High-throughput phenotyping to characterise range use behaviour in broiler chickens.

A key characteristic of free-range chicken farming is to enable chickens to spend time outdoors. However, each chicken may use the available areas for roaming in variable ways. To check if, and how, broilers use their outdoor range at an individual level, we need to reliably characterise range use behaviour. Traditional methods relying on visual scans require significant time investment and only provide discontinuous information. Passive RFID (Radio Frequency Identification) systems enable tracking individually tagged chickens' when they go through pop-holes; hence, they only provide partial information on the movements of individual chickens. Here, we describe a new method to measure chickens' range use and test its reliability on three ranges each containing a different breed. We used an active RFID system to localise chickens in their barn, or in one of nine zones of their range, every 30 seconds and assessed range-use behaviour in 600 chickens belonging to three breeds of slow- or medium-growing broilers used for outdoor production (all <40 g daily weight gain). From those real-time locations, we determined five measures to describe daily range use: time spent in the barn, number of outdoor accesses, number of zones visited in a day, gregariousness (an index that increases when birds spend time in zones where other birds are), and numbers of zone changes. Principal Component Analyses (PCAs) were performed on those measures, in each production system, to create two synthetic indicators of chickens' range use behaviour. The first two PCA axes represented over 90% of the variance of the five measures and were both consistent over time and correlated with independent visual scans. Contributions of the five measures to the PCAs were similar among breeds, except for the correlation between the number of outdoor accesses and the four other measures. PC1 correlated with time spent inside the barn and zone changes frequency, whilst PC2 was explained by exploration of the range. Taken together, PC1 and PC2 indicators showed that range use increased with age, outdoor temperature (in spring), and did not differ between males and females. Importantly, daily scores for both indicators were repeatable among individuals - particularly in PC1 - showing inter-individual variability on range-use. The characterisation of broiler behaviour around their range with these reliable and repeatable indicators provides novel tools to help understand individual variations of range-use in free-range farming.

Allantoic fluid metabolome reveals specific metabolic signatures in chicken lines different for their muscle glycogen content.

Nutrient availability in eggs can affect early metabolic orientation in birds. In chickens divergently selected on the Pectoralis major ultimate pH, a proxy for muscle glycogen stores, characterization of the yolk and amniotic fluid revealed a different nutritional environment. The present study aimed to assess indicators of embryo metabolism in pHu lines (pHu+ and pHu-) using allantoic fluids (compartment storing nitrogenous waste products and metabolites), collected at days 10, 14 and 17 of embryogenesis and characterized by 1H-NMR spectroscopy. Analysis of metabolic profiles revealed a significant stage effect, with an enrichment in metabolites at the end of incubation, and an increase in interindividual variability during development. OPLS-DA analysis discriminated the two lines. The allantoic fluid of pHu- was richer in carbohydrates, intermediates of purine metabolism and derivatives of tryptophan-histidine metabolism, while formate, branched-chain amino acids, Krebs cycle intermediates and metabolites from different catabolic pathways were more abundant in pHu+. In conclusion, the characterization of the main nutrient sources for embryos and now allantoic fluids provided an overview of the in ovo nutritional environment of pHu lines. Moreover, this study revealed the establishment, as early as day 10 of embryo development, of specific metabolic signatures in the allantoic fluid of pHu+ and pHu- lines.

Research Note: Divergent selection for breast muscle ultimate pH affects egg quality traits in broiler breeders.

