Genetical genomics of growth in a chicken model

BACKGROUND

The genetics underlying body mass and growth are key to understanding a wide range of topics in biology, both evolutionary and developmental. Body mass and growth traits are affected by many genetic variants of small effect. This complicates genetic mapping of growth and body mass. Experimental intercrosses between individuals from divergent populations allows us to map naturally occurring genetic variants for selected traits, such as body mass by linkage mapping. By simultaneously measuring traits and intermediary molecular phenotypes, such as gene expression, one can use integrative genomics to search for potential causative genes.

RESULTS

In this study, we use linkage mapping approach to map growth traits (N = 471) and liver gene expression (N = 130) in an advanced intercross of wild Red Junglefowl and domestic White Leghorn layer chickens. We find 16 loci for growth traits, and 1463 loci for liver gene expression, as measured by microarrays. Of these, the genes TRAK1, OSBPL8, YEATS4, CEP55, and PIP4K2B are identified as strong candidates for growth loci in the chicken. We also show a high degree of sex-specific gene-regulation, with almost every gene expression locus exhibiting sex-interactions. Finally, several trans-regulatory hotspots were found, one of which coincides with a major growth locus.

CONCLUSIONS

These findings not only serve to identify several strong candidates affecting growth, but also show how sex-specificity and local gene-regulation affect growth regulation in the chicken.

Effects of dietary concentrations of methionine on growth performance and oxidative status of broiler chickens with different hatching weight

1. A study was conducted to evaluate the effects of two hatching weight (HW) levels and two dietary concentrations of methionine on the growth performance and oxidative status of broilers. Male Arbor Acres chickens were divided into two groups on their HW (low and high HW, H and L). Each HW group was then distributed into two subgroups, of similar HW, receiving either low or high dietary concentrations of methionine (4.9 g methionine/kg, LM; 5.9 g methionine/kg, HM). Thus, all day-old birds were distributed into 4 treatments (H-LM, H-HM, L-LM, L-HM) × 6 replicates × 10 birds for 21 d. 2. Broilers with high HW were heavier than those with low HW during the 21 d assay, which appeared to result from increased body weight gain rather than improved feed conversion efficiency. A higher dietary concentration of methionine (5.9 g/kg) improved growth performance of broilers with low HW in terms of body weight gain and feed conversion ratio. 3. Broilers with different HW had similar antioxidant status both in serum and liver. 4. Broilers given a diet containing 5.9 g/kg methionine had enhanced serum superoxide dismutase (SOD) activity and decreased hepatic malondialdehyde (MDA) content at day 7. 5. Broilers given a diet containing 5.9 g/kg methionine had a higher hepatic reduced glutathione (GSH):glutathione disulphide (GSSG) ratio than those given a diet containing 4.9 g/kg methionine at day 21. High dietary methionine concentration reduced hepatic GSH content and glutathione peroxidase (GPX) activity of broilers with high HW at day 7 and at day 21, respectively, but increased hepatic GSH content of broilers with low HW at day 7. 6. Although broilers with different HW had similar oxidative status as indicated by several parameters in blood and liver, HW can have positive effects on the subsequent growth performance of broilers, and a higher dietary methionine concentration (5.9 g/kg) can improve growth performance and antioxidant status in broilers exhibiting low HW.

Association of a missense nucleotide polymorphism in the MT-ND2 gene with mitochondrial reactive oxygen species production in the Tibet chicken embryo incubated in normoxia or simulated hypoxia

NADH dehydrogenase (complex I) catalyzes the transfer of electrons from NADH to ubiquinone with pumping protons across the mitochondrial inner membrane and produces reactive oxygen species as a major source in mitochondria. A missense mutation in the mitochondrially encoded NADH dehydrogenase 2 (MT-ND2) gene, which could produce a change in the protein's secondary structure, has been found in the Tibet chicken breed. In this study, breeding eggs of the Tibet chicken breed with the two genotypes were divided into two groups. One group was incubated in normoxia (20.9% oxygen concentration) and the other in simulated hypoxia (14.5% oxygen concentration). On the 16th day of incubation, complex I activity and mitochondrial reactive oxygen species production in the Tibet chicken embryonic liver with different genotypes in each group were measured. Results showed that: (1) hypoxia reduced complex I activity standardized and mitochondrial reactive oxygen species production significantly compared with normoxia and (2) the missense mutation in the MT-ND2 gene was significantly associated with the production of reactive oxygen species in mitochondria while not associated with the standardized or unstandardized activity of complex I.

