Polymorphisms identified in the proximal promoter and coding regions of the <i>ELOVL6</i> gene.

1<p>Positions relative to the transcription start site using, as reference, the GenBank NW_003610943 sequence.</p>2<p>Referring to the coding region (GenBank:AB529461).</p>3<p>SNPs genotyped in the BC1_LD population.</p

Reduction of the QTL interval by GWAS and LDLA analyses and gene mapping of <i>ELOVL6</i>.

<p>Plot of GWAS (blue points) and LDLA patterns (red line) for palmitic (A) and palmitoleic (B) acids. The X-axis represents chromosome 8 positions in Mb and the Y-axis shows the –log10 (p-value). The vertical green line represents the position of the <i>ELOVL6</i> gene on SSC8. Horizontal dashed lines mark the genome-wide significance level (FDR-based q-value≤0.05). Positions in Mb are relative to <i>Sscrofa10.2 assembly</i> of the pig genome.</p

Significant region obtained in GWAS for liver gene expression.

<p>Association analysis between the liver <i>ELOVL6</i> expression level and SNP genotypes for SSC4. Positions in Mb are relative to <i>Sscrofa10.2 assembly</i> of the pig genome. Vertical, dashed lines indicate the location of positional candidate genes. Horizontal, dashed lines mark the chromosome-wide significance level (FDR-based q-value≤0.1).</p

A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits

<div><p>Copy number variations (CNVs) are important genetic variants complementary to SNPs, and can be considered as biomarkers for some economically important traits in domestic animals. In the present study, a genomic analysis of porcine CNVs based on next-generation sequencing data was carried out to identify CNVs segregating in an Iberian x Landrace backcross population and study their association with fatty acid composition and growth-related traits. A total of 1,279 CNVs, including duplications and deletions, were detected, ranging from 106 to 235 CNVs across samples, with an average of 183 CNVs per sample. Moreover, we detected 540 CNV regions (CNVRs) containing 245 genes. Functional annotation suggested that these genes possess a great variety of molecular functions and may play a role in production traits in commercial breeds. Some of the identified CNVRs contained relevant functional genes (e.g., <i>CLCA4</i>, <i>CYP4X1</i>, <i>GPAT2</i>, <i>MOGAT2</i>, <i>PLA2G2A</i> and <i>PRKG1</i>, among others). The variation in copy number of four of them (<i>CLCA4</i>, <i>GPAT2</i>, <i>MOGAT2</i> and <i>PRKG1</i>) was validated in 150 BC1_LD (25% Iberian and 75% Landrace) animals by qPCR. Additionally, their contribution regarding backfat and intramuscular fatty acid composition and growth–related traits was analyzed. Statistically significant associations were obtained for CNVR112 (<i>GPAT2</i>) for the C18:2(n-6)/C18:3(n-3) ratio in backfat and carcass length, among others. Notably, GPATs are enzymes that catalyze the first step in the biosynthesis of both triglycerides and glycerophospholipids, suggesting that this CNVR may contribute to genetic variation in fatty acid composition and growth traits. These findings provide useful genomic information to facilitate the further identification of trait-related CNVRs affecting economically important traits in pigs.</p></div

Fatty acid composition of different <i>ELOVL6:c.-533C>T</i> genotypes in muscle and backfat.

<p>Data include: percentage of C16:0 (A) and C16:1(n-7) fatty acids (B) in muscle and backfat; and the elongation ratios C18:0/C16:0 (C) and C18:1(n-7)+C18:1(n-9)/C16:0 (D) in muscle and backfat. Data represent mean ± SEM. Values with different superscript letters (a, b and c) indicate significant differences between groups (p-value < 0.05), as determined by a single stratum analysis of variance considering sex and batch as fixed effects.</p

Co-association networks based on the AWM approach.

<p><b>A</b>) Full network formed by 1,747 nodes, representing genes and SNPs, and a total of 316,166 edges, accounting for the interactions among them. <b>B</b>) Network formed by 513 nodes and 639 edges representing genes and interactions among the top trio of transcription factors. Colours corresponded to different functions according to the legend.</p

Data_Sheet_1_Influence of dietary n-3 long-chain fatty acids on microbial diversity and composition of sows’ feces, colostrum, milk, and suckling piglets’ feces.docx

IntroductionVery little is known about the impact of n-3 long-chain fatty acids (n-3 LCFAs) on the microbiota of sows and their piglets. The aim of this study was to evaluate the effect of n-3 LCFA in sow diets on the microbiota composition of sows’ feces, colostrum, and milk as well as that of piglets’ feces.MethodsTwenty-two sows were randomly assigned to either a control or an n-3 LCFA diet from service to weaning. Sows’ and piglets’ performance was monitored. The gestating and lactating sows’ microbiomes in feces, colostrum, and milk were characterized by 16s ribosomal RNA gene sequencing. The fecal microbiome from the two lowest (>800 g) and the two highest birth weight piglets per litter was also characterized, and the LPS levels in plasma were analyzed at weaning.Results and Discussionn-3 LCFA increased microbiota alpha diversity in suckling piglets’ and gestating sows’ feces. However, no effects were observed in colostrum, milk, or lactating sows’ feces. Dietary n-3 LCFA modified the microbiota composition of gestating sows’ feces, milk, and suckling piglets’ feces, without affecting lactating sows’ feces or colostrum. In gestating sows’ feces and milk, the decrease in genus Succinivibrio and the increase of Proteobacteria phylum, due to the increased genera Brenneria and Escherichia, respectively, stand out. In the feces of suckling piglets, the higher abundance of the beneficial genus Akkermansia and Bacteroides, and different species of Lactobacillus are highlighted. In addition, positive correlations for families and genera were found between lactating sows’ feces and milk, milk and suckling piglets’ feces, and lactating sows’ feces and suckling piglets’ feces. To conclude, dietary n-3 LCFA had a positive impact on the microbiome of suckling piglet’s feces by increasing microbial diversity and some beneficial bacteria populations, had a few minor modifications on the microbiome of milk and gestating sows’ feces and did not change the microbiome in lactating sows’ feces or colostrum. Therefore, this study shows the effect of dietary n-3 LCFA on the microbiota of sows, colostrum, milk, and suckling piglets during the lactation period providing crucial information on the microbiota status at the early stages of life, which have an impact on the post-weaning.</p

Summary of CNVs of the seven analyzed pigs.

<p>Summary of CNVs of the seven analyzed pigs.</p

Association of <i>ELOVL6: c.-533C>T</i> genotypes on gene expression in backfat.

<p>A SNP genome-wide association study was performed with <i>ELOVL6</i> relative expression levels measured by RT-qPCR in 110 samples from backfat, liver and muscle. Data include: Schematic representation of the elongation pathway of 16-carbon fatty acid (A), <i>ELOVL6</i> expression levels in backfat (B), liver (C) and muscle (D). Data represent means ± SEM. Values with different superscript letters (a, b and c) indicate significant differences between groups (p-value < 0.05), as determined by a single stratum analysis of variance considering sex and batch as fixed effects.</p

Phenotypic traits registered in the BC1_LD (F1× Landrace) and in the BC (F2× Landrace) and F3 generations of the Iberian × Landrace cross.

<p>Phenotypic traits registered in the BC1_LD (F1× Landrace) and in the BC (F2× Landrace) and F3 generations of the Iberian × Landrace cross.</p