Multitissue transcriptomics demonstrates the systemic physiology of methionine deficiency in broiler chickens

Methionine (Met) supplementation is common practice in broilers to support nutrition, yet there are gaps in the understanding of its role in systemic physiology. Furthermore, several different Met sources are available that may have different physiological effects. This study evaluated the mode of action of Met deficiency (no Met-supplementation) and supplementation (0.25% DL- or L-Met, 0.41% liquid methionine hydroxy analog-free acid (MHA-FA)), and of Met source (DL-, L- or MHA-FA) in broiler chickens, via host transcriptomics. Biological pathway activation modeling was performed to predict the likely phenotypic effects of differentially expressed genes (DEGs) in tissue samples from the jejunum, liver and breast obtained at 10, 21 and 34/35 d of age from three experiments in a combined analysis. Animal performance data showed that Met deficiency reduced BW, daily BW gain, daily feed intake, and breast yield, and increased feed conversion ratio in all experiments (P < 0.05). Effects of Met deficiency on gene expression were least evident in the jejunum and most evident in the liver and breast, as evidenced by the number of DEG and activated pathways. Activated pathways suggested Met deficiency was associated with inhibited protein turnover, gut barrier integrity, and adaptive immunity functions in the jejunum, that predicted reduced breast yield. There was an interaction with age; in Met-deficient birds, there were 333 DEGs in the jejunum of starter vs finisher birds suggesting young birds were more sensitive to Met deficiency than older birds. In the liver, Met deficiency activated pathways associated with lipid turnover, amino acid metabolism, oxidative stress, and the immune system, whereas in breast, it activated pathways involved in metabolic regulation, hemostasis, the neuronal system, and oxidative stress, again predicting a negative impact on breast yield. In the starter phase, supplementation with DL-Met compared to MHA-FA inhibited gamma-aminobutyric acid activity and oxidative stress in breast tissue. When data from all tissues were integrated, increased expression of a liver gene (ENSGALG00000042797) was found to be correlated with the expression of several genes that best explained variation due to the Met deficiency in jejunum and breast muscle. Some of these genes were involved in anti-oxidant systems. Overall, the findings indicate that impaired growth performance due to Met deficiency results from an array of tissue-specific molecular mechanisms in which oxidative stress plays a key systemic role. Young birds are more sensitive to Met-deficiency and DL-Met was a preferential source of Met than L- or MHA-FA during the starter phase.

The Effect of Increased Temperatures on Viability, Morphology, Infectivity, and Development of Eimeria tenella

Commonly found in backyard and commercial poultry production, coccidiosis, caused by Eimeria species, presents a self-limiting intestinal infection based on the number of ingested oocysts. Heat stress (HS) is one of the major environmental stressors in poultry, predisposing broiler chickens to immunosuppression and rendering them susceptible to diseases. There are suggestions that HS reduces Eimeria oocyst shedding in chickens; however, the relationship between HS and coccidiosis is not well elucidated. The objective of this study was to investigate the effect of temperature on viability, morphology, infectivity, and development of Eimeria tenella in vitro, and merozoite production and oocyst shedding in vivo. In vitro exposure of sporozoites to 55 C for at least 60 min reduced sporozoites viability as shown by morphological changes and rendering them unable to invade Mardin-Darbi bovine kidney (MDBK) cells. Intracellular development of merozoites was significantly reduced by an increase in 2 C in the optimal temperature of incubation in vitro. Most importantly, the induction of HS in the live chickens caused significantly lower lesion scores, reduced merozoite production, and oocyst shedding, resulting in a much less severe disease outcome.

Effect of heat stress on amino acid digestibility and transporters in meat-type chickens

