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.

Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL.

BACKGROUND: The understanding of the biological determinism of meat ultimate pH, which is strongly related to muscle glycogen content, is a key point for the control of muscle integrity and meat quality in poultry. In the present study, we took advantage of a unique model of two broiler lines divergently selected for the ultimate pH of the pectoralis major muscle (PM-pHu) in order to decipher the genetic control of this trait. Two complementary approaches were used: detection of selection signatures generated during the first five generations and genome-wide association study for PM-pHu and Sartorius muscle pHu (SART-pHu) at the sixth generation of selection. RESULTS: Sixty-three genomic regions showed significant signatures of positive selection. Out of the 10 most significant regions (detected by HapFLK or FLK method with a p-value below 1e-6), 4 were detected as soon as the first generation (G1) and were recovered at each of the four following ones (G2-G5). Another four corresponded to a later onset of selection as they were detected only at G5. In total, 33 SNPs, located in 24 QTL regions, were significantly associated with PM-pHu. For SART-pHu, we detected 18 SNPs located in 10 different regions. These results confirmed a polygenic determinism for these traits and highlighted two major QTL: one for PM-pHu on GGA1 (with a Bayes Factor (BF) of 300) and one for SART-pHu on GGA4 (with a BF of 257). Although selection signatures were enriched in QTL for PM-pHu, several QTL with strong effect haven't yet responded to selection, suggesting that the divergence between lines might be further increased. CONCLUSIONS: A few regions of major interest with significant selection signatures and/or strong association with PM-pHu or SART-pHu were evidenced for the first time in chicken. Their gene content suggests several candidates associated with diseases of glycogen storage in humans. The impact of these candidate genes on meat quality and muscle integrity should be further investigated in chicken.

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.

The Family Secrets of Avian Egg-Specific Ovalbumin and Its Related Proteins Y and X.

The ovalbumin gene family in Gallus gallus is composed of three homologous genes located within a 46 kb locus on chromosome 2: ovalbumin, ovalbumin-related protein Y (OVAY), and ovalbumin-related protein X (OVAX) genes. The expression of these genes in hen oviduct is under estrogen control, but their relative hormonal responsiveness and subsequent protein concentration in egg, is distinctive. Interestingly, all three proteins lack the classical signal peptide for secretion. Ovalbumin, OVAX, and OVAY belong to the serine protease inhibitor (serpin) family whose members share a common tertiary structure. Ovalbumin and OVAX are one of the few members of this family that do not express any protease inhibition activity whereas OVAY has been predicted to be inhibitory, by comparison with the consensus sequence for inhibitory serpins. In contrast to ovalbumin and OVAY, OVAX interacts with heparin, a negatively charged glycosaminoglycan, via a positively charged domain exposed at the surface of the molecule. Ovalbumin is the major egg white protein and might be a source of amino acids for the developing embryo. The physiological function of OVAY is not known, but recent data have revealed a possible role of this protein in early embryonic development. Considering the antibacterial activities of OVAX, this protein might play a role in egg defense. This review sheds light on the expression, biochemistry, and structural specificities of these three highly similar paralogs. It gives new clues in favor of diverging functions, which are likely to have arisen by duplication events from a common ancestral gene.

Variation in macrominerals and trace elements in cows' retail milk and implications for consumers nutrition.

Based on previous farm-level studies, this study hypothesised that production system (conventional, CON; organic, ORG; channel island, CHA) and season would cause variation in the concentrations of macrominerals and trace elements in retail milk. On average, milk retained its status as an excellent source of Ca, P, I, and Mo across different demographics, and a very good source of K, Mg, and Zn for children. Compared with CON and ORG, CHA milk contained higher concentrations of Ca, Mg, P, Cu, Mn, and Zn; and lower concentrations of K and I. Macrominerals did not show a clear seasonal pattern but trace elements were all at lower concentrations during the typical grazing season. Variation in mineral concentrations can have implications to Ca and P supply in children, and I and Zn supply across different consumer demographics; while the seasonal variation was more pronounced than that associated with production system.

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.

Metabolomics and lipidomics reveal the effects of the toxic dinoflagellate Alexandrium catenella on immune cells of the blue mussel, Mytilus edulis.

The increasing occurrence of harmful algal blooms, mostly of the dinoflagellate Alexandrium catenella in Canada, profoundly disrupts mussel aquaculture. These filter-feeding shellfish feed on A. catenella and accumulate paralytic shellfish toxins, such as saxitoxin, in tissues, making them unsafe for human consumption. Algal toxins also have detrimental effects upon several physiological functions in mussels, but particularly on the activity of hemocytes - the mussel immune cells. The objective of this work was to determine the effects of experimental exposure to A. catenella upon hemocyte metabolism and activity in the blue mussel, Mytilus edulis. To do so, mussels were exposed to cultures of the toxic dinoflagellate A. catenella for 120 h. The resulting mussel saxitoxin load had measurable effects upon survival of hemocytes and induced a stress response measured as increased ROS production. The neutral lipid fraction of mussel hemocytes decreased two-fold, suggesting a differential use of lipids. Metabolomic 1H nuclear magnetic resonance (NMR) analysis showed that A. catenella modified the energy metabolism of hemocytes as well as hemocyte osmolyte composition. The modified energy metabolism was reenforced by contrasting plasma metabolomes between control and exposed mussels, suggesting that the blue mussel may reduce feed assimilation when exposed to A. catenella.

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.

Mineral Concentrations in Bovine Milk from Farms with Contrasting Grazing Management.

