Development of a 64 SNV panel for breed authentication in Iberian pigs and their derived meat products.

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.

Direct and maternal additive effects are not the main determinants of Iberian piglet perinatal mortality.

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.

Adipose tissue transcriptional response of lipid metabolism genes in growing Iberian pigs fed oleic acid v. carbohydrate enriched diets.

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.

Assessing effective population size, coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed.

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.

Effects of dietary fat saturation on fatty acid composition and gene transcription in different tissues of Iberian pigs.

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.

Dietary energy source largely affects tissue fatty acid composition but has minor influence on gene transcription in Iberian pigs.

A trial was performed to compare the effects of different dietary sources of MUFA on the fatty 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. Animals 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 lipid 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 several biological functions including lipid metabolic processes. 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 prostanoid synthesis, with LEP, RXRG, and PTGS2 genes playing mayor roles.

Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics.

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.

Recombination rates across porcine autosomes inferred from high-density linkage maps.

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.

Joint effects of porcine leptin and leptin receptor polymorphisms on productivity and quality traits.

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.

Effects of porcine MC4R and LEPR polymorphisms, gender and Duroc sire line on economic traits in Duroc × Iberian crossbred pigs.

Polymorphisms MC4R c.1426 A>G (p.Asp298Asn) and LEPR c.2002 C>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.2002 C>T mutation, were detected on the main traits. LEPR c.2002 T allele increased body weight (2.5 ± 0.7 kg), backfat thickness (1.5 ± 0.4mm), 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.2002 T 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.1426 A>G SNP were identified. A genetic test based on the LEPR c.2002 C>T SNP may be useful to select Duroc sires to reduce undesirable heterogeneity of carcasses and premium cuts of crossbred animals.

Divergence time estimates of East Asian and European pigs based on multiple near complete mitochondrial DNA sequences.

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.

Evaluation of FABP2 as candidate gene for a fatty acid composition QTL in porcine chromosome 8.

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 F(2) 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.

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.

Identification of mitochondrial markers for genetic traceability of European wild boars and Iberian and Duroc pigs.

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.

Mitochondrial genome polymorphisms associated with longissimus muscle composition in Iberian pigs.

We carried out a study to investigate the associations between mitochondrial DNA polymorphisms and meat quality traits (intramuscular fat and protein content of the longissimus) in an Iberian porcine line named Torbiscal. The studied pigs (n = 319) belong to 9 maternal lineages and were previously assigned to 6 mitochondrial haplotypes (H1 to H6), based on Cytochrome b and Dloop sequences. Statistical analyses, following a bivariate mixed model, show a greater fat content and lower protein content in H3 haplotype carriers than H1, H2, H4, H5, and H6 haplotype carriers. The magnitudes of these differences are close to 1 g of fat and -0.5 g of protein per 100 g of muscle. To identify the causative mutation of these effects on intramuscular fat and protein contents, the complete mitochondrial DNA sequence of 6 individuals was determined, each one carrying a different mitochondrial haplotype. The alignments of these 6 complete mitochondrial sequences allowed identification of 32 substitutions and 2 indels. Two polymorphic positions were exclusively detected in H3 carriers: a synonymous transition 9104C > T in the gene-coding region of Cytochrome c oxidase subunit III and a substitution 715A > G in 12S rRNA. Genotyping results of a larger number of Torbiscal samples showed the exclusive presence of 9104T and 715G alleles in H3 carriers. The detected candidate substitutions are located in essential mitochondrial genes, and although they do not change the amino acid composition, we cannot disregard a potential change in the secondary structure of their corresponding mRNA. The usefulness of these polymorphisms as markers in selection programs requires validation of the consistency of these results in other Iberian pig lines.

Effect of exercise on skeletal muscle proteolytic enzyme activity and meat quality characteristics in Iberian pigs.

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: 5.2kg). Pigs were randomly distributed in three groups. Two groups receiving the same diet were reared in confinement, one housed in individual pens of 8m(2) (sedentary group) and the other was housed outdoor with daily (up to 2km) forced walking (exercise group). And 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.

QTL detection on porcine chromosome 12 for fatty-acid composition and association analyses of the fatty acid synthase, gastric inhibitory polypeptide and acetyl-coenzyme A carboxylase alpha genes.

Refinement of previous QTL on porcine chromosome 12 for fatty-acid composition and a candidate gene association analysis were conducted using an Iberian x 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.

Characterization of the porcine acyl-CoA synthetase long-chain 4 gene and its association with growth and meat quality traits.

Summary Long-chain acyl-CoA synthetase (ACSL) catalyses the formation of long-chain acyl-CoA from fatty acid, ATP and CoA, activating fatty acids for subsequent reactions. Long-chain acyl-CoA synthetase thus plays an essential role in both lipid biosynthesis and fatty acid degradation. The ACSL4 gene was evaluated as a positional candidate gene for the quantitative trait loci (QTL) located between SW2456 and SW1943 on chromosome X. We have sequenced 4906 bp of the pig ACSL4 mRNA. Sequence analysis allowed us to identify 10 polymorphisms located in the 3'-UTR region and to elucidate two ACSL4 haplotypes. Furthermore, a QTL and an association study between polymorphisms of the ACSL4 gene and traits of interest were carried out in an Iberian x Landrace cross. We report QTL that have not been previously identified, and we describe an association of the ACSL4 polymorphisms with growth and percentage of oleic fatty acid. Finally, we have determined allelic frequencies in 140 pigs belonging to the Iberian, Landrace, Large White, Meishan, Pietrain, Duroc, Vietnamese, Peccary and Babirusa populations.

Characterization of OCA2 cDNA in different porcine breeds and analysis of its potential effect on skin pigmentation in a red Iberian strain.

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.