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.

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.

Mapping QTL for white striping in relation to breast muscle yield and meat quality traits in broiler chickens.

BACKGROUND: White striping (WS) is an emerging muscular defect occurring on breast and thigh muscles of broiler chickens. It is characterized by the presence of white striations parallel to the muscle fibers and has significant consequences for meat quality. The etiology of WS remains poorly understood, even if previous studies demonstrated that the defect prevalence is related to broiler growth and muscle development. Moreover, recent studies showed moderate to high heritability values of WS, which emphasized the role of genetics in the expression of the muscle defect. The aim of this study was to identify the first quantitative trait loci (QTLs) for WS as well as breast muscle yield (BMY) and meat quality traits using a genome-wide association study (GWAS). We took advantage of two divergent lines of chickens selected for meat quality through Pectoralis major ultimate pH (pHu) and which exhibit the muscular defect. An expression QTL (eQTL) detection was further performed for some candidate genes, either suggested by GWAS analysis or based on their biological function. RESULTS: Forty-two single nucleotide polymorphisms (SNPs) associated with WS and other meat quality traits were identified. They defined 18 QTL regions located on 13 chromosomes. These results supported a polygenic inheritance of the studied traits and highlighted a few pleiotropic regions. A set of 16 positional and/or functional candidate genes was designed for further eQTL detection. A total of 132 SNPs were associated with molecular phenotypes and defined 21 eQTL regions located on 16 chromosomes. Interestingly, several co-localizations between QTL and eQTL regions were observed which could suggest causative genes and gene networks involved in the variability of meat quality traits and BMY. CONCLUSIONS: The QTL mapping carried out in the current study for WS did not support the existence of a major gene, but rather suggested a polygenic inheritance of the defect and of other studied meat quality traits. We identified several candidate genes involved in muscle metabolism and structure and in muscular dystrophies. The eQTL analyses showed that they were part of molecular networks associated with WS and meat quality phenotypes and suggested a few putative causative genes.

Genetic Determinism of Fearfulness, General Activity and Feeding Behavior in Chickens and Its Relationship with Digestive Efficiency.

The genetic relationships between behavior and digestive efficiency were studied in 860 chickens from a cross between two lines divergently selected on digestive efficiency. At 2 weeks of age each chick was video-recorded in the home pen to characterize general activity and feeding behavior. Tonic immobility and open-field tests were also carried out individually to evaluate emotional reactivity (i.e. the propensity to express fear responses). Digestive efficiency was measured at 3 weeks. Genetic parameters of behavior traits were estimated. Birds were genotyped on 3379 SNP markers to detect QTLs. Heritabilities of behavioral traits were low, apart from tonic immobility (0.17-0.18) and maximum meal length (0.14). The genetic correlations indicated that the most efficient birds fed more frequently and were less fearful. We detected 14 QTL (9 for feeding behavior, 3 for tonic immobility, 2 for frequency of lying). Nine of them co-localized with QTL for efficiency, anatomy of the digestive tract, feed intake or microbiota composition. Four genes involved in fear reactions were identified in the QTL for tonic immobility on GGA1.

Serum and Muscle Metabolomics for the Prediction of Ultimate pH, a Key Factor for Chicken-Meat Quality.

Variations in muscle glycogen storage are highly correlated with variations in meat ultimate pH (pHu), a key factor for poultry meat quality. A total of two chicken lines were divergently selected on breast pHu to understand the biological basis for variations in meat quality (i.e., the pHu- and the pHu+ lines that are characterized by a 17% difference in muscle glycogen content). The effects of this selection on bird metabolism were investigated by quantifying muscle metabolites by high-resolution NMR ((1)H and (31)P) and serum metabolites by (1)H NMR. A total of 20 and 26 discriminating metabolites between the two lines were identified by orthogonal partial least-squares discriminant analysis (OPLS-DA) in the serum and muscle, respectively. There was over-representation of carbohydrate metabolites in the serum and muscle of the pHu- line, consistent with its high level of muscle glycogen. However, the pHu+ line was characterized by markers of oxidative stress and muscle catabolism, probably because of its low level of energy substrates. After OPLS-DA multiblock analysis, a metabolic set of 15 high-confidence biomarkers was identified that could be used to predict the quality of poultry meat after validation on an independent population.

Genetic parameters of white striping in relation to body weight, carcass composition, and meat quality traits in two broiler lines divergently selected for the ultimate pH of the pectoralis major muscle.