Genetic variation in feed consumption, growth, nutrient utilization efficiency and mitochondrial function within a farmed population of channel catfish (Ictalurus punctatus)

We evaluated the effects of diets (32/4 or 36/6 percent protein/fat) and six channel catfish families for growth performance characteristics. Two families with fast- (C) and slow- (D) growth rate and with low and high feed efficiency (FE) were selected for analyses of mitochondrial complex enzymatic activities (I, II, III, and IV) and gene expression (ND1, CYTB, COX1, COX2, ATP6) levels in liver, muscle, and intestine. There were significant differences in growth rate and nutrient retention among the families. Mitochondrial enzymatic complex activities (I-V) in the tissues were all lower in family C. Four of the five genes were down-regulated in the liver and up-regulated in the muscle for the fast growing family C. There were significant differences between diets for some mitochondrial respiratory chain enzyme activities and gene expression levels. Significant diet×family interactions were observed for some enzyme activities and gene expression levels. Changes in mitochondrial respiratory chain enzyme activities and gene expression levels provide insight into the cellular mechanisms of fish with differences in growth rate and feed efficiency. Results also suggest that genotype×diet interactions should be accounted for when considering strategies for using mitochondrial function as a criteria in channel catfish selection programs for improved growth performance characteristics.

Muscle characteristics and meat quality traits are affected by divergent selection on residual feed intake in pigs

Residual feed intake (RFI) is defined as the difference between the observed feed intake and that expected based on requirements for maintenance and production. A divergent selection was conducted during 4 generations in Large White male pigs to produce low and high RFI lines. The present study aims at determining the influence of this selection on biochemical and histological traits of skeletal muscle, and relating these changes to correlated effects on growth, carcass composition, and meat quality traits. At 8 d preslaughter, biopsies from the LM were taken in the fed state on 14 females from each RFI line fed ad libitum. Animals were slaughtered at 107.8 ± 8.0 kg of BW without any previous fasting. Samples of LM, semimembranosus (SM), biceps femoris (BFM), and rhomboideus muscles were taken at both 30 min and 24 h postmortem. Myofiber typing was only assessed in LM. Low RFI pigs ("efficient") had leaner carcasses with greater muscle content (P < 0.001), less backfat thickness (P < 0.001), and less intramuscular fat content in all 4 muscles (P < 0.01 to P = 0.04). Their greater muscle content was associated with hypertrophy of all fast-twitch fibers. Glycogen content in all glycolytic muscles (i.e., LM, SM and BFM), was greater in low than high RFI pigs. The greater accumulation of glycogen in LM of low RFI pigs was specifically located in the fast-twitch glycolytic IIBW fibers, which correspond to fibers containing IIb, IIb + IIx, or IIx myosin heavy chains. The difference in muscle glycogen content between RFI line pigs was more significant in the living animals (P = 0.0003) than at 30 min postmortem (P = 0.08). This was associated with a decreased ultimate pH (P = 0.001), and greater lightness of color (P = 0.002) and drip loss (P = 0.04) in LM of low than high RFI line pigs, suggesting that selection for reduced RFI may impair some meat quality traits, such as water-holding capacity. Pigs from the low RFI line exhibited a greater (P = 0.02) percentage of IIBW fibers in LM and tended (P < 0.10) to have less lipid β-oxidative capacity in LM, SM, and BFM. In contrast, no difference (P > 0.10) between lines was found for citrate synthase and lactate dehydrogenase activities, mitochondrial activity, and expression of genes coding for uncoupling proteins 2 and 3. Differences between RFI pigs in plasma leptin, cortisol, and thyroid hormone concentrations are presented and discussed. In conclusion, selection for low RFI influenced muscle properties in a way favoring muscle mass, but likely impairing meat quality.

Membrane potential and H2O2 production in duodenal mitochondria from broiler chickens (Gallus gallus domesticus) with low and high feed efficiency

Increased hydrogen peroxide (H2O2) production was observed in duodenal mitochondria obtained from broiler chickens with low feed efficiency (FE). As a decrease in mitochondrial membrane potential (Deltapsi(m)) due to mild uncoupling of oxidative phosphorylation reduces reactive oxygen species production, this study was conducted to evaluate the effect of uncoupling on Deltapsi(m) and H2O2 production in duodenal mitochondria isolated from broilers with low (0.48+/-0.02) and high (0.68+/-0.01) FE. Membrane potential and H2O2 production were measured fluorometrically and in the presence of different levels of an uncoupler, carbonylcyanide-p-trifluoromethoxyphenylhydrazone (FCCP). The Deltapsi(m) was higher (P<or=0.05) in high FE mitochondria at 0 to 600 nM FCCP. A decrease in Deltapsi(m) was observed at 600 and 1000 nM FCCP in the low and high FE groups, respectively. H2O2 generation was higher in the low FE mitochondria at all FCCP levels except at 200 nM. Adding 200 to 800 nM FCCP decreased H2O2 production in low but not in high FE mitochondria. These results showed that FCCP-induced uncoupling lowered H2O2 production in low FE but not in high FE duodenal mitochondria and suggest that Deltapsi(m) may influence H2O2 production in low FE mitochondria.