The present study was conducted to investigate the effect of heat stress (HS) on performance, digestibility, and molecular transporters of amino acids in broilers. Cobb 500 chicks were raised from hatch till 13 d in floor pens. At d 14, 48 birds were randomly and equally divided between a control group (25°C) and a HS treatment group (35°C). Birds in both treatment classes were individually caged and fed ad libitum on a diet containing 18.7% CP and 3,560 Kcal ME/Kg. Five birds per treatment at one and 12 d post treatment were euthanized and the Pectoralis major (P. major) and ileum were sampled for gene expression analysis. At d 33, ileal contents were collected and used for digestibility analysis. Broilers under HS had reduced growth and feed intake compared to controls. Although the apparent ileal digestibility (AID) was consistently higher for all amino acids in the HS group, it was not significant except for hydroxylysine. The amino acid consumption and retention were significantly lower in the HS group when compared to the control group. Meanwhile, the retention of amino acids per BWG was higher in the HS group when compared to the control group except for hydroxylysine and ornithine. The dynamics of amino acid transporters in the P. major and ileum was influenced by HS. In P. major and ileum tissues at d one, transporters SNAT1, SNAT2, SNAT7, TAT1, and b0,+AT, were down-regulated in the HS group. Meanwhile, LAT4 and B0AT were down-regulated only in the P. major in the treatment group. The amino acid transporters B0AT and SNAT7 at d 12 post HS were down-regulated in the P. major and ileum, but SNAT2 was down-regulated only in the ileum and TAT1 was down-regulated only in the P. major compared with the control group. These changes in amino acid transporters may explain the reduced growth in meat type chickens under heat stress.

Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ

Background

Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today’s broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens.

Methods

We used the Del-Mar 14 K Chicken Integrated Systems microarray to take time-course snapshots of global gene transcription in abdominal fat of juvenile [1-11 weeks of age (wk)] chickens divergently selected on bodyweight at two ages (8 and 36 wk). Further, a RNA sequencing analysis was completed on the same abdominal fat samples taken from high-growth (HG) and low-growth (LG) cockerels at 7 wk, the age with the greatest divergence in body weight (3.2-fold) and visceral fatness (19.6-fold).

Results

Time-course microarray analysis revealed 312 differentially expressed genes (FDR ≤ 0.05) as the main effect of genotype (HG versus LG), 718 genes in the interaction of age and genotype, and 2918 genes as the main effect of age. The RNA sequencing analysis identified 2410 differentially expressed genes in abdominal fat of HG versus LG chickens at 7 wk. The HG chickens are fatter and over-express numerous genes that support higher rates of visceral adipogenesis and lipogenesis. In abdominal fat of LG chickens, we found higher expression of many genes involved in hemostasis, energy catabolism and endocrine signaling, which likely contribute to their leaner phenotype and slower growth. Many transcription factors and their direct target genes identified in HG and LG chickens could be involved in their divergence in adiposity and growth rate.

Conclusions

The present analyses of the visceral fat transcriptome in chickens divergently selected for a large difference in growth rate and abdominal fatness clearly demonstrate that abdominal fat is a very dynamic metabolic and endocrine organ in the chicken. The HG chickens overexpress many transcription factors and their direct target genes, which should enhance in situ lipogenesis and ultimately adiposity. Our observation of enhanced expression of hemostasis and endocrine-signaling genes in diminished abdominal fat of LG cockerels provides insight into genetic mechanisms involved in divergence of abdominal fatness and somatic growth in avian and perhaps mammalian species, including humans.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4035-5) contains supplementary material, which is available to authorized users.

Genetic analysis of bone quality traits and growth in a random mating broiler population

We report the genetic relationship between growth and bone quality traits in a random mating broiler control population. Traits studied were growth rates from week 0 to 4 [body weight gain (BWG) 0 to 4], from week 0 to 6 (BWG 0 to 6), and residual feed intake (RFI) from week 5 to 6 (RFI 5 to 6). Bone quality traits were obtained at 6 weeks of age. These traits were shank weight (SW), shank length (SL), shank diameter (SDIAM), tibia weight (TW), tibia length (TL), and tibia diameter (TDIAM). Likewise, tibia was used to obtain the tibia density (TDEN), tibia breaking strength (TBS), tibia mineral density (TMD), tibia mineral content (TMC), and tibia ash content (TAC). At the phenotypic level, growth traits were positively correlated with most of the bone quality traits except with TDEN and TAC which tended to show unfavorable associations (-0.04 to -0.31). Heritability of bone quality traits ranged from 0.08 to 0.54. The additive genetic associations of growth traits with weight, length, and diameter of shank and tibia were positive (0.37 to 0.80). A similar pattern was observed with TMD and TMC (0.06 to 0.65). In contrast, growth traits showed unfavorable genetic associations with TDEN, TBS, and TAC (-0.03 to -0.18). It was concluded that bone quality traits have an additive genetic background and they can be improved by means of genetic tools. It appears that selection for growth is negatively correlated with some traits involved in the integrity, health, and maturity of leg bones.