BACKGROUND: White striping (WS) is an emerging quality defect with adverse consequences for the sensorial, technological, and nutritional qualities of breast meat in broiler chickens. The genetic determinism of this defect is little understood and thus the aim of the study presented here was to estimate the genetic parameters of WS in relation to other traits of economic importance such as body weight, carcass composition, and technological meat quality in an experimental population consisting of two divergent lines selected for high (pHu + line) or low (pHu- line) ultimate pH (pHu) of the pectoralis major (p. major) muscle. RESULTS: The incidence of WS in the whole population was 50.7%, with 36.7% of broilers being moderately and 14% being severely affected. A higher incidence of moderate (p < 0.001) and severe (p < 0.0001) WS was observed in the pHu + line, and strong genetic determinism (h(2) = 0.65 ± 0.08) was evidenced for WS in the studied lines. In addition, WS was significantly genetically correlated with body weight (rg = 0.33 ± 0.15), and breast meat yield (0.68 ± 0.06), but not with the percentage of leg or abdominal fat. Increased body weight and breast muscle yield were significantly associated with increased incidence and severity of WS regardless of the line. Significant rg were observed between WS and several meat quality traits, including breast (0.21 ± 0.08) and thigh (0.31 ± 0.10) pHu, and breast cooking loss (0.30 ± 0.15). WS was also strongly genetically correlated with the intramuscular fat content of the pectoralis major muscle (0.64 ± 0.09), but not with the lipid oxidation index of this muscle. CONCLUSIONS: This study highlighted the role of genetics as a major determinant of WS. The estimated genetic correlations showed that WS was more highly related to muscle development than to the overall growth of the body. The positive genetic association reported in this study between WS and muscle pHu indicated a possible relationship between the ability of muscle to store energy as a carbohydrate and its likelihood of developing WS. Finally, the strong genetic determinism of WS suggested that selection can be an efficient means of reducing the incidence of WS and of limiting its undesirable consequences on meat quality in broiler chickens.

A medium density genetic map and QTL for behavioral and production traits in Japanese quail.

BACKGROUND: Behavioral traits such as sociability, emotional reactivity and aggressiveness are major factors in animal adaptation to breeding conditions. In order to investigate the genetic control of these traits as well as their relationships with production traits, a study was undertaken on a large second generation cross (F2) between two lines of Japanese Quail divergently selected on their social reinstatement behavior. All the birds were measured for several social behaviors (social reinstatement, response to social isolation, sexual motivation, aggression), behaviors measuring the emotional reactivity of the birds (reaction to an unknown object, tonic immobility reaction), and production traits (body weight and egg production). RESULTS: We report the results of the first genome-wide QTL detection based on a medium density SNP panel obtained from whole genome sequencing of a pool of individuals from each divergent line. A genetic map was constructed using 2145 markers among which 1479 could be positioned on 28 different linkage groups. The sex-averaged linkage map spanned a total of 3057 cM with an average marker spacing of 2.1 cM. With the exception of a few regions, the marker order was the same in Japanese Quail and the chicken, which confirmed a well conserved synteny between the two species. The linkage analyses performed using QTLMAP software revealed a total of 45 QTLs related either to behavioral (23) or production (22) traits. The most numerous QTLs (15) concerned social motivation traits. Interestingly, our results pinpointed putative pleiotropic regions which controlled emotional reactivity and body-weight of birds (on CJA5 and CJA8) or their social motivation and the onset of egg laying (on CJA19). CONCLUSION: This study identified several QTL regions for social and emotional behaviors in the Quail. Further research will be needed to refine the QTL and confirm or refute the role of candidate genes, which were suggested by bioinformatics analysis. It can be hoped that the identification of genes and polymorphisms related to behavioral traits in the quail will have further applications for other poultry species (especially the chicken) and will contribute to solving animal welfare issues in poultry production.

Detection of QTL controlling feed efficiency and excretion in chickens fed a wheat-based diet.

