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.

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.

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.

Eggshell decalcification and skeletal mineralization during chicken embryonic development: defining candidate genes in the chorioallantoic membrane.

During chicken embryonic development, skeleton calcification mainly relies on the eggshell, whose minerals are progressively solubilized and transported to the embryo via the chorioallantoic membrane (CAM). However, the molecular components involved in this process remain undefined. We assessed eggshell demineralization and calcification of the embryo skeleton after 12 and 16 d of incubation, and analyzed the expression of several candidate genes in the CAM: carbonic anhydrases that are likely involved in secretion of protons for eggshell dissolution (CA2, CA4, CA9), ions transporters and regulators (CALB1, SLC4A1, ATP6V1B2, SGK1, SCGN, PKD2) and vitamin-D binding protein (GC). Our results confirmed that eggshell weight, thickness, and strength decreased during incubation, with a concomitant increase in calcification of embryonic skeletal system. In the CAM, the expression of CA2 increased during incubation while CA4 and CA9 were expressed at similar levels at both stages. SCL4A1 and SCGN were expressed, but not differentially, between the two stages, while the expression of ATP6V1B2 and PKD2 genes decreased. The expression of SGK1 and TRPV6 increased over time, although the expression of the latter gene was barely detectable. In parallel, we analyzed the expression of these candidate genes in the yolk sac (YS), which mediates the transfer of yolk minerals to the embryo during the first half of incubation. In YS, CA2 expression increases during incubation, similar to the CAM, while the expression of the other candidate genes decreases. Moreover, CALB1 and GC genes were found to be expressed during incubation in the YS, in contrast to the CAM where no expression of either was detected. This study demonstrates that the regulation of genes involved in the mobilization of egg minerals during embryonic development is different between the YS and CAM extraembryonic structures. Identification of the full suite of molecular components involved in the transfer of eggshell calcium to the embryo via the CAM should help to better understand the role of this structure in bone mineralization.

Improving the efficiency of feed utilization in poultry by selection. 1. Genetic parameters of anatomy of the gastro-intestinal tract and digestive efficiency.

BACKGROUND: Feed costs represent about 70% of the costs of raising broilers. The main way to decrease these costs is to improve feed efficiency by modification of diet formulation, but one other possibility would be to use genetic selection. Understanding the genetic architecture of the gastro-intestinal tract (GIT) and the impact of the selection criterion on the GIT would be of particular interest. We therefore studied the genetic parameters of AMEn (Apparent metabolisable energy corrected for zero nitrogen balance), feed efficiency, and GIT traits in chickens.Genetic parameters were estimated for 630 broiler chickens of the eighth generation of a divergent selection experiment on AMEn. Birds were reared until 23 d of age and fed a wheat-based diet. The traits measured were body weight (BW), feed conversion ratio (FCR), AMEn, weights of crop, liver, gizzard and proventriculus, and weight, length and density of the duodenum, jejunum and ileum. RESULTS: The heritability estimates of BW, FCR and AMEn were moderate. The heritability estimates were higher for the GIT characteristics except for the weights of the proventriculus and liver. Gizzard weight was negatively correlated with density (weight to length ratio) of duodenum, jejunum and ileum. Proventriculus and gizzard weights were more strongly correlated with AMEn than with FCR, which was not the case for intestine weight and density. CONCLUSIONS: GIT traits were largely dependent on genetics and that selecting on AMEn or FCR would modify them. Phenotypic observations carried out in the divergent lines selected on AMEn were consistent with estimated genetic correlations between AMEn and GIT traits.

Improving the efficiency of feed utilization in poultry by selection. 2. Genetic parameters of excretion traits and correlations with anatomy of the gastro-intestinal tract and digestive efficiency.

BACKGROUND: Poultry production has been widely criticized for its negative environmental impact related to the quantity of manure produced and to its nitrogen and phosphorus content. In this study, we investigated which traits related to excretion could be used to select chickens for lower environmental pollution.The genetic parameters of several excretion traits were estimated on 630 chickens originating from 2 chicken lines divergently selected on apparent metabolisable energy corrected for zero nitrogen (AMEn) at constant body weight. The quantity of excreta relative to feed consumption (CDUDM), the nitrogen and phosphorus excreted, the nitrogen to phosphorus ratio and the water content of excreta were measured, and the consequences of such selection on performance and gastro-intestinal tract (GIT) characteristics estimated. The genetic correlations between excretion, GIT and performance traits were established. RESULTS: Heritability estimates were high for CDUDM and the nitrogen excretion rate (0.30 and 0.29, respectively). The other excretion measurements showed low to moderate heritability estimates, ranging from 0.10 for excreta water content to 0.22 for the phosphorus excretion rate. Except for the excreta water content, the CDUDM was highly correlated with the excretion traits, ranging from -0.64 to -1.00. The genetic correlations between AMEn or CDUDM and the GIT characteristics were very similar and showed that a decrease in chicken excretion involves an increase in weight of the upper part of the GIT, and a decrease in the weight of the small intestine. CONCLUSION: In order to limit the environmental impact of chicken production, AMEn and CDUDM seem to be more suitable criteria to include in selection schemes than feed efficiency traits.

