Using transcriptome profiling to characterize QTL regions on chicken chromosome 5

<p>Abstract</p> <p>Background</p> <p>Although many QTL for various traits have been mapped in livestock, location confidence intervals remain wide that makes difficult the identification of causative mutations. The aim of this study was to test the contribution of microarray data to QTL detection in livestock species. Three different but complementary approaches are proposed to improve characterization of a chicken QTL region for abdominal fatness (AF) previously detected on chromosome 5 (GGA5).</p> <p>Results</p> <p>Hepatic transcriptome profiles for 45 offspring of a sire known to be heterozygous for the distal GGA5 AF QTL were obtained using a 20 K chicken oligochip. mRNA levels of 660 genes were correlated with the AF trait. The first approach was to dissect the AF phenotype by identifying animal subgroups according to their 660 transcript profiles. Linkage analysis using some of these subgroups revealed another QTL in the middle of GGA5 and increased the significance of the distal GGA5 AF QTL, thereby refining its localization. The second approach targeted the genes correlated with the AF trait and regulated by the GGA5 AF QTL region. Five of the 660 genes were considered as being controlled either by the AF QTL mutation itself or by a mutation close to it; one having a function related to lipid metabolism (HMGCS1). In addition, a QTL analysis with a multiple trait model combining this 5 gene-set and AF allowed us to refine the QTL region. The third approach was to use these 5 transcriptome profiles to predict the paternal Q versus q AF QTL mutation for each recombinant offspring and then refine the localization of the QTL from 31 cM (100 genes) at a most probable location confidence interval of 7 cM (12 genes) after determining the recombination breakpoints, an interval consistent with the reductions obtained by the two other approaches.</p> <p>Conclusion</p> <p>The results showed the feasibility and efficacy of the three strategies used, the first revealing a QTL undetected using the whole population, the second providing functional information about a QTL region through genes related to the trait and controlled by this region (HMGCS1), the third could drastically refine a QTL region.</p

Transcriptome profiling of the feeding-to-fasting transition in chicken liver

<p>Abstract</p> <p>Background</p> <p>Starvation triggers a complex array of adaptative metabolic responses including energy-metabolic responses, a process which must imply tissue specific alterations in gene expression and in which the liver plays a central role. The present study aimed to describe the evolution of global gene expression profiles in liver of 4-week-old male chickens during a 48 h fasting period using a chicken 20 K oligoarray.</p> <p>Results</p> <p>A large number of genes were modulated by fasting (3532 genes with a pvalue corrected by Benjamini-Hochberg < 0.01); 2062 showed an amplitude of variation higher than +/- 40% among those, 1162 presented an human ortholog, allowing to collect functional information. Notably more genes were down-regulated than up-regulated, whatever the duration of fasting (16 h or 48 h). The number of genes differentially expressed after 48 h of fasting was 3.5-fold higher than after 16 h of fasting. Four clusters of co-expressed genes were identified by a hierarchical cluster analysis. Gene Ontology, KEGG and Ingenuity databases were then used to identify the metabolic processes associated to each cluster. After 16 h of fasting, genes involved in ketogenesis, gluconeogenesis and mitochondrial or peroxisomal fatty acid beta-oxidation, were up-regulated (cluster-1) whereas genes involved in fatty acid and cholesterol synthesis were down-regulated (cluster-2). For all genes tested, the microarray data was confirmed by quantitative RT-PCR. Most genes were altered by fasting as already reported in mammals. A notable exception was the <it>HMG-CoA synthase 1 </it>gene, which was up-regulated following 16 and 48 h of fasting while the other genes involved in cholesterol metabolism were down-regulated as reported in mammalian studies. We further focused on genes not represented on the microarray and candidates for the regulation of the target genes belonging to cluster-1 and -2 and involved in lipid metabolism. Data are provided concerning PPARa, SREBP1, SREBP2, NR1H3 transcription factors and two desaturases (FADS1, FADS2).</p> <p>Conclusion</p> <p>This study evidences numerous genes altered by starvation in chickens and suggests a global repression of cellular activity in response to this stressor. The central role of lipid and acetyl-CoA metabolisms and its regulation at transcriptional level are confirmed in chicken liver in response to short-term fasting. Interesting expression modulations were observed for <it>NR1H3, FADS1 </it>and <it>FADS2 </it>genes. Further studies are needed to precise their role in the complex regulatory network controlling lipid metabolism.</p

Layers response to a suboptimal diet through phenotype and transcriptome changes in four tissues

Poultry meat and eggs are major sources of nutrients in the human diet. The long production career of laying hens expose them to biotic or abiotic stressors, lowering their production. Understanding the mechanisms of adaptation to stress is crucial for selecting robust animals and meeting the needs of a growing human population. In this study, financed by the French ChickStress and the European Feed-a-Gene (grant agreement no. 633531) programs, we compared the effects of a 15%-energy-reduced diet (feed stress, FS) vs a commercial diet (control, CT) on phenotypic traits and adipose, blood, hypothalamus and liver transcriptomes in two feed-efficiency-diverging lines. Phenotypic traits showed differences between lines or diets, but no line × diet interaction. In the FS group, feed intake (FI) increased and hens had lower body- and abdominal adipose weight, compared to CT group. We found no differences in egg production or quality. At the transcriptomic level, 16,461 genes were expressed in one or more tissues, 41% of which were shared among tissues. We found differentially expressed genes between lines or diet in all tissues, and almost no line × diet interactions. Focusing on diet, adipose and liver transcriptomes were unaffected. In blood, pathways linked to amino acids, monosaccharides, and steroid metabolism were affected, while in the hypothalamus, changes were observed in fatty acid metabolism and endocannabinoid signalling. Given the similarities in egg production, the FS animals seem to have adapted to the stress by increasing FI and by mobilizing adipose reserves. Increase in FI did not appear to affect liver metabolism, and the mobilization of adipose reserves was apparently not driven at the transcriptomic level. In blood, the pathways linked to metabolic processes suggest a metabolic role for this tissue in chicken, whose erythrocytes are nucleated and contain mitochondria. FI increase might be linked to the hypothalamic pathway of endocannabinoid signalling, which are lipid-based neurotransmitters, notably involved in the regulation of appetite