Two divergently selected broiler lines were created by selection for low (pHu-) or high (pHu+) Pectoralis major ultimate pH (pHu) in order to better understand the molecular mechanisms underlying meat quality traits in broilers and are also unique genetic resources reflecting low and high glycogen levels in chicken muscle. The present study aimed to reveal the correlated phenotypical changes of egg quality traits in broiler breeders from the 2 divergent lines at the 14th generation. Birds were reared on littered floor system until 18 wk of age and in individual cages up to 42 wk. Individual egg production was recorded daily from age at first egg to 42 wk. External (egg weight: EW and shape index: SI), internal (albumen height: AH, Haugh unit: HU, yolk index: YI, and yolk color: YC), and shell (shell percentage: ESP, thickness: EST and strength: ESS) characteristics of eggs in pHu- and pHu+ lines were measured in all eggs for 4 consecutive days at 26, 27, 28, 30, 31, 32, 41, and 42 wk of age. The pHu- line had significantly higher egg percentage than pHu+ (55.9 and 49.1%, respectively). The EW in pHu- line (57.2 g) was significantly lower than in pHu+ (59.0 g) and increased with age in both lines. The mean ESP, EST and ESS were lower in the pHu+ eggs compared to the pHu- line. ESP and EST decreased mainly from 26 to 27 wk of age and they had a stable trend with advancing age in the remaining weeks. AH and YI were lower in pHu- line eggs than in pHu+. YC was more intense and HU higher in pHu+ eggs than pHu- in pre-peak and peak laying period. In conclusion, these results showed that a divergent selection for muscle energy metabolism has led to correlated responses on internal and external egg quality traits and suggest that the production of good-quality eggs may be impaired in broiler breeders with low energy reserves.

A Divergent Selection on Breast Meat Ultimate pH, a Key Factor for Chicken Meat Quality, is Associated With Different Circulating Lipid Profiles.

Background: Chicken meat has become a major source of protein for human consumption. However, the quality of the meat is not yet under control, especially since pH values that are too low or too high are often observed. In an attempt to get a better understanding of the genetic and biochemical determinants of the ultimate pH, two genetic lines of broilers were divergently selected for low (pHu-) or high (pHu+) breast meat pHu. In this study, the serum lipidome of 17-day-old broilers from both lines was screened for pHu markers using liquid-chromatography coupled with mass spectrometry (LC-HRMS). Results: A total of 185 lipids belonging to 4 groups (glycerolipids, glycerophospholipids, sterols, sphingolipids) were identified in the sera of 268 broilers from the pHu lines by targeted lipidomics. The glycerolipids, which are involved in energy storage, were in higher concentration in the blood of pHu- birds. The glycerophospholipids (phosphatidylcholines, phosphatidylethanolamines) with long and polyunsaturated acyl chains were more abundant in pHu+ than in pHu- while the lysophosphatidylcholines and lysophosphatidylethanolamines, known to be associated with starch, were observed in higher quantity in the serum of the pHu- line. Finally, the concentration of the sterols and the ceramides, belonging to the sphingolipids class, were higher in the pHu+ and pHu-, respectively. Furthermore, orthogonal partial least-squares analyses highlighted a set of 68 lipids explaining 77% of the differences between the two broilers lines (R2Y = 0.77, Q2 = 0.67). Among these lipids, a subset of 40 predictors of the pHu value was identified with a Root Mean Squared Error of Estimation of 0.18 pH unit (R2Y = 0.69 and Q2 = 0.62). The predictive model of the pHu value was externally validated on 68 birds with a Root Mean Squared Error of Prediction of 0.25 pH unit. Conclusion: The sets of molecules identified will be useful for a better understanding of relationship between serum lipid profile and meat quality, and will contribute to define easily accessible pHu biomarkers on live birds that could be useful in genetic selection.

Nutrient sources differ in the fertilised eggs of two divergent broiler lines selected for meat ultimate pH.

The pHu+ and pHu- lines, which were selected based on the ultimate pH (pHu) of the breast muscle, represent a unique model to study the genetic and physiological controls of muscle energy store in relation with meat quality in chicken. Indeed, pHu+ and pHu- chicks show differences in protein and energy metabolism soon after hatching, associated with a different ability to use energy sources in the muscle. The present study aimed to assess the extent to which the nutritional environment of the embryo might contribute to the metabolic differences observed between the two lines at hatching. Just before incubation (E0), the egg yolk of pHu+ exhibited a higher lipid percentage compared to the pHu- line (32.9% vs. 27.7%). Although 1H-NMR spectroscopy showed clear changes in egg yolk composition between E0 and E10, there was no line effect. In contrast, 1H-NMR analysis performed on amniotic fluid at embryonic day 10 (E10) clearly discriminated the two lines. The amniotic fluid of pHu+ was richer in leucine, isoleucine, 2-oxoisocaproate, citrate and glucose, while choline and inosine were more abundant in the pHu- line. Our results highlight quantitative and qualitative differences in metabolites and nutrients potentially available to developing embryos, which could contribute to metabolic and developmental differences observed after hatching between the pHu+ and pHu- lines.