Dietary Phosphorus and Calcium Utilization in Growing Pigs: Requirements and Improvements.

The sustainability of animal production relies on the judicious use of phosphorus (P). Phosphate, the mined source of agricultural phosphorus supplements, is a non-renewable resource, but phosphorus is essential for animal growth, health, and well-being. P must be provided by efficient and sustainable means that minimize the phosphorus footprint of livestock production by developing precise assessment of the bioavailability of dietary P using robust models. About 60% of the phosphorus in an animal's body occurs in bone at a fixed ratio with calcium (Ca) and the rest is found in muscle. The P and Ca requirements must be estimated together; they cannot be dissociated. While precise assessment of P and Ca requirements is important for animal well-being, it can also help to mitigate the environmental effects of pig farming. These strategies refer to multicriteria approaches of modeling, efficient use of the new generations of phytase, depletion and repletion strategies to prime the animal to be more efficient, and finally combining these strategies into a precision feeding model that provides daily tailored diets for individuals. The industry will need to use strategies such as these to ensure a sustainable plant-animal-soil system and an efficient P cycle.

Phenotypic timeline of gastrointestinal tract development in broilers divergently selected for digestive efficiency.

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, to favor the use of a wider variety of feedstuffs. The objective of the study was to better characterize the kinetics of development of the digestive tract in broilers, in relationship with digestive efficiency by measuring various digestive parameters as well as serum color. Absolute and relative growth of gastrointestinal tract organs were compared between 2 divergent chicken lines selected on digestive efficiency (AMEn) during 7 wk of development. We show that as early as 7 d of age, these 2 lines differs for several organs developments and that these differences remain visible later on. In addition, the allometry of the gizzard and intestine segments is different between the 2 lines, with efficient birds putting more effort in the upper part of the digestive tract during postnatal development and less-efficient birds putting more effort in the lower part of the gastrointestinal tract. Interestingly, we also showed that differences in serum pigmentation, which is a good biomarker for digestive capacity, could be a convenient diagnostic tool to discriminate between chickens with high or low digestive efficiency at early stages of development. In conclusion, this study showed that selection of chickens for AMEn had large impacts in gastrointestinal development including at early stages and is a valuable resource for further studies on the genetic and physiological control of the response of the animal to feed variations.

Lipid metabolism and antioxidant status in sucrose vs. potato-fed rats.

OBJECTIVE: Consumption of high levels of simple carbohydrates is associated with several metabolic disorders in humans and in laboratory animals, including symptoms of an early stage of metabolic syndrome (syndrome X). This disorder has several cardiovascular risk factors, such as hypertriglyceridemia, and is associated with an increase in oxidative stress. In contrast to sucrose, potato, a source of complex carbohydrates and antioxidant micronutrients, was thought to improve lipid metabolism and antioxidant protection. METHODS: We investigated the effects of diets containing i) complex dietary carbohydrates and antioxidant micronutrients (potato Solanum tuberosum L.), ii) complex carbohydrates (starch) and iii) a simple carbohydrate (sucrose) on lipid metabolism and antioxidant status in rats. RESULTS: An increase in short chain fatty acid (SCFA) pools was observed in the cecum of rats fed a potato-based diet, resulting from an increase in all SCFAs, especially propionate (+360%, P < 0.0001). Feeding rats a potato-based diet for 3 weeks led to a decrease in cholesterol (-37%, potato vs. control and -32%, potato vs. sucrose) and triglycerides (-31%, potato vs. control and -43%, potato vs. sucrose) concentrations in triglyceride-rich lipoproteins (TGRLP) fractions. The antioxidant status was decreased by sucrose consumption and improved by potato consumption. CONCLUSIONS: Our present results suggest that consumption of complex carbohydrates (provided as cooked potatoes), in combination with different antioxidant micronutrients, may enhance the antioxidant defences and improve lipid metabolism, when compared with starch (complex carbohydrates) and to sucrose consumption (source of simple sugar). These effects limit oxidative stress and reduce the risk of developing the associated degenerative diseases, including cardiovascular disease, and could have potential in cardiovascular disease prevention.

