Bar chart example.

<p>(A) NQ plot displaying linear normalized quantity (NQ) vs sample. (B) NQ plot by group displaying logarithmic (Log₂) normalized quantity (NQ) of each group (1 and 2) vs target.</p

Comparisons of data.

<p>(A) Comparison of data obtained with the 2^−ΔΔCT method (DataAssist™) vs the relative standard quantification (DAG Expression). (B) Comparison of data obtained with the Pfaffl model vs the relative standard quantification (DAG Expression). The coefficient of correlation (r) is shown above each plot.</p

DAG Expression; (A) Import window; (B) Assay data table (left) and sample data table (right) work area; (C) Standard curve with a four-fold dilution series (1/4, 1/16, 1/64, 1/256, 1/1024) used to extrapolate the quantity values of Unknown samples; (D) Control-gene stability analysis.

<p>M-values for 4 selected control genes; (E) Results table with different parameters presented for each assay.</p

Results of the haplotype association analysis for the common QTL regions in the merged dataset and each individual backcross.

<p>Results of the haplotype association analysis for the common QTL regions in the merged dataset and each individual backcross.</p

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

<div><p>One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0–3 Mb, for body weight, on SSC2, 3–9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in <i>PDE10A</i>, <i>DHCR7</i>, <i>MFN2 and CCNY</i> genes located within the common QTL regions and those identified near <i>ssc-mir-103-1</i> considered <i>PANK3</i> regulators to be further analysed.</p></div

Phenotypic traits recorded for the backcrossed pigs analyzed.

Number of individuals (N), mean and standard deviation (SD) were calculated. Measures of body weight at 150 days of mean age (BW150), backfat thickness measured at 75 kg (BFT75) and at slaughter (BFTS), mean weights of hams (HW) shoulders (SW) and loin bone-in (LBW) and intramuscular fat content (IMF) in Longissimus dorsi muscle.</p

Distribution of the density of indels across chromosomes calculated as number of indels per Mb.

Chromosomes are sorted in increasing order of density value.</p

Common QTL regions identified.

<p>QTL detected for body weight at 150 days (BW150), ham weight (HW), shoulder weight (SH), loin bone-in weight (LBW) and intramuscular fat (IMF): region name, associated trait, genomic position, dataset where the QTL was identified and actual backcross segregation.</p

Weighted Venn diagram showing the number of indels shared between the three indel detection programs: <i>Dindel</i>, <i>Pindel</i> and <i>SAMtools mpileup</i>.

A total of 1,928,746 indels were found in common.</p

Selection of the ten genotyped indels with the alternative allele frequency in the Iberian (Freq. IB) and Landrace (Freq. LD) founders and their consequence predicted by the <i>VEP</i> platform.

Selection of the ten genotyped indels with the alternative allele frequency in the Iberian (Freq. IB) and Landrace (Freq. LD) founders and their consequence predicted by the VEP platform.</p