Thirty conventional and twenty-four organic dairy farms were divided into equal numbers within system groups: high-pasture, standard-pasture, and low-pasture groups. Milk samples were collected monthly for 12 consecutive months. Milk from high-pasture organic farms contained less fat and protein than standard- and low-pasture organic farms, but more lactose than low-pasture organic farms. Grazing, concentrate feed intake and the contribution of non-Holstein breeds were the key drivers for these changes. Milk Ca and P concentrations were lower in standard-pasture conventional farms than the other conventional groups. Milk from low-pasture organic farms contained less Ca than high- and standard-pasture organic farms, while high-pasture organic farms produced milk with the highest Sn concentration. Differences in mineral concentrations were driven by the contribution of non-Holstein breeds, feeding practices, and grazing activity; but due to their relatively low numerical differences between groups, the subsequent impact on consumers' dietary mineral intakes would be minor.

Macromineral and trace element concentrations and their seasonal variation in milk from organic and conventional dairy herds.

To study the effects of dairy production system on milk macromineral and trace element concentrations, milk samples were collected monthly in 2019 from 43 conventional and 27 organic farms. Organic milk contained more Ca (1049.5 vs. 995.8 mg/kg), K (1383.6 vs. 1362.4 mg/kg), P (806.5 vs. 792.5 mg/kg) and Mo (73.3 vs. 60.6 µg/kg) but less Cu (52.4 vs. 60.6 µg/kg), Fe (0.66 vs 2.03 mg/kg), Mn (28.8 vs. 45.0 µg/kg), Zn (4.51 vs. 5.00 mg/kg) and Al (0.32 vs. 1.14 µg/kg) than conventional milk. Significant seasonal variation was observed in all determined minerals' concentrations. Milk I concentration was not consistently affected by production system, whereas organic milk contained less I in June and July than conventional milk. Dietary factors contributing to different milk mineral concentrations between production systems included intakes of maize silage, dry-straights and oils (higher in conventional diets), and pasture, clover and wholecrop (higher in organic diets).

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.

A multiplatform metabolomic approach to characterize fecal signatures of negative postnatal events in chicks: a pilot study.

BACKGROUND: Negative experiences in early life can induce long-lasting effects on the welfare, health, and performance of farm animals. A delayed placement of chicks in rearing houses has negative effects on their performance, and results in fecal-specific odors detectable by rats. Based on this observation, the volatile organic compounds (VOCs) and metabolites from the feces of 12-day-old chickens were screened for early markers of response to negative events using gas-chromatography and liquid-chromatography coupled with mass spectrometry (GC-MS, LC-HRMS). RESULTS: The low reproducibility of solid-phase micro-extraction of the VOCs followed by GC-MS was not suitable for marker discovery, in contrast to liquid extraction of metabolites from freeze-dried feces followed by GC-MS or LC-HRMS analysis. Therefore, the fecal metabolome from 12-day-old chicks having experienced a normal or delayed placement were recorded by GC-MS and LC-HRMS in two genotypes from two experiments. From both experiments, 25 and 35 metabolites, respectively explaining 81% and 45% of the difference between delayed and control chickens, were identified by orthogonal partial least-squares discriminant analysis from LC-HRMS and GC-MS profiling. CONCLUSION: The sets of molecules identified will be useful to better understand the chicks' response to negative events over time and will contribute to define stress or welfare biomarkers. .

Does lipidomic serum analysis support the assessment of digestive efficiency in chickens?

The increasing cost of conventional feedstuffs used in poultry diets has bolstered interest in genetic selection for digestive efficiency (DE) to improve the adaptation of the birds to various alternative feedstuffs. However, DE measurement through AMEn is time-consuming and constraining. To simplify selection for DE, the potential of serum composition to predict AMEn was evaluated based on 40 birds from two broiler lines (D+ and D-) divergently selected on the fecal AMEn of a difficult-to-digest wheat-based diet. Differences in serum coloration were suspected between the two lines, and thus a spectrophotometric analysis was carried out, revealing a significant difference in absorption between 430 nm and 516 nm, corresponding to the signature of orange-red lipophilic pigments such as xanthophylls. To go further, the liposoluble fraction of the serum was explored for its lipidome by mass spectrometry. Discriminant analysis revealed that a pattern of 10 metabolites, including zeaxanthin/lutein, can explain 82% of the lipidomic differences between the two lines. Colorimetry combined with lipidomics studies confirmed the relationship between digestive efficiency and serum composition, which opens up new possibilities for using it as a quick and easy proxy of digestive efficiency.

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.

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.

Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken.

The processing ability and sensory quality of chicken breast meat are highly related to its ultimate pH (pHu), which is mainly determined by the amount of glycogen in the muscle at death. To unravel the molecular mechanisms underlying glycogen and meat pHu variations and to identify predictive biomarkers of these traits, a transcriptome profiling analysis was performed using an Agilent custom chicken 8 × 60 K microarray. The breast muscle gene expression patterns were studied in two chicken lines experimentally selected for high (pHu+) and low (pHu-) pHu values of the breast meat. Across the 1,436 differentially expressed (DE) genes found between the two lines, many were involved in biological processes related to muscle development and remodelling and carbohydrate and energy metabolism. The functional analysis showed an intensive use of carbohydrate metabolism to produce energy in the pHu- line, while alternative catabolic pathways were solicited in the muscle of the pHu+ broilers, compromising their muscle development and integrity. After a validation step on a population of 278 broilers using microfluidic RT-qPCR, 20 genes were identified by partial least squares regression as good predictors of the pHu, opening new perspectives of screening broilers likely to present meat quality defects.