Adaptive response of broilers to dietary phosphorus and calcium restrictions.

The aim of this study was to evaluate the capacity of chickens to adapt to and compensate for early dietary restriction of non-phytate P ( NPP: ) and/or Ca (10 to 21 d) in a later phase (22 to 35 d), and to determine whether compensatory processes depend on the P and Ca concentrations in the finisher diet. Four diets were formulated and fed to broilers from 10 to 21 d in order to generate birds with different mineral status: L1 (0.6% Ca, 0.30% NPP), L2 (0.6% Ca, 0.45% NPP), H1 (1.0% Ca, 0.30% NPP), and H2 (1.0% Ca, 0.45% NPP). On d 22, each group was divided into three groups which received a low (L, 0.48% Ca, 0.24% NPP), moderate (M, 0.70% Ca, 0.35% NPP), or high (H, 0.90% Ca, 0.35% NPP) finisher diet until 35 d, resulting in a total of 12 treatments. Lowering the Ca level enhanced apparent ileal digestibility of P (P AID) at 21 d especially with the high NPP level (Ca × NPP, P < 0.01). The lower bone mineralization observed at 21 d in broilers fed the L1 diet compared to those fed the H2 diet had disappeared by 35 d with long-term stimulation of the P AID with the low NPP level (P < 0.001). Although P AID and growth performance were improved in birds fed the L1L compared to the L1H and H2H treatments, tibia characteristics tended to be lower in birds fed the L1L compared to those fed the L1H treatment. Birds fed the H1M treatment had higher P AID, growth performance and tibia ash content than those fed the H1H treatment. A significant increase in the mRNA levels of several genes encoding Ca and P transporters was observed at 35 d in birds fed the L1 followed by the L diet compared to birds fed the L1 followed by the M diet. In conclusion, chickens are able to adapt to early dietary changes in P and Ca through improvement of digestive efficiency in a later phase, and the extent of the compensation in terms of growth performance and bone mineralization depends on the P and Ca levels in the subsequent diet.

Genetic determinism of bone and mineral metabolism in meat-type chickens: A QTL mapping study.

Skeletal integrity in meat-type chickens is affected by many factors including rapid growth rate, nutrition and genetics. To investigate the genetic basis of bone and mineral metabolism, a QTL detection study was conducted in an intercross between two lines of meat-type chickens divergently selected for their high (D +) or low (D -) digestive efficiency. Tibia size (length, diameter, volume) and ash content were determined at 3 weeks of age as well as phosphorus (P) retention and plasma concentration. Heritability of these traits and their genetic correlations with digestive efficiency were estimated. A QTL mapping study was performed using 3379 SNP markers. Tibia size, weight, ash content and breaking strength were highly heritable (0.42 to 0.61). Relative tibia diameter and volume as well as P retention were strongly and positively genetically correlated with digestive efficiency (0.57 to 0.80). A total of 35 QTL were identified (9 for tibia weight, 13 for tibia size, 5 for bone strength, 5 for bone mineralization, 2 for plasma P concentration and 1 for P retention). Six QTL were genome-wide significant, and 3 QTL for tibia relative volume, weight and ash weight on chromosome 6 were fixed, the positive allele coming from the D-line. For two QTL for ash content on chromosome 18 and relative tibia length on chromosome 26, the confidence intervals were small enough to identify potential candidate genes. These findings support the evidence of multiple genetic loci controlling bone and mineral metabolism. The identification of candidate genes may provide new perspectives in the understanding of bone regulation, even beyond avian species.

Impact of Selection for Digestive Efficiency on Microbiota Composition in the Chicken.

OBJECTIVES: Feed efficiency and its digestive component, digestive efficiency, are key factors in the environmental impact and economic output of poultry production. The interaction between the host and intestinal microbiota has a crucial role in the determination of the ability of the bird to digest its food and to the birds' feed efficiency. We therefore investigated the phenotypic and genetic relationships between birds' efficiency and the composition of the cecal microbiota in a F2 cross between broiler lines divergently selected for their high or low digestive efficiency. METHODS: Analyses were performed on 144 birds with extreme feed efficiency values at 3 weeks, with feed conversion values of 1.41±0.05 and 2.02±0.04 in the efficient and non-efficient groups, respectively. The total numbers of Lactobacillus, L. salivarius, L. crispatus, C. coccoides, C. leptum and E. coli per gram of cecal content were measured. RESULTS: The two groups mainly differed in larger counts of Lactobacillus, L. salivarius and E. coli in less efficient birds. The equilibrium between bacterial groups was also affected, efficient birds showing higher C. leptum, C. coccoides and L. salivarius to E. coli ratios. The heritability of the composition of microbiota was also estimated and L. crispatus, C. leptum, and C. coccoides to E. coli ratios were moderately but significantly heritable (0.16 to 0.24). The coefficient of fecal digestive use of dry matter was genetically and positively correlated with L. crispatus, C. leptum, C. coccoides (0.50 to 0.76) and negatively with E. coli (-0.66). Lipid digestibility was negatively correlated with E. coli (-0.64), and AMEn positively correlated with C. coccoides and with the C. coccoides to Lactobacillus ratio (0.48 to 0.64). We also detected 14 Quantitative Trait Loci (QTL) for microbiota on the host genome, mostly on C. leptum and Lactobacillus. The QTL for C. leptum on GGA6 was close to genome-wide significance. This region mainly includes genes involved in anti-inflammatory responses and in the motility of the gastrointestinal tract.