Profiles of genetic parameters of body weight and feed efficiency in two divergent broiler lines for meat ultimate pH.

BACKGROUND: Selection for feed efficiency is one of the best ways to decrease poultry production costs and environmental impacts. While literature on its genetic determinism is abundant, it is limited to one or a few periodic values over the animals' lifespans. With the development of new phenotyping tools, kinetics of growth and feed intake are now available, providing access to daily data on feed efficiency. In this study, over the course of 6 weeks, we described the kinetics of body weight (BW), average daily weight gain (ADG), feed intake (FI), and daily cumulative feed conversion ratio (DCFCR) using electronic feed stations. We then estimated the genetic parameters of daily data in two fast growing lines of chicken divergently selected for breast meat ultimate pH (heritability and genetic correlations with breast meat yield and pH). RESULTS: Birds from the line selected to have a more acidic meat (pHu-), were more efficient than those selected to have a less acidic meat (pHu+), with a 4.3% higher BW from d7 to d29 and 5.0% better feed efficiency from d12 to slaughter. The line effect for ADG and DCFCR appeared to be significant as early as d5, which is consistent with the early age at which metabolic differences between the two lines appear. Genetic parameters estimated within each line revealed different genetic determinisms of growth and feed efficiency, with a higher impact of maternal effects on BW during the growing phase (d10 to d20) in the pHu+ line and much higher heritability values of DCFCR during the finishing phase (d26-d42) in the pHu- line. CONCLUSION: Genetic profiles of daily performance highlighted the difference between both lines. Their behavior during dietary transitions reinforced the already known impact of these periods in the animals' lives. Based on the profiles of genetic parameters within each line, it seems feasible to identify early criteria for selecting feed efficiency, but they must be defined for each line, as the genetic determinism of these traits is line-dependent.

Foraging Behavior Shows Individual-Consistency Over Time, and Predicts Range Use in Slow-Growing Free-Range Male Broiler Chickens.

Recent research on free-range chickens shows that individual behavioral differences may link to range use. However, most of these studies explored individual behavioral differences only at one time point or during a short time window, assessed differences when animals were out of their social group and home environment (barn and range), and in specific tests or situations. Therefore, it is yet unclear how different behaviors relate to range use and how consistent these behaviors are at the individual level. To fill this gap, we here aimed to describe the behavioral budget of slow-growing male broiler chickens (S757N) when in their social group and home environment during the whole rearing period (from the second week of life to the twelfth week, before slaughter), and to relate observed behavioral differences to range use. For this, we followed a sample of individuals in two flocks (n = 60 focal chickens out of 200 chickens per flock), over two seasons, during three periods: before range access (from 14 to 25 days old), during early range access (first weeks of range access, from 37 to 53 days old), and during late range access (last weeks of range access, from 63 to 87 days old). By the end of each period, individual tests of exploration and social motivation were also performed, measuring exploration/activity and sociability propensities. Our results show that foraging (i.e., pecking and scratching at the ground) was the only behavior that correlated to range use for all three rearing periods, independent of the season. Foraging was also the only behavior that showed within-individual consistency from an early age and across the three rearing periods. Foraging may, therefore, serve as a useful behavioral predictor of range use in free-range broiler chickens. Our study increases the knowledge of how behaviors develop and relate to each other in a domesticated and intensely selected species, and improves our understanding of the biology of free-range broiler chickens. These findings can, ultimately, serve as a foundation to increase range use and improve chicken welfare.

Revealing Pathways Associated with Feed Efficiency and Meat Quality Traits in Slow-Growing Chickens.

