL32, SDHA, TBP and YWHAZ) were evaluated to determine the most stable internal reference for quantitative PCR normalization in the two main commercial muscles (pectoralis major (breast) and biceps femoris (thigh)), liver and abdominal fat. Four statistical methods (geNorm, NormFinder, CV and BestKeeper) were used in the evaluation of the most suitable combination of reference genes. Additionally, a comprehensive ranking was established with the RefFinder tool. This analysis identified YWHAZ and TBP as the recommended combination for the analysis of biceps femoris and liver, YWHAZ and RPL32 for pectoralis major and RPL32 and B2M for abdominal fat and across-tissue studies. The final ranking for each tool changed slightly but overall the results, and most particularly the ability to discard the least robust candidates, were consistent between tools. The selection and number of reference genes were validated using SCD, a target gene related to fat metabolism. Overall, the results can be directly used to quantitate target gene expression in different tissues or in validation studies from larger transcriptomic experiments.

Associations between pig adiponectin (ADIPOQ) genotype and serum lipid levels are modulated by age-specific modifiers.

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

DECR1 and ME1 genotypes are associated with lipid composition traits in Duroc pigs.

Variation at the porcine DECR1 and ME1 genes has been associated with meat quality traits and backfat thickness in Landrace pigs, respectively. However, it has not been investigated yet whether DECR1 and ME1 genotypes influence lipid composition. With this aim, we have genotyped two missense DECR1 substitutions (c.160G>C and c.437G>C) and one silent ME1 (c.576C>T) polymorphism in 361 Duroc barrows distributed in five half-sib families and phenotyped for serum lipid concentrations and intramuscular fat content and composition traits. At the whole-population level, relevant associations, that is, with a posterior probability of the allele substitution effect to be over or below zero (PPN0) > 0.90, were observed between DECR1 genotype and serum cholesterol (CHOL) (PPN0 = 0.932) and LDL concentrations (PPN0 = 0.945) at 190 days, as well as between ME1 genotype and longissimus dorsi saturated fatty acid content (PPN0 = 0.924). At the within-family level, we found relevant associations between DECR1 and ME1 genotypes and diverse lipid composition traits, but most of them were family-specific. Discrepancies in allele substitution effects estimated in half-sib families might be produced by many factors such as number of individuals, marker allele frequencies and informativeness in each family, unaccounted random genetic and environmental effects, epistasis and family-specific differences in the linkage phase or amount of linkage disequilibrium between causal and marker mutations. This lack of consistency across families, combined with the fact that the ME1 mutation is synonymous and that the two DECR1 polymorphisms are conservative, suggests that the associations found are not causative.

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.

Transcriptional analysis of intramuscular fatty acid composition in the longissimus thoracis muscle of Iberian × Landrace back-crossed pigs.

This study aimed at identifying differential gene expression conditional on the fatty acid profile of the longissimus thoracis (Lt) muscle, a prime cut of economic relevance for fresh and cured pork production. A population of 110 Iberian (25%) × Landrace (75%) back-crossed pigs was used, because these two breeds exhibit extreme profiles of intramuscular saturated fatty acid, monounsaturated fatty acid (MUFA) and polyunsaturated fatty acid (PUFA) contents. Total RNA from Lt muscle was individually hybridized to GeneChip Porcine Genome arrays (Affymetrix). A principal component analysis was performed with data from the 110 animals to select 40 extreme animals based on the total fatty acid profile and the MUFA composition (MAP). Comparison of global transcription levels between extreme fatty acid profile pigs (n = 40) resulted in 219 differentially expressed probes (false discovery rate <0.10). Gene ontology, pathway and network analysis indicated that animals with higher percentages of PUFA exhibit a shift toward a more oxidative muscular metabolism state, with a raise in mitochondria function (PPARGC1A, ATF2), fatty acid uptake and oxidation (FABP5, MGLL). On the other hand, 87 probes were differentially expressed between MUFA composition groups (n = 40; false discovery rate <0.10). In particular, muscles rich in n-7 MUFA expressed higher levels of genes involved in lipid metabolism (GLUL, CRAT, PLA2G15) and lower levels of fatty acid elongation genes (ELOVL5). Moreover, the chromosomal position of FABP5, PAQR3, MGLL, PPARGC1A, GLUL and ELOVL5 co-localized with very relevant QTL for fat deposition and composition described in the same resource population. This study represents a complementary approach to identifying genes underlying these QTL effects.

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.

Association analysis with lipid traits of 2 candidate genes (LRP12 and TRIB1) mapping to a SSC4 QTL for serum triglyceride concentration in pigs.

The performance of a genome scan for serum lipid traits at 45 and 190 d in 5 half-sib families of Duroc pigs allowed us to detect several pig chromosomal regions with significant effects on these phenotypes. In the current work, we aimed to refine the position of 1 chromosome 4 (SSC4) genome-wide significant QTL for serum triglyceride concentration at 190 d. Genotyping of 4 additional microsatellites allowed reduction of the 90% confidence interval of this QTL to the genomic interval between markers SW2409 and SW839. Sequencing experiments were performed to characterize the variability of 2 lipid-related genes, the lipoprotein receptor-related protein 12 (LRP12) and tribbles homolog 1 (TRIB1) loci, that map to this region. In this way, 2 (c.771A > G and c.1101A > G) and 1 (c.*156_157del) polymorphisms were identified at the LRP12 coding region and TRIB1 3' untranslated region, respectively. Association analyses between LRP12 and TRIB1 genotypes did not reveal any significant effect on serum lipid concentrations, suggesting that variation of these two loci does not explain the segregation of the SSC4 QTL. However, highly significant associations were observed for gluteus medius saturated fatty acid content (LRP12 c.1101A > G, P = 0.0006; TRIB1 c.*156_157del, P = 0.0003). In the light of these and other findings, the potential involvement of LRP12 and TRIB1 in muscle lipid metabolism deserves to be further explored.

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.

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.

Mapping and tissue mRNA expression analysis of the pig solute carrier 27A (SLC27A) multigene family.

Solute-carrier family 27A molecules are integral transmembrane proteins that play a fundamental role in the uptake of long-chain fatty acids into mammalian cells. Our goal was to characterize this multigene family in pigs. Chromosomal location of the six porcine SLC27A genes was determined by radiation hybrid mapping and indicated that the six genes map to six different chromosomal locations. Moreover, we analyzed SLC27A mRNA expression in six pig tissues by quantitative RT-PCR. While SLC27A1, SLC27A3 and SLC27A4 were expressed in most, if not all, analyzed tissues, SLC27A2, SLC27A5 and SLC27A6 were predominantly expressed in the liver. In general, pig and human SLC27A mRNA expression profiles were remarkably concordant, although important differences were observed for SLC27A1 and SLC27A6 mRNAs. Discrepancies between mRNA expression profiles have been observed even in closely related primate species, and they might reflect the acquisition of regulatory changes promoting evolutionary adaptation.