Tom E. Porter

Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways.

The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation—fasting and re-feeding—in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortiums efforts to help launch the new era of functional genomics in the chicken.

Identification of QTL controlling meat quality traits in an F2 cross between two chicken lines selected for either low or high growth rate

BackgroundMeat technological traits (i.e. meat pH, water retention and color) are important considerations for improving further processing of chicken meat. These quality traits were originally characterized in experimental lines selected for high (HG) and low (LG) growth. Presently, quantitative trait loci (QTL) for these traits were analyzed in an F2 population issued from the HG × LG cross. A total of 698 animals in 50 full-sib families were genotyped for 108 microsatellite markers covering 21 linkage groups.ResultsThe HG and LG birds exhibit large differences in body weight and abdominal fat content. Several meat quality traits [pH at 15 min post-slaughter (pH15) and ultimate pH (pHu), breast color-redness (BCo-R) and breast color-yellowness (BCo-Y)] were lower in HG chickens. In contrast, meat color-lightness (BCo-L) was higher in HG chickens, whereas meat drip loss (DL) was similar in both lines. HG birds were more active on the shackle line. Association analyses were performed using maximum-likelihood interval mapping in QTLMAP. Five genome-wide significant QTLs were revealed: two for pH15 on GGA1 and GGA2, one for DL on GGA1, one for BCo-R and one for BCo-Y both on GGA11. In addition, four suggestive QTLs were identified by QTLMAP for BCo-Y, pHu, pH15 and DL on GGA1, GGA4, GGA12 and GGA14, respectively. The QTL effects, averaged on heterozygous families, ranged from 12 to 31% of the phenotypic variance. Further analyses with QTLExpress confirmed the two genome-wide QTLs for meat color on GGA11, failed to identify the genome-wide QTL for pH15 on GGA2, and revealed only suggestive QTLs for pH15 and DL on GGA1. However, QTLExpress qualified the QTL for pHu on GGA4 as genome-wide.ConclusionThe present study identified genome-wide significant QTLs for all meat technological traits presently assessed in these chickens, except for meat lightness. This study highlights the effects of divergent selection for growth rate on some behavioral traits, muscle biochemistry and ultimately meat quality traits. Several QTL regions were identified that are worthy of further characterization. Some QTLs may in fact co-localize, suggesting pleiotropic effects for some chromosomal regions.

Transcriptional profiling of cecal gene expression in probiotic- and Salmonella-challenged neonatal chicks

Probiotics are currently used to improve health and reduce enteric pathogens in poultry. However, the mechanisms by which they reduce or prevent disease are not known. Salmonella are intracellular pathogens that cause acute gastroenteritis in humans, and infections by nontyphoid species of Salmonella also can result in diarrhea, dehydration, and depression in poultry. Frequently, however, no clinical signs of infection are apparent in poultry flocks. In this study, day-of-hatch chicks were challenged with Salmonella enterica serovar Enteritidis (SE) and treated 1 h later with a poultry-derived, Lactobacillus-based probiotic culture (FloraMax-B11, Pacific Vet Group USA Inc., Fayetteville, AR). Cecae were collected 12 and 24 h posttreatment for Salmonella detection and RNA isolation for microarray analysis of gene expression. At both 12 and 24 h, SE was significantly reduced in chicks treated with the probiotic as compared with the birds challenged with only SE (P < 0.05). Microarray analysis revealed gene expression differences among all treatment groups. At 12 h, 170 genes were expressed at significantly different levels (P < 0.05), with a minimum difference in expression of 1.2-fold. At 24 h, the number of differentially regulated genes with a minimum 1.2-fold change was 201. Pathway analysis revealed that at both time points, genes associated with the nuclear factor kappa B complex, as well as genes involved in apoptosis, were significantly regulated. Based on this analysis, probiotic-induced differential regulation of the genes growth arrest-specific 2 (GAS2) and cysteine-rich, angiogenic inducer, 61 (CYR61) may result in increased apoptosis in the cecae of chicks. Because Salmonella is an intracellular pathogen, we suggest that increased apoptosis may be a mechanism by which the probiotic culture reduces Salmonella infection.

