Additional file 1 of Multi-tissue metabolic and transcriptomic responses to a short-term heat stress in swine

Additional file 1. Table of the DEGs identified in the seven tissues. Cutoff for adjusted p-value was fixed at 0.05

Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing

<div><p>Reciprocal translocations are the most frequently occurring constitutional structural rearrangements in mammalian genomes. In phenotypically normal pigs, an incidence of 1/200 is estimated for such rearrangements. Even if constitutional translocations do not necessarily induce defects and diseases, they are responsible for significant economic losses in domestic animals due to reproduction failures. Over the last 30 years, advances in molecular and cytogenetic technologies have led to major improvements in the resolution of the characterization of translocation events. Characterization of translocation breakpoints helps to decipher the mechanisms that lead to such rearrangements and the functions of the genes that are involved in the translocation. Here, we describe the fine characterization of a reciprocal translocation t(3;4) (p1.3;q1.5) detected in a pig line. The breakpoint was identified at the base-pair level using a positional cloning and chromosome walking strategy in somatic cell hybrids that were generated from an animal that carries this translocation. We show that this translocation occurs within the <i>ADAMTSL4</i> gene and results in a loss of expression in homozygous carriers. In addition, by taking this translocation as a model, we used a whole-genome next-generation mate-pair sequencing approach on pooled individuals to evaluate this strategy for high-throughput screening of structural rearrangements.</p></div

Map of the SSC4 region containing the breakpoint.

<p>All the markers (microsatellites, SNPs and STS) used in each round of PCR amplification are indicated on the map corresponding to the 106.5–120.5 Mb interval (a) or on a zoom of the 107.80–107.96 Mb interval (b). The successive batches of STS are indicated by a number in brackets following the STS names. Screening results obtained for each marker on Hb1.8 are represented by colors (blue: positive, grey: negative). The smallest interval on the SSC4 map is highlighted in white and the names of the two adjacent STS are indicated in bold.</p

Map of the SSC3 region containing the breakpoint.

<p>All the markers (microsatellites, SNPs and STS) used in each round of PCR amplification are indicated on the map corresponding to the 22–32 Mb interval (a) or on a zoom of the 23.80–23.87 Mb interval (b). The successive batches of STS are indicated by a number in brackets following the STS names. Screening results obtained for each marker on Hb1.8 are represented by colors (yellow: positive, grey: negative). The smallest interval on the SSC3 map is highlighted in white and the names of the two adjacent STS are indicated in bold.</p

Fluorescent in situ hybridization of the pIRS-PCR probe, derived from hybrid Hb1.8, on normal pig metaphase chromosomes.

<p>pIRS-PCR products label the entire length of chromosomes 1, 8, 10, 16, X, and partially chromosomes 3, 4 and 5. Chromosomes 3 and 4 are indicated with yellow and blue arrows respectively (a), and are magnified in (b). On these two chromosomes, signals are observed on the p arm for SSC3 and in the p15-q22 region for SSC4, confirming the presence of the translocated derivative chromosome der(4) in Hb1.8 hybrid clone.</p

Distribution of discordant mate-pairs linking SSC3 to SSC4.

<p>Each circle represents a single mate-pair with one read mapped to SSC3 (x-axis) and the other read mapped to SSC4 (y-axis). In total, more than 12,000 mate-pairs link the two chromosomes, underlining the high background noise due to false-positive discordant mate-pairs. The dark green circle, where the two dashed lines cross, highlights a concentration of mate-pairs linking the two regions involved in the translocation.</p

Results obtained by PCR-screening of each hybrid clone with microsatellite markers.

<p>Results obtained by PCR-screening of each hybrid clone with microsatellite markers.</p

Karyotype of the balanced reciprocal translocation t(3;4)(p1.3;q1.5).

<p>(a): G-band karyotype obtained from a LW female, heterozygous for the translocation. The breakpoint positions on SSC3 and SSC4 are indicated with arrows. (b): Schematic representation of SSC3 and SSC4 pairs including one normal SSC3 or SSC4 chromosome (N) and one translocated chromosome der(3) or der(4).</p

^1HNMR-Based metabolomic profiling method to develop plasma biomarkers for sensitivity to chronic heat stress in growing pigs

<div><p>The negative impact of heat stress (HS) on the production performances in pig faming is of particular concern. Novel diagnostic methods are needed to predict the robustness of pigs to HS. Our study aimed to assess the reliability of blood metabolome to predict the sensitivity to chronic HS of 10 F1 (Large White × Creole) sire families (SF) reared in temperate (TEMP) and in tropical (TROP) regions (n = 56±5 offsprings/region/SF). Live body weight (BW) and rectal temperature (RT) were recorded at 23 weeks of age. Average daily feed intake (AFDI) and average daily gain were calculated from weeks 11 to 23 of age, together with feed conversion ratio. Plasma blood metabolome profiles were obtained by Nuclear Magnetic Resonance spectroscopy (^1HNMR) from blood samples collected at week 23 in TEMP. The sensitivity to hot climatic conditions of each SF was estimated by computing a composite index of sensitivity (I_<i>sens</i>) derived from a linear combination of <i>t</i> statistics applied to familial BW, ADFI and RT in TEMP and TROP climates. A model of prediction of sensitivity was established with sparse Partial Least Square Discriminant Analysis (<i>s</i>PLS-DA) between the two most robust SF (n = 102) and the two most sensitive ones (n = 121) using individual metabolomic profiles measured in TEMP. The sPLS-DA selected 29 buckets that enabled 78% of prediction accuracy by cross-validation. On the basis of this training, we predicted the proportion of sensitive pigs within the 6 remaining families (n = 337). This proportion was defined as the predicted membership of families to the sensitive category. The positive correlation between this proportion and I_<i>sens</i> (r = 0.97, P < 0.01) suggests that plasma metabolome can be used to predict the sensitivity of pigs to hot climate.</p></div

List of the 43 haplotypes defined with the 35 SNP of the chip surrounding <i>SOX9</i>.

<p>The haplotypes were classified according to the p-value obtained for each marker (sharing of the transmitted allele from the most significant SNP to the less significant one). For each marker the preferentially transmitted allele was noted “1”, the alternative allele “0” and the log(1/p) obtained with the TDT analysis was reported. On the right, the frequency of each haplotype among the affected animals is reported (the 3 most frequent ones are indicated in red). The marker shown in red box is the marker closest to the gene <i>SOX9</i>.</p