BACKGROUND: Improving feed efficiency is a major goal in poultry production in order to reduce production costs, increase the possibility of using alternative feedstuffs and decrease the volume of manure. However, in spite of their economic and environmental impact, very few quantitative trait loci (QTL) have been reported on these traits. Thus, we undertook the detection of QTL on 820 meat-type chickens from a F2 cross between D- and D+ lines that were divergently selected on low or high digestive efficiency at 3 weeks of age. Birds were measured for growth between 0 and 23 days, feed intake and feed conversion ratio between 9 and 23 days, breast and abdominal fat yields at 23 days, and the anatomy of their digestive tract (density, relative weight and length of the duodenum, jejunum, ileum, and ratio of proventriculus to gizzard weight) was examined. To evaluate excretion traits, fresh and dry weight, water content, pH, nitrogen to phosphorus ratio from 0 to 23 days, and pH of gizzard and jejunum contents at 23 days were measured. A set of 3379 single nucleotide polymorphisms distributed on 28 Gallus gallus (GGA) autosomes, the Z chromosome and one unassigned linkage group was used for QTL detection. RESULTS: Using the QTLMap software developed for linkage analyses by interval mapping, we detected 16 QTL for feed intake, 13 for feed efficiency, 49 for anatomy-related traits, seven for growth, six for body composition and ten for excretion. Nine of these QTL were genome-wide significant (four for feed intake on GGA1, one for feed efficiency on GGA2, and four for anatomy on GGA1, 2, 3 and 4). GGA16, 19, and 26 carried many QTL for different types of traits that co-localize at the same position. CONCLUSIONS: This study identified several QTL regions that are involved in the control of digestive efficiency in chicken. Further studies are needed to identify the genes that underlie these effects, and to validate these in other commercial populations and for different breeding environments.

Nutrigenetics of carotenoid metabolism in the chicken: a polymorphism at the ß,ß-carotene 15,15'-mono-oxygenase 1 (BCMO1) locus affects the response to dietary ß-carotene.

The enzyme ß,ß-carotene-15,15'-mono-oxygenase 1 (BCMO1) is responsible for the symmetrical cleavage of ß-carotene into retinal. We identified a polymorphism in the promoter of the BCMO1 gene, inducing differences in BCMO1 mRNA levels (high in adenines (AA) and low in guanines (GG)) and colour in chicken breast muscle. The present study was designed to test whether this polymorphism could affect the response to dietary ß-carotene. Dietary ß-carotene supplementation did not change the effects of the genotypes on breast muscle properties: BCMO1 mRNA levels were lower and xanthophyll contents higher in GG than in AA chickens. Lower vitamin E levels in the plasma and duodenum, plasma cholesterol levels and body weight were also observed in GG than in AA chickens. In both genotypes, dietary ß-carotene increased vitamin A storage in the liver; however, it reduced numerous parameters such as SCARB1 (scavenger receptor class B type I) in the duodenum, BCMO1 in the liver, vitamin E levels in the plasma and tissues, xanthophyll contents in the pectoralis major muscle and carcass adiposity. However, several diet × genotype interactions were observed. In the GG genotype, dietary ß-carotene increased ISX (intestine-specific homeobox) and decreased BCMO1 mRNA levels in the duodenum, decreased xanthophyll concentrations in the duodenum, liver and plasma, and decreased colour index and HDL-cholesterol concentration in the plasma. Retinol accumulation following dietary ß-carotene supplementation was observed in the duodenum of AA chickens only. Therefore, the negative feedback control on ß-carotene conversion through ISX appears as functional in the duodenum of GG but not of AA chickens. This could result in a higher availability of ß-carotene in the duodenum of GG chickens, reducing the uptake of xanthophylls, liposoluble vitamins and cholesterol.

Detection of QTL controlling digestive efficiency and anatomy of the digestive tract in chicken fed a wheat-based diet.

BACKGROUND: Improving digestive efficiency is a major goal in poultry production, to reduce production costs, make possible the use of alternative feedstuffs and decrease the volume of manure produced. Since measuring digestive efficiency is difficult, identifying molecular markers associated with genes controlling this trait would be a valuable tool for selection. Detection of QTL (quantitative trait loci) was undertaken on 820 meat-type chickens in a F2 cross between D- and D+ lines divergently selected on low or high AMEn (apparent metabolizable energy value of diet corrected to 0 nitrogen balance) measured at three weeks in animals fed a low-quality diet. Birds were measured for 13 traits characterizing digestive efficiency (AMEn, coefficients of digestive utilization of starch, lipids, proteins and dry matter (CDUS, CDUL, CDUP, CDUDM)), anatomy of the digestive tract (relative weights of the proventriculus, gizzard and intestine and proventriculus plus gizzard (RPW, RGW, RIW, RPGW), relative length and density of the intestine (RIL, ID), ratio of proventriculus and gizzard to intestine weight (PG/I); and body weight at 23 days of age. Animals were genotyped for 6000 SNPs (single nucleotide polymorphisms) distributed on 28 autosomes, the Z chromosome and one unassigned linkage group. RESULTS: Nine QTL for digestive efficiency traits, 11 QTL for anatomy-related traits and two QTL for body weight at 23 days of age were detected. On chromosome 20, two significant QTL at the genome level co-localized for CDUS and CDUDM, i.e. two traits that are highly correlated genetically. Moreover, on chromosome 16, chromosome-wide QTL for AMEn, CDUS, CDUDM and CDUP, on chromosomes 23 and 26, chromosome-wide QTL for CDUS, on chromosomes 16 and 26, co-localized QTL for digestive efficiency and the ratio of intestine length to body weight and on chromosome 27 a chromosome-wide QTL for CDUDM were identified. CONCLUSIONS: This study identified several regions of the chicken genome involved in the control of digestive efficiency. Further studies are necessary to identify the underlying genes and to validate these in commercial populations and breeding environments.

