Functional analysis of differentially expressed genes between partridges with high and low IR.

<p>DAVID Functional Annotation Cluster (FAC) analysis was conducted on two independent gene lists containing 509 up-regulated genes and 40 down-regulated genes (0 ≤ q ≤ 0.5) under high stringency ease scores. <i>In black</i>: grouped FACs for up-regulated genes. <i>In grey</i>: grouped FACs for down-regulated genes.</p

Transcriptomic Characterization of Innate and Acquired Immune Responses in Red-Legged Partridges (<i>Alectoris rufa</i>): A Resource for Immunoecology and Robustness Selection

<div><p>Present and future challenges for wild partridge populations include the resistance against possible disease transmission after restocking with captive-reared individuals, and the need to cope with the stress prompted by new dynamic and challenging scenarios. Selection of individuals with the best immune ability may be a good strategy to improve general immunity, and hence adaptation to stress. In this study, non-infectious challenges with phytohemagglutinin (PHA) and sheep red blood cells allowed the classification of red-legged partridges (<i>Alectoris rufa</i>) according to their overall immune responses (IR). Skin from the area of injection of PHA and spleen, both from animals showing extreme high and low IR, were selected to investigate the transcriptional profiles underlying the different ability to cope with pathogens and external aggressions. RNA-seq yielded 97 million raw reads from eight sequencing libraries and approximately 84% of the processed reads were mapped to the reference chicken genome. Differential expression analysis identified 1488 up- and 107 down-regulated loci in individuals with high IR versus low IR. Partridges displaying higher innate IR show an enhanced activation of host defence gene pathways complemented with a tightly controlled desensitization that facilitates the return to cellular homeostasis. These findings indicate that the immune system ability to respond to aggressions (either diseases or stress produced by environmental changes) involves extensive transcriptional and post-transcriptional regulations, and expand our understanding on the molecular mechanisms of the avian immune system, opening the possibility of improving disease resistance or robustness using genome assisted selection (GAS) approaches for increased IR in partridges by using genes such as <i>AVN</i> or <i>BF2</i> as markers. This study provides the first transcriptome sequencing data of the Alectoris genus, a resource for molecular ecology that enables integration of genomic tools in further studies.</p></div

Gender differences in total antibody (AbTot) and IgG titers, and mitogen stimulation index (MSI) after non-infectious challenges with sheep red blood cells (SRBC) and phytohemagglutinin (PHA), respectively.

<p>^a-b Within row, values with the same letter are not significantly different (P>0.005).</p><p>Values are expressed as means ± standard deviation: titer as log₂ of the reciprocal of the greatest dilution causing visible hemagglutination; skin thickness in cm.</p

Differential gene expression heatmap from RNA-Seq data.

<p>SPL, spleen low IR; SPH, spleen high IR; SKL, skin low IR; SKH, skin high IR.</p

Statistics of genes differentially expressed between individuals with high and low IR.

<p>¹SPL, spleen low IR; SPH, spleen high IR; SKL, skin low IR; SKH, skin high IR.</p><p>Statistics of genes differentially expressed between individuals with high and low IR.</p

Statistics for the filtering and mapping of reads to the reference chicken genome.

<p>¹Complete sample names: SPL1, spleen low IR 1; SPL2, spleen low IR 2; SPH1, spleen high IR 1; SPH2, spleen high IR 2; SKL1, skin low IR 1; SKL2, skin low IR 2; SKH1, skin high IR 1; SKH2, skin high IR 2.</p><p>Statistics for the filtering and mapping of reads to the reference chicken genome.</p

Summary of RNA-seq data from spleen and skin samples from animals displaying extreme IR.

<p>(A) Box plot showing the distribution of fragments per kilobase of exon per million fragments mapped (FPKM) values. (B) Volcano graph showing differentially (in red) and non-differentially (in black) expressed genes. Values of >0 correspond to down-regulated genes, while values of <0 correspond to up-regulated genes. SPL, spleen low IR; SPH, spleen high IR; SKL, skin low IR; SKH, skin high IR.</p

List of chicken genes from KEGG pathway maps differentially expressed in liver from animals supplemented with 5⁻¹ diet and controls, with expression ratio, annotated gene description and KEGG ID.

<p>List of chicken genes from KEGG pathway maps differentially expressed in liver from animals supplemented with 5⁻¹ diet and controls, with expression ratio, annotated gene description and KEGG ID.</p

Dietary Inulin Supplementation Modifies Significantly the Liver Transcriptomic Profile of Broiler Chickens

<div><p>Inclusion of prebiotics in the diet is known to be advantageous, with positive influences both on health and growth. The current study investigated the differences in the hepatic transcriptome profiles between chickens supplemented with inulin (a storage carbohydrate found in many plants) and controls. Liver is a major metabolic organ and has been previously reported to be involved in the modification of the lipid metabolism in chickens fed with inulin. A nutrigenomic approach through the analysis of liver RNA hybridized to the Affymetrix GeneChip Chicken Genome Array identified 148 differentially expressed genes among both groups: 104 up-regulated (≥1.4-fold) and 44 down-regulated (≤0.6-fold). Quantitative real-time PCR analysis validated the microarray expression results for five out of seven genes tested. The functional annotation analyses revealed a number of genes, processes and pathways with putative involvement in chicken growth and performance, while reinforcing the immune status of animals, and fostering the production of long chain fatty acids in broilers supplemented with 5 g of inulin kg⁻¹ diet. As far as we are aware, this is the first report of a microarray based gene expression study on the effect of dietary inulin supplementation, supporting further research on the use of this prebiotic on chicken diets as a useful alternative to antibiotics for improving performance and general immunity in poultry farming, along with a healthier meat lipid profile.</p></div

ANOVA results of the genes studied in the liver by Real-time PCR assay from animals supplemented with 5 g of inulin kg⁻¹ diet and controls.

<p>ANOVA results of the genes studied in the liver by Real-time PCR assay from animals supplemented with 5 g of inulin kg⁻¹ diet and controls.</p