First Detection of Near-Infrared Line Emission from Organics in Young Circumstellar Disks

We present an analysis of high-resolution spectroscopy of several bright T Tauri stars using the VLT/CRIRES and Keck/NIRSPEC spectrographs, revealing the first detections of emission from HCN and C2H2 in circumstellar disks at near-infrared wavelengths. Using advanced data reduction techniques we achieve a dynamic range with respect to the disk continuum of ~500 at 3 microns, revealing multiple emission features of H2O, OH, HCN, and C2H2. We also present stringent upper limits for two other molecules thought to be abundant in the inner disk, CH4 and NH3. Line profiles for the different detected molecules are broad but centrally peaked in most cases, even for disks with previously determined inclinations of greater than 20 degrees, suggesting that the emission has both a Keplerian and non-Keplerian component as observed previously for CO emission. We apply two different modeling strategies to constrain the molecular abundances and temperatures: we use a simplified single-temperature LTE slab model with a Gaussian line profile to make line identifications and determine a best-fit temperature and initial abundance ratios, and we compare these values with constraints derived from a detailed disk radiative transfer model assuming LTE excitation but utilizing a realistic temperature and density structure. Abundance ratios from both sets of models are consistent with each other and consistent with expected values from theoretical chemical models, and analysis of the line shapes suggests the molecular emission originates from within a narrow region in the inner disk (R < 1 AU).Comment: Accepted to the Astrophysical Journa

Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken

<p>Abstract</p> <p>Background</p> <p>Integrative genomics approaches that combine genotyping and transcriptome profiling in segregating populations have been developed to dissect complex traits. The most common approach is to identify genes whose eQTL colocalize with QTL of interest, providing new functional hypothesis about the causative mutation. Another approach includes defining subtypes for a complex trait using transcriptome profiles and then performing QTL mapping using some of these subtypes. This approach can refine some QTL and reveal new ones.</p> <p>In this paper we introduce Factor Analysis for Multiple Testing (FAMT) to define subtypes more accurately and reveal interaction between QTL affecting the same trait. The data used concern hepatic transcriptome profiles for 45 half sib male chicken of a sire known to be heterozygous for a QTL affecting abdominal fatness (AF) on chromosome 5 distal region around 168 cM.</p> <p>Results</p> <p>Using this methodology which accounts for hidden dependence structure among phenotypes, we identified 688 genes that are significantly correlated to the AF trait and we distinguished 5 subtypes for AF trait, which are not observed with gene lists obtained by classical approaches. After exclusion of one of the two lean bird subtypes, linkage analysis revealed a previously undetected QTL on chromosome 5 around 100 cM. Interestingly, the animals of this subtype presented the same q paternal haplotype at the 168 cM QTL. This result strongly suggests that the two QTL are in interaction. In other words, the "q configuration" at the 168 cM QTL could hide the QTL existence in the proximal region at 100 cM. We further show that the proximal QTL interacts with the previous one detected on the chromosome 5 distal region.</p> <p>Conclusion</p> <p>Our results demonstrate that stratifying genetic population by molecular phenotypes followed by QTL analysis on various subtypes can lead to identification of novel and interacting QTL.</p

Constructing a chicken normalised multitissue-cDNA library.

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Implication des protéines PR dans la résistance partielle de la pomme de terre à Phytophthora infestans et Pectobacterium atrosepticum.

Implication des protéines PR dans la résistance partielle de la pomme de terre à Phytophthora infestans et Pectobacterium atrosepticum.Implication des protéines PR dans la résistance partielle de la pomme de terre à Phytophthora infestans et Pectobacterium atrosepticum

Transcriptomics data of liver and adipose tissue highlight lncRNAs as candidates for the lipid metabolism regulation in broilers

Broilers’ body fat is not valued by food industry which must remove fat deposits on broilers’ carcass during slaughter stages. Adiposity variability has a multifactorial origin with a genetic part and genes which regulate lipid metabolism are not all known yet. The aim of this study is to contribute to a better knowledge of these regulatory genes in chicken, and particularly long noncoding (lncRNA) genes, which regulate genes expression implied in a lot of diseases and metabolic processes. Therefore, we used two broilers lines (lean/fat lines) divergently selected on abdominal fat weight and fed with two different diets (high/low fat/fibers). The genotype factor leads to a differential expression (DE) of genes involved in the cholesterol synthesis and the diet factor in the hepatic fatty acid synthesis and secretion. We used RNA‑seq data from two metabolic tissues: 16 livers and 16 adipose tissues and FEELnc has classified more than 6000 expressed lncRNAs. DE analyzes showed 160 (vs. 258) and 266 (vs. 396) lncRNA genes up- and down-regulated respectively between the lean and fat lines in liver (vs. adipose tissue). 30 (vs. 5) and 101 (vs. 1) lncRNA genes are DE between the low and the high fat diet. Amongst them, around 80 lncRNA genes are divergently localized with their nearest coding gene and potentially share a bidirectional promoter. We found some interesting examples concerning key enzymes in cholesterol and fatty acid synthesis for our both factors, genotype and diet which are good candidates for the lipid metabolism regulation in chicken

Comparison of different electrophoretic separations of hen egg white proteins

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