Here, molecular pathways and genes involved in the feed efficiency (FE) and thigh-meat quality of slow-growing Korat chickens were investigated. Individual feed intake values and body weights were collected weekly to the calculate feed conversion ratios (FCR) and residual feed intake. The biochemical composition and meat quality parameters were also measured. On the basis of extreme FCR values at 10 weeks of age, 9 and 12 birds from the high and the low FCR groups, respectively, were selected, and their transcriptomes were investigated using the 8 × 60 K Agilent chicken microarray. A weighted gene co-expression network analysis was performed to determine the correlations between co-expressed gene modules and FE, thigh-meat quality, or both. Groups of birds with different FE values also had different nucleotide, lipid, and protein contents in their thigh muscles. In total, 38 modules of co-expressed genes were identified, and 12 were correlated with FE and some meat quality traits. A functional analysis highlighted several enriched functions, such as biological processes, metabolic processes, nucleotide metabolism, and immune responses. Several molecular factors were involved in the interactions between FE and meat quality, including the assembly competence domain, baculoviral IAP repeat containing 5, cytochrome c oxidase assembly factor 3, and myosin light chain 9 genes.

Working for food is related to range use in free-range broiler chickens.

When animals prefer to make efforts to obtain food instead of acquiring it from freely available sources, they exhibit what is called contrafreeloading. Recently, individual differences in behavior, such as exploration, were shown to be linked to how prone an individual may be to contrafreeload. In this work, our main objective was to test whether and how individual differences in range use of free-range broiler chickens (Gallus gallus domesticus) were related to the individual motivation to contrafreeload. We also verified whether other behavioral variations could relate to range use. To that aim, over three different periods (before range access, first weeks of range access, and last weeks of range access), chickens with different ranging levels (low and high rangers) were submitted to a contrafreeloading test and had different behaviors recorded (such as foraging, resting, locomotion) in their home environment. During the contrafreeloading test, chickens were conditioned to one chamber presenting a foraging substrate and mealworms, while in the other chamber, mealworms were freely available on the floor. During testing trials, chickens had access to both empty chambers, and the time spent in each chamber was quantified. On average, low rangers preferred the chamber where mealworms were easily accessible (without the foraging substrate), while high rangers preferred the chamber where mealworms were accessible with difficulty, showing greater contrafreeloading. Out of ten behaviors recorded in chickens' home environment, foraging was the only one that differed significantly between our two ranging groups, with low rangers foraging, on average, significantly less than high rangers. These results corroborate previous experiences suggesting that range use is probably linked to chickens' exploratory trait and suggest that individual differences in free-range broiler chickens are present even before range access. Increasing our knowledge of individual particularities is a necessary step to improve free-range chicken welfare on the farm.

The kinetics of growth, feed intake, and feed efficiency reveal a good capacity of adaptation of slow and rapid growing broilers to alternative diets.

Poultry production currently relies on the use of soybean as the main protein and energy source. Reducing its proportion in poultry diets and partly replacing it with local feedstuffs would improve sustainability by reducing dependence on importations and the environmental impact of production. In this study, we evaluated the impact of replacing soybean by sunflower meal, fava bean, canola meal, and dried distillers grains with solubles on the performance of rapid and slow growing chickens. Animals were reared in groups and on the floor. Individual BW and feed intake data were collected throughout each animal's life, thanks to an electronic feed station. At 5 wk (for broilers) and 12 wk (for slow growing chickens), the birds were slaughtered to obtain carcass composition and meat quality data. Adaptation to the alternative diet was studied separately for each genotype. Firstly, we performed ANOVA with diet effect on daily data of individual BW, feed intake, and feed conversion ratio. Secondly, the variability of performances within the group was studied by ANOVA with effects of diet, period, and their interaction. Finally, correlations between daily performances and final performances at slaughter were calculated to understand the construction of final phenotypes and to identify early indicators of final performances. The results showed that the animals adapted well to the alternative diet, mean daily and final performances being mostly similar between the 2 diets for both genotypes (<3% on final BW). However, daily observations highlighted the critical importance of periods around dietary transitions by showing impacted performances for both genotypes. For example, feed conversion ratio of Label Rouge-alternative diet was 12 to 14% lower during the 3 d after transitions than during the 3 d before. It underlined the fact that adapting management of the batch to the alternative diet would be necessary. Correlations between daily and final performances showed that the slaughter performances of rapid growing chickens were mostly determined by BW whereas the main criterion was cumulative feed conversion for slow growing chickens. These correlations also suggested that reserves might be modified with the alternative diet, with rapid growing chickens giving rise to more glycogen reserves and less fat reserves.