Fibronectin, laminin, and collagen IV as modulators of cell behavior during adrenal gland development in the human fetus.

The specific development of the human fetal adrenal gland requires cell proliferation, migration, apoptosis, and zone-specific steroidogenic activity. The present work was designed to determine the physiological significance of the previously identified spatial distribution of extracellular matrix components in the fetal gland. Primary cultures of human fetal adrenal cells grown on collagen IV, laminin, or fibronectin revealed that cell morphology was affected by environmental cues. Matrices also modulated the profile of steroid secretion by the fetal cells. Collagen IV favored cortisol secretion after ACTH or angiotensin II stimulation and increased dehydroepiandrosterone production when the AT(2) receptor of angiotensin II was specifically stimulated. These effects were correlated by changes in the mRNA levels of 3beta-hydroxysteroid dehydrogenase and cytochrome P450C17. In contrast, fibronectin and laminin decreased cell responsiveness to ACTH in terms of cortisol secretion, but enhanced ACTH-stimulated androgen secretion. Finally, extracellular matrices were able to orchestrate cell behavior. Collagen IV and laminin enhanced cell proliferation, and fibronectin increased cell death. This study is the first to demonstrate that the nature of extracellular matrix coordinates specific steroidogenic pathways and cell turnover in the developing human fetal adrenal gland.

Effect of potato on acid-base and mineral homeostasis in rats fed a high-sodium chloride diet.

Excessive dietary NaCl in association with a paucity of plant foods, major sources of K alkaline salts, is a common feature in Western eating habits which may lead to acid-base disorders and to Ca and Mg wasting. In this context, to evaluate the effects of potato, rich in potassium citrate, on acid-base homeostasis and mineral retention, Wistar rats were fed wheat starch (WS) or cooked potato (CP) diets with a low (0.5 %) or a high (2 %) NaCl content during 3 weeks. The replacement of WS by CP in the diets resulted in a significant urinary alkalinisation (pH from 5.5 to 7.3) parallel to a rise in citrate and K excretion. Urinary Ca and Mg elimination represented respectively 17 and 62 % of the daily absorbed mineral in rats fed the high-salt WS diet compared with 5 and 28 % in rats fed the high-salt CP diet. The total SCFA concentration in the caecum was 3-fold higher in rats fed the CP diets compared with rats fed the WS diets, and it led to a significant rise in Ca and Mg intestinal absorption (Ca from 39 to 56 %; Mg from 37 to 60 %). The present model of low-grade metabolic acidosis indicates that CP may be effective in alkalinising urine, enhancing citrate excretion and ameliorating Ca and Mg balance.

Entire potato consumption improves lipid metabolism and antioxidant status in cholesterol-fed rat.

BACKGROUND: Vegetables and fruits are rich sources of a variety of nutrients, including vitamins (E and C), trace minerals, and dietary fibers, and many other classes of biologically active compounds such as carotenoids and polyphenols, which are often assumed to protect against degenerative pathologies such as cardiovascular diseases. Although potato is considered as a starchy food, it is also included in the category of vegetables by its micronutrient content. AIM OF THE STUDY: In the present study, we investigated in the rat the effect of a potato-enriched diet on lipid metabolism and antioxidant protection. RESULTS: Feeding rats a potato-enriched diet for 3 weeks led to a significant decrease in cholesterol and triglyceride levels in plasma (respectively, -30%, P<0.0001 and -36%, P<0.05) and cholesterol level in liver (-42%, P<0.0001). Antioxidant status was also improved by potato consumption. TBARS levels in heart were decreased and vitamin E/triglycerides ratio in plasma was improved. CONCLUSIONS: Our present results suggest that consumption of cooked potatoes (consumed with skin) may enhance antioxidant defense and improve the lipid metabolism. These effects could be interesting for prevention of cardiovascular disease.