Genetic analysis of leg problems and growth in a random mating broiler population

Improvement in growth has been widely reported as the cause of increased incidence of leg problems in broiler chickens. We report herein the genetic relationship between growth and leg problems in a random mating broiler control population. The traits studied were valgus (VL), varus (VR), and tibial dyschondroplasia (TD), which were expressed on a binary scale of 0 (normal) and 1 (abnormal); growth rates from 0 to 4 wk (BWG 0-4) and from 0 to 6 wk of age (BWG 0-6); and residual feed intake from 5 to 6 wk of age (RFI 5-6). A threshold-linear mixed model was employed for the joint analysis of the categorical and linear traits. Incidences of VL, VR, and TD were 26, 4, and 2%, respectively. Heritability of leg problems ranged from 0.11 to 0.13. Phenotypic correlations alluded to an unfavorable relationship between growth and leg problems; however, the genetic relationship between growth and leg problems was extremely weak, ranging from 0.01 to 0.08. There is, therefore, a basis for genetic improvement in leg problems. However, improved management practices would also be important to reduce incidence of leg problems in broiler chickens.

Transcriptomic analysis of genes in the nitrogen recycling pathway of meat-type chickens divergently selected for feed efficiency

The understanding of the dynamics of ammonia detoxification and excretion in uricotelic species is lagging behind ureotelic species. The relative expression of genes involved in nitrogen recycling and feed efficiency in chickens is unknown. The objective of this study was to investigate the transcriptomics differences in key genes in the nitrogen (N) metabolism and purine biosynthesis pathway in a chicken population divergently selected for low (LRFI) or high (HRFI) residual feed intake at days 35 and 42 using duodenum, liver, pectoralis major (P. major) and kidney. There was a significant positive correlation between RFI and fecal N. The purine salvage pathway was activated in the LRFI compared with HRFI at days 42. The birds in the LRFI population attained greater feed efficiency by having lower FI, increasing their protein retention and producing adequate glutamine to maintain growth compared with the HRFI line. To maintain growth, excess N is deaminated mostly to generate purine nucleotides. Generating purine nucleotides primarily from the purine biosynthesis pathway is energetically costly, and to preserve energy, they preferentially generate nucleotides from the purine salvage pathway. The LRFI birds need to generate sufficient nucleotides to maintain growth despite reduced FI that then results in reduced fecal N.

Effects of balanced dietary protein levels on egg production and egg quality parameters of individual commercial layers

The effects of a series of balanced dietary protein levels on egg production and egg quality parameters of laying hens from 18 through 74 wk of age were investigated. One hundred forty-four pullets (Bovans) were randomly assigned to individual cages with separate feeders including 3 different protein level series of isocaloric diets. Diets were separated into 4 phases of 18-22, 23-32, 33-44, and 45-74 wk of age. The high protein (H) series contained 21.62, 19.05, 16.32, and 16.05% CP, respectively. Medium protein (M) and low protein (L) series were 2 and 4% lower in balanced dietary protein. The results clearly demonstrated that the balanced dietary protein level was a limiting factor for BW, ADFI, egg weight, hen day egg production (HDEP), and feed per kilogram of eggs. Feeding with the L series resulted in lower ADFI and HDEP (90.33% peak production) and more feed per kilogram of eggs compared with the H or M series (HDEP; 93.23 and 95.68% peak production, monthly basis). Egg weight responded in a linear manner to balanced dietary protein level (58.78, 55.94, and 52.73 g for H, M, and L, respectively). Feed intake of all hens, but especially those in the L series, increased considerably after wk 54 when the temperature of the house decreased due to winter conditions. Thus, hens fed the L series seemed particularly dependent on house temperature to maintain BW, ADFI, and HDEP. For egg quality parameters, percent yolk, Haugh units, and egg specific gravity were similar regardless of diets. Haugh units were found to be greatly affected by the variation of housing temperature (P = 0.025). Maximum performance cannot always be expected to lead to maximum profits. Contrary to the idea of a daily amino acid requirement for maximum performance, these results may be used to determine profit-maximizing levels of balanced dietary protein based on the cost of protein and returns from different possible protein levels that may be fed.