Early Growth and Protein-Energy Metabolism in Chicken Lines Divergently Selected on Ultimate pH.

In chickens, a divergent selection on the Pectoralis major pHu allowed the creation of the pHu+ and pHu- lines, which represent a unique model for studying the biological control of carbohydrate storage in muscle. The present study aimed to describe the early mechanisms involved in the establishment of pHu+ and pHu- phenotypes. At hatching, pHu+ chicks were slightly heavier but exhibited lower plasma glucose and triglyceride and higher uric acid. After 5 days, pHu+ chicks exhibited higher breast meat yield compared to pHu- while their body weight was no different. At both ages, in vivo muscle glycogen content was lower in pHu+ than in pHu- muscles. The lower ability of pHu+ chicks to store carbohydrate in their muscle was associated with the increased expression of SLC2A1 and SLC2A3 genes coding glucose transporters 1 and 3, and of CS and LDHα coding key enzymes of oxidative and glycolytic pathways, respectively. Reduced muscle glycogen content at hatching of the pHu+ was concomitant with higher activation by phosphorylation of S6 kinase 1/ribosomal protein S6 pathway, known to activate protein synthesis in chicken muscle. In conclusion, differences observed in muscle at slaughter age in the pHu+ and pHu- lines are already present at hatching. They are associated with several changes related to both carbohydrate and protein metabolism, which are likely to affect their ability to use eggs or exogenous nutrients for muscle growth or energy storage.

Molecular Phenotyping of White Striping and Wooden Breast Myopathies in Chicken.

The White Striping (WS) and Wooden Breast (WB) defects are two myopathic syndromes whose occurrence has recently increased in modern fast-growing broilers. The impact of these defects on the quality of breast meat is very important, as they greatly affect its visual aspect, nutritional value, and processing yields. The research conducted to date has improved our knowledge of the biological processes involved in their occurrence, but no solution has been identified so far to significantly reduce their incidence without affecting growing performance of broilers. This study aims to follow the evolution of molecular phenotypes in relation to both fast-growing rate and the occurrence of defects in order to identify potential biomarkers for diagnostic purposes, but also to improve our understanding of physiological dysregulation involved in the occurrence of WS and WB. This has been achieved through enzymatic, histological, and transcriptional approaches by considering breast muscles from a slow- and a fast-growing line, affected or not by WS and WB. Fast-growing muscles produced more reactive oxygen species (ROS) than slow-growing ones, independently of WS and WB occurrence. Within fast-growing muscles, despite higher mitochondria density, muscles affected by WS or WB defects did not show higher cytochrome oxidase activity (COX) activity, suggesting altered mitochondrial function. Among the markers related to muscle remodeling and regeneration, immunohistochemical staining of FN1, NCAM, and MYH15 was higher in fast- compared to slow-growing muscles, and their amount also increased linearly with the presence and severity of WS and WB defects, making them potential biomarkers to assess accurately their presence and severity. Thanks to an innovative histological technique based on fluorescence intensity measurement, they can be rapidly quantified to estimate the injuries induced in case of WS and WB. The muscular expression of several other genes correlates also positively to the presence and severity of the defects like TGFB1 and CTGF, both involved in the development of connective tissue, or Twist1, known as an inhibitor of myogenesis. Finally, our results suggested that a balance between TGFB1 and PPARG would be essential for fibrosis or adiposis induction and therefore for determining WS and WB phenotypes.

Interest in the serum color as an indirect criterion of selection of digestive efficiency in chickens.

Improving the digestive efficiency of birds is becoming increasingly important with the diversification of feedstuffs used in poultry diets. Compared with time-consuming chemical analyses that were previously used to measure digestive efficiency, near-infrared spectroscopy has been a great advance as it was fast and thus allowed measurements to be taken from a large number of animals, as required for genetic studies. However, it still implies to rear the birds in cages to collect feces, which is questionable in terms of welfare. The purpose of this study was thus to establish whether the serum color could be used as a biomarker of digestive efficiency that would be easy and fast to measure on floor-reared animals. We first compared the serum color of 2 lines of chickens divergently selected for high or low digestive efficiency when fed with a wheat-based diet. Digestive efficiency was assessed by nitrogen-corrected apparent metabolizable energy. Color was assessed by the absorbance of the serum between 300 and 572 nm. Color differed between the 2 lines between 430 and 572 nm, which corresponds to the absorption zone of carotenoids such as lutein and zeaxanthin. In a second step, we estimated the heritability of serum color measurements and their genetic correlations with digestive efficiency. Taking these parameters into account, in our experimental conditions the best trait among those tested that can be used as a biomarker of digestive efficiency is serum absorbance at 492 nm, with a heritability estimate of 0.31 ± 0.09 and a genetic correlation with digestive efficiency of 0.84 ± 0.28.

Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species.

Efforts to elucidate the causes of biological differences between wild fowls and their domesticated relatives, the chicken, have to date mainly focused on the identification of single nucleotide mutations. Other types of genomic variations have however been demonstrated to be important in avian evolution and associated to variations in phenotype. They include several types of sequences duplicated in tandem that can vary in their repetition number. Here we report on genome size differences between the red jungle fowl and several domestic chicken breeds and selected lines. Sequences duplicated in tandem such as rDNA, telomere repeats, satellite DNA and segmental duplications were found to have been significantly re-shaped during domestication and subsequently by human-mediated selection. We discuss the extent to which changes in genome organization that occurred during domestication agree with the hypothesis that domesticated animal genomes have been shaped by evolutionary forces aiming to adapt them to anthropized environments.

Differential expression and co-expression gene network analyses reveal molecular mechanisms and candidate biomarkers involved in breast muscle myopathies in chicken.

The broiler industry is facing an increasing prevalence of breast myopathies, such as white striping (WS) and wooden breast (WB), and the precise aetiology of these occurrences remains poorly understood. To progress our understanding of the structural changes and molecular pathways involved in these myopathies, a transcriptomic analysis was performed using an 8 × 60 K Agilent chicken microarray and histological study. The study used pectoralis major muscles from three groups: slow-growing animals (n = 8), fast-growing animals visually free from defects (n = 8), or severely affected by both WS and WB (n = 8). In addition, a weighted correlation network analysis was performed to investigate the relationship between modules of co-expressed genes and histological traits. Functional analysis suggested that selection for fast growing and breast meat yield has progressively led to conditions favouring metabolic shifts towards alternative catabolic pathways to produce energy, leading to an adaptive response to oxidative stress and the first signs of inflammatory, regeneration and fibrosis processes. All these processes are intensified in muscles affected by severe myopathies, in which new mechanisms related to cellular defences and remodelling seem also activated. Furthermore, our study opens new perspectives for myopathy diagnosis by highlighting fine histological phenotypes and genes whose expression was strongly correlated with defects.

Predicting the Quality of Meat: Myth or Reality?

This review is aimed at providing an overview of recent advances made in the field of meat quality prediction, particularly in Europe. The different methods used in research labs or by the production sectors for the development of equations and tools based on different types of biological (genomic or phenotypic) or physical (spectroscopy) markers are discussed. Through the various examples, it appears that although biological markers have been identified, quality parameters go through a complex determinism process. This makes the development of generic molecular tests even more difficult. However, in recent years, progress in the development of predictive tools has benefited from technological breakthroughs in genomics, proteomics, and metabolomics. Concerning spectroscopy, the most significant progress was achieved using near-infrared spectroscopy (NIRS) to predict the composition and nutritional value of meats. However, predicting the functional properties of meats using this method-mainly, the sensorial quality-is more difficult. Finally, the example of the MSA (Meat Standards Australia) phenotypic model, which predicts the eating quality of beef based on a combination of upstream and downstream data, is described. Its benefit for the beef industry has been extensively demonstrated in Australia, and its generic performance has already been proven in several countries.

Transcriptional profiling and pathway analysis reveal differences in pituitary gland function, morphology, and vascularization in chickens genetically selected for high or low body weight.

