Additional file 6: Table S6. of Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location

Complete list of key upstream regulators proposed in response to diets in subcutaneous adipose tissue and associated biological processes. (XLSX 18 kb

Additional file 4: Table S4. of Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location

Detail list of genes associated with different biological process within a small interconnected module in perirenal adipose tissue of pigs fed a high-fat high-fiber diet. (XLSX 11 kb

Additional file 2: Table S2. of Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location

Summary of the biological processes shared by genes being commonly regulated by diet across adipose tissue. (DOCX 23 kb

Additional file 1: Table S1. of Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location

List of differentially expressed probes commonly regulated by diets across perirenal and subcutaneous adipose tissues. (XLSX 207 kb

Additional file 3: Table S3. of Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location

List of co-expressed probes within a small module mainly attributed to perirenal adipose tissue related responses to diet. (XLSX 40 kb

Additional file 7: Table S7. of Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location

Primers used for qPCR analysis. (DOCX 17 kb

Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken

In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments

Distribution of functional polymorphisms.

<p>1: Number of SNPs having a potential impact on protein function; Number of total SNPs affecting protein sequence is given in brackets.</p><p>2: Number of SNPs having a nonsense impact; Number of amino acids and percentage of protein sequence that are lost are given in brackets.</p><p>3: Number of coding indels; Number of amino acids and percentage of protein sequence that are lost are given in brackets.</p><p>Distribution of functional polymorphisms.</p

Chromosomal location of present and previously published QTLs related to abdominal fat weight.

<p>Empty boxes encompass the confidence interval of the QTL, when available. Plain boxes point out the QTL peak location, when available. QTLs colored in red are genome-wide significant (<i>p</i><0.05), while those colored in blue are suggestive QTLs (<i>p</i><0.2). QTLs described in the present study are colored in orange. ^a Ankra-Badu <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-AnkraBadu1" target="_blank">[30]</a>, ^b Zhou <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Zhou1" target="_blank">[54]</a>, ^c McElroy <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-McElroy1" target="_blank">[55]</a>, ^d Jennen <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Jennen1" target="_blank">[56]</a>, ^e Tatsuda <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Tatsuda1" target="_blank">[57]</a>, ^f Ikeobi <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Ikeobi1" target="_blank">[28]</a>, ^g Lagarrigue <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Lagarrigue1" target="_blank">[27]</a>, ^h Park <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Park1" target="_blank">[58]</a>, ⁱ Wang <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Wang1" target="_blank">[59]</a>, ^j Nadaf <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Nadaf1" target="_blank">[60]</a>, ^k Demeure <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Demeure1" target="_blank">[9]</a>, ^l Tian <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111299#pone.0111299-Tian1" target="_blank">[61]</a>.</p

Number of analyzed RNA and DNA sequences in the study (after alignment to Galgal4).

<p>Number of analyzed RNA and DNA sequences in the study (after alignment to Galgal4).</p