Transcriptional analysis of abdominal fat in genetically fat and lean chickens reveals adipokines, lipogenic genes and a link between hemostasis and leanness

BackgroundThis descriptive study of the abdominal fat transcriptome takes advantage of two experimental lines of meat-type chickens (Gallus domesticus), which were selected over seven generations for a large difference in abdominal (visceral) fatness. At the age of selection (9 wk), the fat line (FL) and lean line (LL) chickens exhibit a 2.5-fold difference in abdominal fat weight, while their feed intake and body weight are similar. These unique avian models were originally created to unravel genetic and endocrine regulation of adiposity and lipogenesis in meat-type chickens. The Del-Mar 14K Chicken Integrated Systems microarray was used for a time-course analysis of gene expression in abdominal fat of FL and LL chickens during juvenile development (1–11 weeks of age).ResultsMicroarray analysis of abdominal fat in FL and LL chickens revealed 131 differentially expressed (DE) genes (FDR≤0.05) as the main effect of genotype, 254 DE genes as an interaction of age and genotype and 3,195 DE genes (FDR≤0.01) as the main effect of age. The most notable discoveries in the abdominal fat transcriptome were higher expression of many genes involved in blood coagulation in the LL and up-regulation of numerous adipogenic and lipogenic genes in FL chickens. Many of these DE genes belong to pathways controlling the synthesis, metabolism and transport of lipids or endocrine signaling pathways activated by adipokines, retinoid and thyroid hormones.ConclusionsThe present study provides a dynamic view of differential gene transcription in abdominal fat of chickens genetically selected for fatness (FL) or leanness (LL). Remarkably, the LL chickens over-express a large number of hemostatic genes that could be involved in proteolytic processing of adipokines and endocrine factors, which contribute to their higher lipolysis and export of stored lipids. Some of these changes are already present at 1 week of age before the divergence in fatness. In contrast, the FL chickens have enhanced expression of numerous lipogenic genes mainly after onset of divergence, presumably directed by multiple transcription factors. This transcriptional analysis shows that abdominal fat of the chicken serves a dual function as both an endocrine organ and an active metabolic tissue, which could play a more significant role in lipogenesis than previously thought.

Effects of BDNF, T3, and corticosterone on expression of the hypothalamic obesity gene network in vivo and in vitro

Hypothalamic neuropeptides, neurotrophins, and systemic hormones modulate food intake and body composition. Although advances toward elucidating these interactions have been made, many aspects of the underlying mechanisms remain vague. Hypothalami from fat and lean chicken lines were assessed for differential expression of anabolic/orexigenic and catabolic/anorexigenic genes. Effects of triiodothyronine (T(3)), corticosterone (Cort), and brain-derived neurotrophic factor (BDNF) on expression of anabolic/orexigenic and catabolic/anorexigenic genes were tested in cultures of hypothalamic neurons. From this, we found that BDNF increased and T(3) decreased gene expression for BDNF, leptin receptor (LEPR), pro-opiomelanocortin (POMC), thyrotropin releasing hormone (TRH), and agouti-related protein (AGRP). Thyroid hormone levels were manipulated during development to show that T(3) inhibited BDNF, TRH, and BDNF receptor gene expression. Delivery of T(3), Cort, T(3) plus Cort, or vehicle in vivo continuously for 72 h indicated that Cort and T(3) have overlapping roles in regulating TRH, LEPR, and POMC gene expression and that Cort and T(3) regulate BDNF, neuropeptide Y, and AGRP in opposite directions. Collectively, these findings suggest that interactions between the neuropeptide BDNF and the hormones T(3) and/or Cort may constitute a homeostatic mechanism that links hypothalamic energy regulation controlling body composition.

Transcriptional and pathway analysis in the hypothalamus of newly hatched chicks during fasting and delayed feeding.