BACKGROUND: Though intensive genetic selection has led to extraordinary advances in growth rate and feed efficiency in production of meat-type chickens, endocrine processes controlling these traits are still poorly understood. The anterior pituitary gland is a central component of the neuroendocrine system and plays a key role in regulating important physiological processes that directly impact broiler production efficiency, though how differences in pituitary gland function contribute to various growth and body composition phenotypes is not fully understood. RESULTS: Global anterior pituitary gene expression was evaluated on post-hatch weeks 1, 3, 5, and 7 in male broiler chickens selected for high (HG) or low (LG) growth. Differentially expressed genes (DEGs) were analyzed with gene ontology categorization, self-organizing maps, gene interaction network determination, and upstream regulator identification to uncover novel pituitary genes and pathways contributing to differences in growth and body composition. A total of 263 genes were differentially expressed between HG and LG anterior pituitary glands (P ≤ 0.05 for genetic line-by-age interaction or main effect of line; ≥1.6-fold difference between lines), including genes encoding four anterior pituitary hormones. Genes involved in signal transduction, transcriptional regulation, and vesicle-mediated transport were differentially expressed and are predicted to influence expression and secretion of pituitary hormones. DEGs involved in immune regulation provide evidence that inflammation and response to cellular stressors may compromise pituitary function in LG birds, affecting their ability to adequately produce pituitary hormones. Many DEGs were also predicted to function in processes that regulate organ morphology and angiogenesis, suggesting pituitary gland structure differs between the divergently selected lines. CONCLUSIONS: The large number of DEGs within the anterior pituitary gland of birds selected for high or low body weight highlights the importance of this gland in regulating economically important traits such as growth and body composition in broiler chickens. Intracellular signaling, transcriptional regulation, and membrane trafficking are important cellular processes contributing to proper hormone production and secretion. The data also suggest that pituitary function is intimately tied to structure, and organization of the gland could influence hypothalamic and systemic metabolic inputs and delivery of hormones regulating growth and metabolism into peripheral circulation.

Functional genomics of the digestive tract in broilers.

BACKGROUND: The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. The aim of the project was to improve the understanding of genes involved in digestive functions by characterizing the transcriptome of different sections of the digestive tract: the junction between the proventriculus and the gizzard, the gizzard, the gastroduodenal junction, and the jejunum. RESULTS: Total RNA from the four tissues were sequenced on a HiSeq2500 for six 23-day-old chickens from a second generation (F2) cross between two lines that were divergent for their digestive efficiency (D+/D-). Bioinformatics and biostatistics analyses of the RNA-seq data showed a total of 11,040 differentially expressed transcripts between the four tissues. In total, seven clusters of genes with markedly different expression profiles were identified. Functional analysis on gene groups was performed using "Gene Ontology" and semantic similarity. It showed a significant enrichment of body immune defenses in the jejunum, and an enrichment of transcriptional activity in the gizzard. Moreover, an interesting enrichment for neurohormonal control of muscle contraction was found for the two gizzard's junctions. CONCLUSION: This analysis allows us to draw the first molecular portrait of the different sections of the digestive tract, which will serve as a basis for future studies on the genetic and physiological control of the response of the animal to feed variations.

Relationships between digestive efficiency and metabolomic profiles of serum and intestinal contents in chickens.

The increasing cost of conventional feedstuffs has bolstered interest in genetic selection for digestive efficiency (DE), a component of feed efficiency, assessed by apparent metabolisable energy corrected to zero nitrogen retention (AMEn). However, its measurement is time-consuming and constraining, and its relationship with metabolic efficiency poorly understood. To simplify selection for this trait, we searched for indirect metabolic biomarkers through an analysis of the serum metabolome using nuclear magnetic resonance (1H NMR). A partial least squares (PLS) model including six amino acids and two derivatives from butyrate predicted 59% of AMEn variability. Moreover, to increase our knowledge of the molecular mechanisms controlling DE, we investigated 1H NMR metabolomes of ileal, caecal, and serum contents by fitting canonical sparse PLS. This analysis revealed strong associations between metabolites and DE. Models based on the ileal, caecal, and serum metabolome respectively explained 77%, 78%, and 74% of the variability of AMEn and its constitutive components (utilisation of starch, lipids, and nitrogen). In our conditions, the metabolites presenting the strongest associations with AMEn were proline in the serum, fumarate in the ileum and glucose in caeca. This study shows that serum metabolomics offers new opportunities to predict chicken DE.