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Hepatic transcriptional profiling of juvenile broiler chickens divergently selected for high or low body weight

ABSTRACT: Divergently selected chickens for either high growth (HG genotype) or low growth (LG genotype) developed at SRA-INRA, France were used to profile hepatic gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The HG and LG chickens are different in various phenotypic and metabolic measurements, including growth rate, abdominal fat, plasma glycemia, insulinemia, T4, T3, triglyceride and NEFA. The HG and LG chickens are valuable as a model for biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in liver during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with a two-stage mixed model. A total number of 531 differentially expressed genes were identified. The greatest number of genes was detected at 7 weeks of age where 178 genes were up-regulated in the HG and 162 genes up-regulated in the LG. The differentially expressed genes include metabolic enzymes, acute phase proteins, immune factors and transcription factors involved in various pathways (i.e., fatty acid and amino acid metabolism, glycolysis, oxidative phosphorylation, growth factor signaling and immune defense). Several of these functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the HG and LG lines. Keywords: divergently selected chickens, growth, transcriptional profiling, differentially expressed genes

ORGANISM(S): Gallus gallus

PROVIDER: GSE7254 | GEO | 2007/05/30

SECONDARY ACCESSION(S): PRJNA98007

REPOSITORIES: GEO

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Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile abdominal adipose gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in abdominal adipose during juvenile development using a balanced block hybridization design. Fluorescence intensities were normalized within array (without background subtraction), and between array (aquantile method) in LIMMA package R [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3] producing M-values (log-2 expression ratios) and A-values (average log-2 expression values). Normalized values were analyzed using a two factor ANOVA model. A total of 3,669 unique differentially expressed functional genes were identified (FDR<0.05). Genes were determined to have a significant effect of age (3,222), genotype (344), or an age by genotype interaction (254). The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes

Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile abdominal adipose gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in abdominal adipose during juvenile development using a balanced block hybridization design. Fluorescence intensities were normalized within array (without background subtraction), and between array (aquantile method) in LIMMA package R [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3] producing M-values (log-2 expression ratios) and A-values (average log-2 expression values). Normalized values were analyzed using a two factor ANOVA model. A total of 1,020 differentially expressed functional genes were identified (FDR<0.05). Genes were determined to have a significant effect of age (422), genotype (344), or an age by genotype interaction (254). The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes A balanced block design was used for microarray hybridizations, where half of the birds of each genotype and age were labeled with Alexa Flour 647 (red) and the other half with Alexa Flour 555 (green). Four biological replicates were used for each genotype (FL or LL) at six different ages (1, 3, 5, 7, 9 and 11 wk).

Project description:Several processes governing growth and metabolism are regulated by the neuroendocrine system, particularly the trophic hormones produced in the anterior pituitary gland. However, many of the differences that exist in pituitary gene expression and functional gene networks associated with divergent growth characteristics are still largely unknown. Using the Del-Mar 14K Chicken Integrated Systems microarray, this experiment evaluated global gene expression in the anterior pituitary gland during the first 7 weeks of post-hatch growth in two lines of chickens genetically selected for high growth (HG) or low growth (LG) at SRA-INRA, France. The HG and LG chickens differ in body weight, abdominal fat content, and plasma hormone and metabolite levels, making them a valuable model for both biomedical and agricultural traits. Amplified total RNA extracted from individual anterior pituitary glands collected from 4 birds from each line at each age (n=4) was produced. Cy-3 labeled cDNA from these samples was hybridized with an aliquot of Cy-5 labeled cDNA made from a pool of total RNA from all 32 samples. Data were analyzed as log2-(Cy3intensity (norm)/Cy5intensity (raw)) by two-way ANOVA using a linear mixed model procedure (PROC MIXED; SAS institute Inc., Cary, NC), and a total of 2,310 spots were significantly different (P<0.05) by line (1,100), age (1,058), or the line-by-age interaction (353). Of these, we identified 291 spots representing 263 genes as differentially expressed between HG and LG birds, where there was a >160% difference between the highest expression in one line and the lowest expression in the other and a significant line-by-age (110) or line (181) effect. Four anterior pituitary hormones were contained in this set of differentially expressed genes: thyroid-stimulating hormone ?-subunit, luteinizing hormone ?-subunit, and follicle-stimulating hormone ?-subunit mRNA levels were higher in the HG line; and growth hormone mRNA was elevated in the LG line. Pathway analysis revealed differences in expression between HG and LG lines associated with molecular transport, endocrine system development and function, organ and tissue morphology, and cellular compromise. Potential alteration in pituitary function between the two lines was highlighted in a network containing genes associated with hormone expression and secretion, as well as those potentially involved in pituitary gland morphology and vascularization.

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Hepatic transcriptional profiling of juvenile broiler chickens divergently selected for high or low body weight

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