Differential Expression of Mitochondrial and Extramitochondrial Proteins in Lymphocytes of Male Broilers with Low and High Feed Efficiency

Studies were conducted to investigate relationships between mitochondrial and extramitochondrial protein expression, and protein oxidation in lymphocytes obtained from broilers in which individual feed efficiencies were obtained. Lymphocytes were isolated from male broilers from a single line that were shown to exhibit either low (0.48 +/- 0.02, n = 8) or high (0.68 +/- 0.01, n = 7) feed efficiency (FE). Western blot analysis showed that, compared with lymphocytes from high FE broilers, lymphocytes from low FE broilers exhibited a) higher amounts of oxidized proteins (protein carbonyls), b) lower amounts of 3 mitochondrial proteins [core I, cyt c 1 (complex III), and ATP synthase (complex V)], and c) higher amounts of 2 proteins [30 S (complex II) and COX II (complex IV)]. Two-dimensional gel electrophoresis revealed that the intensities of 25 protein spots from pooled samples of lymphocytes from high and low FE broilers differed by 5-fold or more. Three of these protein spots were picked from the gel and subjected to matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis. One protein spot of ~33 kDa was tentatively identified by MALDI-TOF as a fragment of collapsin-2, a component of semaphorin 3D. The results of this study provide further evidence of increased oxidation associated with low FE and further evidence of differential protein expression associated with the phenotypic expression of feed efficiency.

Feed efficiency and mitochondrial function

Studies have been conducted in our laboratory to assess differences in mitochondrial function and biochemistry in male broilers with high and low feed efficiency (FE) from the same genetic line and fed the same diet. Mitochondria obtained from broilers with low FE exhibited greater uncoupling of the electron transport chain (ETC) that was apparently due to site-specific defects in electron transport resulting in higher amounts of reactive oxygen species (ROS) compared with high FE mitochondria. Higher amounts of ROS production in Low FE mitochondria were likely responsible for higher protein carbonyl levels, indicative of higher protein oxidation compared with High FE mitochondria and tissue. In turn, higher protein damage in Low FE mitochondria may have contributed to lower activity of electron transport chain complexes relative to values observed in high FE mitochondria. Low FE mitochondria did not exhibit a compromised ability to carryout oxidative phosphorylation, and although there were differences in expression of certain electron transport chain proteins, there was nothing that would indicate that differences in coupling and respiratory chain activity could be due to a general decrease in protein expression between low and high FE mitochondria. The results of these studies provide insight into understanding cellular mechanisms associated with the phenotypic expression of feed efficiency in broilers.

Biochemical evaluation of mitochondrial respiratory chain in duodenum of low and high feed efficient broilers

Increased H2O2 production, indicating higher oxidative stress, and lower mitochondrial function was previously observed in duodenal mitochondria isolated from broilers with low feed efficiency (FE, gain:feed). Thus, experiments were conducted to 1) evaluate the activity of the respiratory chain complexes (complexes I to V) and 2) assess protein oxidation and mitochondrial protein expression in broilers with low and high FE. Duodenal mitochondria were isolated from broiler breeders with low (0.52 +/- 0.01) and high (0.68 +/- 0.01) FE (n = 8/group). Respiratory chain complex activities were measured spectrophotometrically, whereas mitochondrial protein expression and protein oxidation (carbonyls) were assessed with Western blots. The activities of all complexes, except complex IV, were lower in the low FE compared with high FE mitochondria, whereas protein carbonyl levels were higher in low FE mitochondria. Steady-state levels of 6 out of 7 nuclear-encoded respiratory chain subunits [70S(FP), core I, core II, cytochrome c (cyt c)1, iron-sulfur protein (ISP), and ATPase-alpha] were higher, whereas 3 out of 6 mitochondrial-encoded subunits (ND4, ND6-C, and COX II) were lower in the low FE group, suggesting that sensitivity of mitochondrial proteins to H2O2 or oxidation varies. The general reduction in complex activity and differential protein expression concomitant with higher oxidized proteins in low FE mitochondria suggest that oxidative stress could be contributing to the lower mitochondrial function observed in low FE duodenal mitochondria.