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.

Genetic evaluation for growth, body composition, feed efficiency, and leg soundness

A multiple trait linear-threshold model was used to analyze data for BW, residual feed intake, breast meat yield (BMY), conformation score (CS), area (AR), tibial dyschondroplasia, valgus, varus, and rotated tibia. Leg soundness traits were considered as binary responses. At the liability scale, the model included the fixed effects of flock-week of hatch, and sex of the bird and the genetic additive effect, and the error terms as random. The random maternal effect was included in the model only for BW. A full Bayesian implementation of the model was straightforward even though large number of traits and missing records were present. As expected, binary traits have the lowest heritability. Heritability ranged from 0.12 for tibial dyschondroplasia to 0.44 for BMY. Genetic correlations between BW and conformation traits were moderate to high. Residual feed intake was negatively correlated with BW (-0.15), AR (-0.13), BMY (-0.04), and CS (-0.12). Genetic correlation between leg soundness traits were generally low and negative with the exception of the correlation between valgus and varus (-0.70) and between varus and rotated tibia (-0.39). Genetic correlations between BW, BMY, CS, and AR with leg soundness traits were in general negative and low in magnitude. Thus, selecting for improved leg soundness will have minimal effect on BW and carcass traits. Furthermore, genetic improvement in residual feed intake will result in improvements in carcass traits. Simultaneous genetic improvement in leg soundness and innovative husbandry practices should improve broiler welfare without significant adverse effects on production efficiency.

Incorporation of economic values into the component traits of a ratio: feed efficiency

Direct selection on a ratio (R) of 2 traits (x1/x2) does not have a mechanism to accommodate the relative economic values (a1 and a2) between x1 and x2 because selection criteria x1/x2 and a1x1/a2x2 rank animals in the same order. This study presented a procedure to incorporate the economic weights into ratio traits through linear transformation. The partial derivatives of a nonlinear profit function evaluated at the means were widely taken as economic weights in the literature. This study showed that the economic weights derived in this manner were erroneous because they actually contain a mixture of actual economic weights and transformation effects. The ratios 1/2 and 2/4 are considered equal by selection on R, but are treated differently by the linear index. In addition, this study presented a unified approach to compare 4 different selection strategies for genetic improvement of ratio traits: linear index (I), selection on the ratio (R), selection on difference between x1 and x2 (D), and selection on x1 alone. This study considered 3 levels of heritability each for variables x1 and x2 and 2 levels of genetic correlations (γG), 2 ratios of means (µ1/µ2), and 4 ratios of phenotypic variances giving a total of 96 scenarios. Linear index I was the most efficient of the 4 criteria compared in all 96 scenarios studied. The superiority of index I over R, D, and selection on x1 alone are particularly remarkable when x1 and x2 have a large difference in heritability and are highly correlated. Selection on x1 alone is an economically viable alternative to criterion I or R for the improvement of ratio traits particularly when x1 is more heritable than x2 and when x2 is costly to measure. Selection on D is more efficient than direct selection on R or selection on x1 alone when x1 is less heritable than x2 and the difference between µ1 and µ2 is small.

The effects of growth rate on leg morphology and tibia breaking strength, mineral density, mineral content, and bone ash in broilers