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.

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

BACKGROUND: This 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). RESULTS: Microarray 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. CONCLUSIONS: The 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.

Genome-wide interval mapping using SNPs identifies new QTL for growth, body composition and several physiological variables in an F2 intercross between fat and lean chicken lines.

BACKGROUND: For decades, genetic improvement based on measuring growth and body composition traits has been successfully applied in the production of meat-type chickens. However, this conventional approach is hindered by antagonistic genetic correlations between some traits and the high cost of measuring body composition traits. Marker-assisted selection should overcome these problems by selecting loci that have effects on either one trait only or on more than one trait but with a favorable genetic correlation. In the present study, identification of such loci was done by genotyping an F2 intercross between fat and lean lines divergently selected for abdominal fatness genotyped with a medium-density genetic map (120 microsatellites and 1302 single nucleotide polymorphisms). Genome scan linkage analyses were performed for growth (body weight at 1, 3, 5, and 7 weeks, and shank length and diameter at 9 weeks), body composition at 9 weeks (abdominal fat weight and percentage, breast muscle weight and percentage, and thigh weight and percentage), and for several physiological measurements at 7 weeks in the fasting state, i.e. body temperature and plasma levels of IGF-I, NEFA and glucose. Interval mapping analyses were performed with the QTLMap software, including single-trait analyses with single and multiple QTL on the same chromosome. RESULTS: Sixty-seven QTL were detected, most of which had never been described before. Of these 67 QTL, 47 were detected by single-QTL analyses and 20 by multiple-QTL analyses, which underlines the importance of using different statistical models. Close analysis of the genes located in the defined intervals identified several relevant functional candidates, such as ACACA for abdominal fatness, GHSR and GAS1 for breast muscle weight, DCRX and ASPSCR1 for plasma glucose content, and ChEBP for shank diameter. CONCLUSIONS: The medium-density genetic map enabled us to genotype new regions of the chicken genome (including micro-chromosomes) that influenced the traits investigated. With this marker density, confidence intervals were sufficiently small (14 cM on average) to search for candidate genes. Altogether, this new information provides a valuable starting point for the identification of causative genes responsible for important QTL controlling growth, body composition and metabolic traits in the broiler chicken.

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.

Analysis of a slow-growing line reveals wide genetic variability of carcass and meat quality-related traits.

BACKGROUND: Slow-growing lines are widely used in France for the production of high quality free-range chickens. While such production is mainly dedicated to the whole carcass market, new prospects are opening up for the development of cuts and processed products. Whether the body composition and meat quality of slow-growing birds can be improved by selection has thus become an important issue. The genetic parameters of growth, body composition and breast meat quality traits were evaluated in relation to behaviour at slaughter in a large pedigree population including 1022 male and female slow-growing birds. RESULTS: The heritability coefficients (h²) of body weight and body composition traits varied from 0.3 to 0.5. Abdominal fat percentage was genetically positively correlated with body weight but negatively correlated with breast muscle yield. The characteristics of the breast meat (i.e., post-mortem fall in pH, colour, drip loss, shear-force and lipid content) were all heritable, with h² estimates ranging from 0.18 to 0.48. The rate and extent of the fall in pH were under different genetic control. Strong negative genetic correlations were found between the ultimate pH and the lightness, yellowness and drip loss of the meat. Wing flapping on the shackle line was significantly heritable and exhibited marked genetic correlations with the pH at 15 min post-slaughter and the redness of the meat. The genetic relationships between meat quality traits, body weight and body composition appeared slightly different between males and females. CONCLUSION: This study suggested that there are a number of important criteria for selection on carcass and breast meat quality in slow-growing birds. Selection for reduced abdominal fatness and increased breast muscle yield should be effective as both traits were found to be highly heritable and favourably correlated. Substantial improvement in meat quality could be achieved by selection on ultimate pH which was highly heritable and strongly correlated with the colour and water-holding capacity of the meat. Moreover, this study revealed for the first time that the behaviour at slaughter is partly genetically determined in the chicken.

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.

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.

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.

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.