BackgroundThe hypothalamus plays a central role in regulating appetite and metabolism. However, the gene networks within the hypothalamus that regulate feed intake and metabolism, and the effects of fasting on those pathways are not completely understood in any species. The present experiment evaluated global hypothalamic gene expression in newly hatched chicks using microarray analysis to elucidate genes and pathways regulated by feeding, fasting, and delayed feeding. Ten groups of chicks were sampled over four days post-hatch, including fed, fasted, and 48 h fasted followed by access to feed for 4 h, 24 h, and 48 h. Hypothalamic samples were collected for microarray analysis (n = 4). Expression patterns of selected genes were confirmed by quantitative real-time PCR. Pathway analysis of the microarray results predicted a network of genes involved in neuropeptide or neurotransmitter signaling. To confirm the functionality of this predicted gene network, hypothalamic neurons from fed and fasted chicks were isolated and cultured in the presence of neuropeptide Y, somatostatin, α-melanocyte stimulating hormone, norepinephrine, and L-phospho-serine. Results confirmed functional relationships among members of the predicted gene network. Moreover, the effects observed were dependant upon the nutritional state of the animals (fed vs. fasted).ResultsDifferences in gene expression (≥ 1.6 fold) were detected in 1,272 genes between treatments, and of those, 119 genes were significantly (P < 0.05) different. Pathway Miner analysis revealed that six genes (SSTR5, NPY5R, POMC, ADRB2, GRM8, and RLN3) were associated within a gene network. In vitro experiments with primary hypothalamic neurons confirmed that receptor agonists involved in this network regulated expression of other genes in the predicted network, and this regulation within the network was influenced by the nutritional status and age of the chick.ConclusionsMicroarray analysis of the hypothalamus during different nutritional states revealed that many genes are differentially regulated. We found that functional interactions exist among six differentially regulated genes associated within a putative gene network from this experiment. Considering that POMC, an important gene in controlling metabolism, was central to this network, this gene network may play an important role in regulation of feeding and metabolism in birds.

Involvement of thyrotropin-releasing hormone receptor, somatostatin receptor subtype 2 and corticotropin-releasing hormone receptor type 1 in the control of chicken thyrotropin secretion.

Thyrotropin or thyroid-stimulating hormone (TSH) secretion in the chicken is controlled by several hypothalamic hormones. It is stimulated by thyrotropin-releasing hormone (TRH) and corticotropin-releasing hormone (CRH), whereas somatostatin (SRIH) exerts an inhibitory effect. In order to determine the mechanism by which these hypothalamic hormones modulate chicken TSH release, we examined the cellular localization of TRH receptors (TRH-R), CRH receptors type 1 (CRH-R1) and somatostatin subtype 2 receptors (SSTR2) in the chicken pars distalis by in situ hybridization (ISH), combined with immunological staining of thyrotropes. We show that thyrotropes express TRH-Rs and SSTR2s, allowing a direct action of TRH and SRIH at the level of the thyrotropes. CRH-R1 expression is virtually confined to corticotropes, suggesting that CRH-induced adrenocorticotropin release is the result of a direct stimulation of corticotropes, whereas CRH-stimulated TSH release is not directly mediated by the known chicken CRH-R1. Possibly CRH-induced TSH secretion is mediated by a yet unknown type of CRH-R in the chicken. Alternatively, a pro-opiomelanocortin (POMC)-derived peptide, secreted by the corticotropes following CRH stimulation, could act as an activator of TSH secretion in a paracrine way.

Identification of the somatostatin receptor subtypes involved in regulation of growth hormone secretion in chickens

The effects of somatostatin (SRIF) are mediated through five distinct G-protein-coupled receptors (SSTR1-5). In the present study, pituitary cells from 6-week-old chickens were subjected to reverse hemolytic plaque assays for growth hormone (GH) in the presence of SSTR subtype specific nonpeptidyl agonists. A SSTR2 selective agonist (L-779,976) potently inhibited both basal and GH-releasing hormone (GHRH)-stimulated GH release at low nanomolar concentrations. A SSTR5 agonist (L-817,818) inhibited GH release only under basal conditions and in a subpopulation of somatotrophs. In contrast, a SSTR4 selective agonist (L-803,087) used at high nanomolar concentrations modestly stimulated GH release under basal conditions but did not influence GHRH-stimulated GH secretion. The SSTR1 and SSTR3 specific agonists did not affect GH secretion under any condition tested. Reverse transcription-polymerase chain reaction (RT-PCR) and Northern blot analysis using a partial cDNA for chicken SSTR2 showed relatively high levels of SSTR2 mRNA in the anterior pituitary (both in the caudal and cephalic lobes) and brain and detectable levels in liver, muscle, heart and small intestine. These results indicate that SSTR2 is the primary mediator of the inhibitory effects of SRIF on GH secretion in chickens.

Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate

BackgroundDelineating the genetic basis of body composition is important to agriculture and medicine. In addition, the incorporation of gene-gene interactions in the statistical model provides further insight into the genetic factors that underlie body composition traits. We used Bayesian model selection to comprehensively map main, epistatic and sex-specific QTL in an F2 reciprocal intercross between two chicken lines divergently selected for high or low growth rate.ResultsWe identified 17 QTL with main effects across 13 chromosomes and several sex-specific and sex-antagonistic QTL for breast meat yield, thigh + drumstick yield and abdominal fatness. Different sets of QTL were found for both breast muscles [Pectoralis (P) major and P. minor], which suggests that they could be controlled by different regulatory mechanisms. Significant interactions of QTL by sex allowed detection of sex-specific and sex-antagonistic QTL for body composition and abdominal fat. We found several female-specific P. major QTL and sex-antagonistic P. minor and abdominal fatness QTL. Also, several QTL on different chromosomes interact with each other to affect body composition and abdominal fatness.ConclusionsThe detection of main effects, epistasis and sex-dimorphic QTL suggest complex genetic regulation of somatic growth. An understanding of such regulatory mechanisms is key to mapping specific genes that underlie QTL controlling somatic growth in an avian model.

Induction of somatotroph differentiation in vivo by corticosterone administration during chicken embryonic development

Somatotroph differentiation in the embryonic pituitary of avian and mammalian species can be stimulated by glucocorticoids in vitro, and this effect can be augmented by concomitant treatment with growth hormone —releasing hormone (GHRH). Owing to its isolation from maternal influences, the chick embryo is a useful model for studying humoral regulation of pituitary cell differentiation. Somatotroph differentiation in chickens occurs between embryonic day (e-) 14 and e-16, and treatment of e-12 pituitary cells with e-16 serum or corticosterone induces growth hormone (GH) cell differentiation within 2 d in culture. The objective of the present study was to determine whether direct administration of embryonic serum and corticosterone to developing chick embryos was effective in vivo in inducing somatotroph differentiation prematurely. The albumen of fertile eggs was injected on e-11 with 300 μL of 0.9% saline or 150 μL of serum from e-12 or e-16 chick embryos diluted 1∶1 with saline. The embryos were allowed to develop until e-14, when pituitaries were dispersed and the resulting pituitary cells were subjected to reverse hemolytic plaque assays (RHPA) and immunocytochemistry to detect GH-secreting and GH-containing cells, respectively. Injection of e-16 serum increased (p<0.01) GH-secreting and GH-containing cells to 11.5±1.0% and 17.4±3.3% of all pituitary cells, compared to 5.0±0.3% and 5.5±0.9% for saline-injected controls, respectively. Day 12 serum increased GH-containing cells to 9.8±0.9%, without changing percentages of GH-secreting cells. In experiment 2, saline, e-16 serum, and corticosterone were injected on e-11, and pituitary cells were subjected to GH RHPA on e-14. GH secretors were increased by e-16 serum and corticosterone. In experiment 3, we tested whether GHRH would magnify the effect of corticosterone, as we had seen in extended 6-d cultures previously. Saline, corticosterone, and corticosterone plus GHRH were injected on e-11, and pituitary cells were subjected to GH RHPA on e-18. Treatment with corticosterone alone and combined with GHRH increased the percentage of GH-secreting cells. However, combined treatment with corticosterone and GHRH was not more effective than corticosterone alone. The present findings demonstrate that glucocorticoid administration can stimulate somatotroph differentiation in living vertebrate embryos isolated from maternal interactions.