Compromised liver mitochondrial function and complex activity in low feed efficient broilers are associated with higher oxidative stress and differential protein expression

Variations in broiler growth and efficiency have been explained in part by differences in mitochondrial function and biochemistry in broilers. To further our knowledge in this regard, 2 experiments were carried out to determine the relationships of a) mitochondrial function and activities of various electron transport chain (ETC) complexes; b) production of H2O2, a reactive oxygen species (ROS), and its association with protein oxidation; and c) mitochondrial protein expression in liver of a single line male broilers with low or high feed efficiency (FE, n = 5 to 8 per group). Mitochondrial function and complex activities were measured polarographically and spectrophotometrically, respectively. H2O2 was measured fluorimetrically, whereas oxidized protein (carbonyls) and specific mitochondrial proteins were analyzed using Western blots. Mitochondrial function (ETC coupling) and activities of ETC complexes (I, II, III, and IV) were higher in high FE compared with low FE broilers. H2O2 and protein carbonyls were higher in the livers of low FE broilers than in high FE broilers. Whereas the expression of 4 immunoreactive proteins [NAD3 (complex I), subunit VII (complex III), cytochrome c oxidase subunits (COX) II, and COX IVb (complex IV)] were higher in low FE liver mitochondria and 2 proteins [subunit 70 (complex II) and a-ATP synthase (complex V)] were higher in high FE birds, there were no differences between groups in the expression of 18 other mitochondrial proteins. In conclusion, increases in oxidative stress in low FE broilers were caused by or may contribute to differences in mitochondrial function (ETC coupling and complex activities) or the differential expression of steady-state levels of some mitochondrial proteins in the liver. Understanding the role of oxidative stress in Low FE broilers will provide clues in understanding the cellular basis of feed efficiency.

Glutathione and respiratory chain complex activity in duodenal mitochondria of broilers with low and high feed efficiency

We previously observed increased reactive oxygen species (ROS) production in intestinal mitochondria obtained from broiler breeder males with low feed efficiency (FE, gain-to-feed). Because antioxidants are critical for combating ROS-mediated oxidative stress and preserving mitochondrial function, the objectives of this study were 1) to determine levels of reduced glutathione (GSH), a major antioxidant in mitochondria, 2) to measure activities of GSH recycling enzymes: GSH peroxidase and GSH reductase, and 3) to establish relationships between antioxidants and respiratory chain complex activities (complexes I, II, III, IV, and V) in broiler breeder males with low and high FE. Duodenal mitochondria were isolated from broilers with low (0.62 +/- 0.01, n = 8) and high (0.80 +/- 0.01, n = 8) FE. Activities of respiratory chain complexes, GSH peroxidase, and GSH reductase, and levels of GSH were measured by UV spectrophotometry. There were no differences in GSH peroxidase or reductase activities or in individual complex activities between groups but GSH levels tended to be higher (P = 0.075) and oxidized to reduced glutathione ratio tended to be lower (P = 0.077) in broilers with high FE. Regression analysis revealed significant correlations (P < or = 0.05) between mitochondrial GSH and activities of complexes II, IV, and V with R2 values of 0.35, 0.56, and 0.49, respectively. These data suggest that GSH may be important in maintaining or enhancing the activity of certain respiratory chain complexes and could be involved in the phenotypic expression of feed efficiency in broilers.

Gene expression, tissue distribution and potential physiological role of uncoupling protein in avian species

Whole-body energy homeostasis and food intake control are essential for an economically sound selection for growth in poultry. The cellular and molecular mechanisms that regulate and link food intake, energy expenditure and energy balance are still poorly understood in poultry. Mitochondrial uncoupling protein-1 (UCP-1) is known to uncouple respiration from ATP synthesis by short circuiting the inward proton flow, resulting in heat production. Its role seems quite well established in adaptive thermogenesis and energy metabolism. However, uncertainty still surrounds the physiological function of the recently discovered UCP-1 homologues, UCP-2 and -3. Most of the functional characterization of these UCPs, to date, has been conducted in mammals. Recently, an avian UCP homologue, which was identified in chicken, hummingbird and king penguin, appears to play a key role in adaptative thermogenesis. Here, we review recent reports describing avian UCP (av-UCP) and discuss progress concerning the molecular mechanisms and potential role of the av-UCP in thermogenesis regulation in avian species.