Desaturation ratio by <i>SCD</i> diplotype and tissue in purebred Duroc.

<p>The presence of haplotype H1 is associated to higher 18∶1/18∶0 ratio both in intramuscular and subcutaneous fat. The H1H1 pigs have a greater 18∶1/18∶0 ratio than the H2H2 animals in the muscles <i>gluteus medius</i> (H1H1−H2H2∶0.65), <i>longissimus dorsi</i> (H1H1−H2H2∶0.67), and <i>semimembranosus</i> (H1H1−H2H2∶0.57), and in the subcutaneous fat (H1H1−H2H2∶0.50), with the heterozygote H1H2 showing an intermediate effect. No difference is observed among diplotypes in liver. Error bars represent standard errors. Columns lacking a common letter within tissue differ (p<0.01, for <i>gluteus medius</i> and <i>longissimus dorsi</i>; p<0.05, for <i>semimembranosus</i> and subcutaneous fat).</p

Characterization of the 5′ flanking region to the transcription start site of the pig <i>SCD</i> gene.

<p>(<b>A</b>) Schematic representation of recognition motifs for several transcription factor binding sites in the proximal 5′ flanking region of the pig <i>SCD</i> gene. The relative position of the three SNPs polymorphisms identified in this promoter (AY487830: <i>g.2108C>T, g.2228T>C</i> and <i>g.2281A>G</i>) are indicated. (<b>B</b>) Sequence encompassing three SNPs polymorphisms in the promoter region of the pig <i>SCD</i> gene. Position numbering is relative to the translation START codon (in blue). The transcription start site is at position −175 (arrow). Coding sequence and the 5′ non-coding region is shown in uppercase and italics, respectively. The motifs for transcription factors SP1, PPARG, NF-1, RAR:RXR and the TATA-box are underlined and notated above the sequence.</p

Desaturation 18∶1/18∶0 ratio and content of 18∶0+18∶1 by batch and <i>SCD</i> diplotype in purebred Duroc.

<p>The haplotype H1 affects the 18∶1/18∶0 ratio in the muscle <i>gluteus medius</i> but not the 18∶0+18∶1 content (in percentage of total fatty acids). H1 exerts a consistent favourable additive effect on the desaturation ratio across all time-batches. Analyses were performed both within batch (1 to 12) and across batches (All). Values are expressed as the least square mean for each trait by genotype. Means lacking a common superscript within trait differ (p<0.05). The number of pigs (n) genotyped per batch ranged from 22 to 109. The frequency of the haplotype H1 (f (H1)) by batch ranged from 0.33 to 0.57.</p

Pork loins with optimal intramuscular fat but different monounsaturated fatty acid content.

<p>The monounsaturated pamitoleic (16∶1) and oleic (18∶1) acids are more abundant in the loin in panel A (4.0% and 44.2%, respectively) than in the loin in panel B (3.0% and 41.4%), expressed as percentage with respect to total fatty acids. The peaks of these two fatty acids in the chromatograms below are labelled accordingly, along with those of their respective precursors, palmitic (16∶0) and stearic (18∶0) acids. The desaturation ratios 16∶1/16∶0 and 18∶1/18∶0 are higher in loin A (0.16 and 3.7, respectively) than in loin B (0.12 and 2.8, respectively). Genotyping for <i>g.2228T>C</i> in the promoter region of the <i>SCD</i> gene revealed that loin A was homozygous for allele T and loin B homozygous for allele C.</p

The haplotype H1 upregulates <i>SCD</i> mRNA expression in muscle.

<p>Pigs H1H1 had higher <i>SCD</i> mRNA expression than the H2H2 pigs in muscle <i>semimembranosus</i> but not in subcutaneous fat and liver. Values are expressed relative to the mean expression in the diplotype with the greater expression in each tissue. Error bars represent standard errors. Columns lacking a common letter within tissue differ (p<0.05). Haplotype H1 had a favorable additive effect on <i>SCD</i> mRNA expression in muscle (24.9±8.2, p<0.01) but not in subcutaneous fat (7.2±12.5, p = 0.57) and liver (−1.5±15.0, p = 0.91).</p

Haplotype frequencies of single nucleotide polymorphisms (SNPs) <i>AY487830:g.2108C>T</i>, <i>g.2228T>C</i>, and <i>g.2281A>G</i> at the promoter region of the <i>SCD</i> gene in different pig populations.

a<p>Purebred pigs include Duroc (DU), Landrace (L), Pietrain, Iberian (IB), and wild boar. Numbers after the breed refer to independent lines from the same breed. The Duroc-1 was the line used for the association analysis (Exp 1) and crossbreds in Exp 2 where those used for the validation analysis.</p

Desaturation ratio in opposite homozygous siblings for <i>SCD</i> haplotypes H1 and H2.

<p>(<b>A</b>) Ratio 18∶1/18∶0, and (<b>B</b>) 18∶0+18∶1 content (in percentage of total fatty acids) in the muscle <i>gluteus medius</i> of homozygous H1H1 and H2H2 sibling pairs (n = 25) are plotted against the sibling pair mean value. The H1H1 pigs showed a greater desaturation ratio (p<0.01) than their H2H2 sibs but the same 18∶0+18∶1 (p = 0.94) content. The associated p-values were determined using a paired t-test. Regression lines were fitted for each diplotype (blue: H1H1; red: H2H2). The difference between homozygotes for 18∶1/18∶0 increased with 18∶1/18∶0 (p<0.05), with H1H1 sibs showing a trend higher than the expected (1.17±0.10) and H2H2 sibs lower (0.83±0.10). The regression of 18∶0+18∶1 on the litter mean value was not different from the average trend (unity) in both genotypes (p = 0.89).</p

Desaturation ratio by <i>SCD</i> diplotype in experimental crossbreds.

<p>The effect of <i>SCD</i> haplotypes on the 18∶1/18∶0 ratio was validated in three experimental genetic types. Sows from the investigated Duroc line (Duroc-1), which was used as control, were sired by boars from an independent Duroc line (DU-3 × DU-1) and by Iberian boars (IB-2 × DU-1), and their progeny contemporarily compared with Large White × Landrace barrows (LW-1 × L-2). The results confirmed that the H1 haplotype increased the 18∶1/18∶0 ratio in the <i>gluteus medius</i> muscle in all genetic types. The H1H1 pigs showed a higher desaturation ratio than H2H2 (0.81 more in Duroc-1 and and 0.61 more in DU-3 × DU-1), H1H2 (0.37 more in IB-2 × DU-1), and H1H3 (0.38 more in LW-1 × L-2) pigs. All LW-1 × L-2 pigs were AA for SNP <i>g.2281A>G</i>, thereby excluding this SNP as a causative mutation. Error bars represent standard errors. Columns lacking a common letter within genetic type differ (p<0.05).</p

Primers used in the real time quantitative PCR assay.

<p>Primers used in the real time quantitative PCR assay.</p

Effect of the genome-wide <i>P</i>-value cutoff on the relative frequencies of <i>trans</i>- and <i>cis</i>-eQTL.

<p>Effect of the genome-wide <i>P</i>-value cutoff on the relative frequencies of <i>trans</i>- and <i>cis</i>-eQTL.</p