Average nrs of pecks±SEM directed to a familiar, readily available food resource in UL and PL parents, and their respective offspring, as measured in a Foraging test.

<p>Significant differences are indicated: * = p<0.05; ** = p<0.01.</p

Weight measurements of surviving birds.

<p>(A) Growth in UL and PL parents; male UL, n = 4; male PL, n = 7; female UL, n = 11; female PL, n = 8. (B) Body weight in offspring of UL and PL parents. The difference between the offspring groups was significant (p<0.01) based on a repeated measure general linear model with parental treatment and sex as independent factors. There was an interaction between parental treatment and sex (p<0.05) illustrated by the small figure in the female diagram. (C) Growth in offspring of UL and PL parents; males with UL parents n = 10; males with PL parents, n = 9; females with UL parents n = 11; females with PL parents n = 10. All values are given as grams with means±SEM.</p

Significantly differentially expressed gene transcripts between parents treated with Unpredictable Light or Predictable Light based on microarray analysis.

<p>M-fold value is the log2 of the difference in expression level, and B-value is the log odds ratio of expression levels; the B-value estimates the certainty of DE vs non-certainty of DE. The criterium used for significant expression was that B>0. Positive M-values indicate that the transcript is higher expressed in birds treated with Unpredictable Light.</p

Immune gene transcripts which had among the 2.5% highest absolute M-values in each sex and generation.

<p>The table shows the same values with same criteria as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006405#pone-0006405-t003" target="_blank">table 3</a> for all transcripts included on the microarray from the two immune related genes Ig light chain, Ig heavy chain. Also included are three MHC-transcripts, which were only top ranked in the parents. If not stated otherwise, all transcripts were down-regulated in parents treated with Unpredictable Light (UL) or offspring of UL parents in relation to parents in Predictable Light or their offspring.</p>*<p>Up-regulated.</p>1<p>Annotation was done using Chicken Discovery System.</p>§<p>NA indicate genes filtered away during analysis as low quality spot on microarray. Filtration is dependent on joint properties on all the arrays in the group, hence could fall out differently in relation to which arrays are included.</p

Food competition at adult age in UL and PL parents and their respective offspring as measured in a Dominance test.

<p>Numbers of pecks in the food are given in means±SEM. Significant differences are indicated: * = p<0.05.</p

Figure 2

<p>Correlations between magnitude of differential expression of genes between parents and offspring. Diagrams show M-values for the differential expression (comparing stressed vs control parents, and offspring of stressed vs offspring of control parents) of the 500 most differentially expressed genes (largest log₂ difference caused by stress in parents) in (a) red junglefowl, and (b) White Leghorns. Each point represents one spot on the microarray. Positive M-values indicate upregulation and negative downregulation by stress (or by having stressed parents). The average correlation line is shown in both comparisons.</p

Weight and food competition capacity in offspring

<p>Birds were weighed within an hour after hatching and at eight days of age. Food competition capacity was estimated as the percentage of time in which each individual occupied the feeder in a pair-wise competition test. The data were analysed with ANOVA, using breed and parental treatment as fixed independent variables. Data (LS Means±SEM) with different superscripts in the table differ significantly at p<0.05.</p

Numbers of genes in parents and offspring brains showing differential expression caused by stress applied to parents.

<p>M-value is the log₂ of the difference in expression level, and B-value is the log odds ratio of expression levels; the B-value estimates the certainty of DE vs non-certainty of DE. Common criteria for significant expression is that M>1 and B>0.</p

Real-time RT-PCR data for nine genes selected for verification of microarray results

<p>Because of the low number of biological replicates, no valid p-values could be estimated, so a gene with M>1 was considered to be differentially expressed in this analysis. All genes with M>1 showed the same direction of regulation (up or down-regulated by stress treatment) as on the microarray. The nine genes were selected based on their high M- and B-values in the microarray analysis. Relative expression levels (M-values) were estimated using β-actin as an internal control. Negative M-values indicate that the expression level was higher in control than in stress birds.</p

Genes differentially expressed both in White Leghorn parents and offspring.

<p>The table shows the 10 genes with highest differential expression in WL offspring, out of those which were among the 100 most differentially expressed genes in both WL parents and offspring. Negative M-values indicate that the expression level was higher in control than in stress birds.</p