Fast-growing broilers are especially susceptible to bone abnormalities, causing major problems for broiler producers. The cortical bones of fast-growing broilers are highly porous, which may lead to leg deformities. Leg problems were investigated in 6-wk-old Arkansas randombred broilers. Body weight was measured at hatch and at 6 wk. There were 8 different settings of approximately 450 eggs each. Two subpopulations, slow-growing (SG; bottom quarter, n=511) and fast-growing (FG; top quarter, n=545), were created from a randombred population based on their growth rate from hatch until 6 wk of age. At 6 wk of age, the broilers were processed and chilled at 4°C overnight before deboning. Shank (78.27±8.06 g), drum stick (190.92±16.91 g), and thigh weights (233.88±22.66 g) of FG broilers were higher than those of SG broilers (54.39±6.86, 135.39±15.45, and 168.50±21.13 g, respectivly; P<0.001). Tibia weights (15.36±2.28 g) of FG broilers were also greater than those of SG broilers (11.23±1.81 g; P<0.001). Shank length (81.50±4.71 g) and tibia length (104.34±4.45 mm) of FG broilers were longer than those of SG broilers (71.88±4.66 and 95.98±4.85 mm, respectively; P<0.001). Shank diameter (11.59±1.60 mm) and tibia diameter (8.20±0.62 mm) of FG broilers were wider than those of SG broilers (9.45±1.74, 6.82±0.58 mm, respectively; P<0.001). Tibia breaking strength (28.42±6.37 kg) of FG broilers was higher than those of SG broiler tibia (21.81±5.89 kg; P<0.001). Tibia density and bone mineral content (0.13±0.01 g/cm2 and 1.29±0.23 g, respectively) of FG broilers were higher than those of SG broiler tibia (0.11±0.01 g/cm2 and 0.79±0.1 g; P<0.001). Tibia percentage of ash content (39.76±2.81) of FG broilers was lower than that of SG broilers (39.99±2.67; P=0.173). Fast-growing broiler bones were longer, wider, heavier, stronger, more dense, and contained more ash than SG ones. After all parameters were calculated per unit of final BW at 6 wk, tibia density and bone ash percentage of FG broilers were lower than those of SG broilers.

The effects of broiler chicken growth rate on valgus, varus, and tibial dyschondroplasia

An experiment was conducted to test the hypothesis that the growth rate of broilers influences their susceptibilities to bone abnormalities, causing major leg problems. Leg angulations, described in the twisted legs syndrome as valgus and bilateral or unilateral varus, were investigated in 2 subpopulations of mixed-sex Arkansas randombred broilers. Valgus angulation was classified as mild (tibia-metatarsus angle between 10 and 25°), intermediate (25-45°), or severe (> 45°). Body weight was measured at hatch and weekly until 6 wk of age. There were 8 different settings of approximately 450 eggs each. Two subpopulations, slow growing (bottom quarter, n = 581) and fast growing (top quarter, n = 585), were created from a randombred population based on their growth rate from hatch until 6 wk of age. At 6 wk of age, tibial dyschondroplasia incidences were determined by making a longitudinal cut across the right tibia. The tibial dyschondroplasia bone lesion is characterized by an abnormal white, opaque, unmineralized, and unvascularized mass of cartilage occurring in the proximal end of the tibia. It was scored from 1 (mild) to 3 (severe) depending on the cartilage plug abnormality size. Mean lesion scores of left and right valgus and tibial dyschondroplasia (0.40, 0.38, and 0.06) of fast-growing broilers were higher than those (0.26, 0.28, and 0.02) of slow-growing broilers (P = 0.0002, 0.0037, and 0.0269), respectively. Growth rate was negatively associated with the twisted legs syndrome and a bone abnormality (tibial dyschondroplasia) in this randombred population.

Genetic interrelationships among phosphorus, nitrogen, calcium, and energy bioavailability in a growing chicken population

A random-mating population was used to study the genetic interrelationship between phytate P (PPB), Ca (CaB), N (NB), and energy bioavailability (EB), BW at 4 wk of age, relative growth (RG), and feed conversion ratio (FCR). Heritability estimates for PPB, CaB, NB, and EB were 0.09, 0.13, 0.16, and 0.10, respectively, and those of BW, RG, and FCR were 0.66, 0.15, and 0.10, respectively. Genetic correlations between PPB and BW, and FCR were moderate and negative, suggesting that improvement in PPB will impair growth. The genetic correlations between PPB and CaB, and EB and RG were positive and moderate, indicating that improvement in PPB would also lead to improved CaB, EB, and RG. Energy bioavailability was positively correlated with CaB, NB, PPB, and BW. Even though the genetic correlation between EB and the other traits measured, except RG and FCR, ranged from low to moderate, improving the ability of birds to utilize caloric energy in the feed would consequently improve PPB as well as growth. Improving PPB would reduce the amount of P in excreta and provide an additional savings if exogenous phytase were not added to poultry feed. The genetic correlation between PPB and NB was low but positive, whereas NB had a positive genetic correlation with BW. Therefore, selecting on NB will result in positive correlated responses in BW and PPB. Improving PPB and NB will not only improve productivity, but also reduce the polluting effects of P and N on the environment.

Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways

The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation—fasting and re-feeding—in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.

Modification of animals versus modification of the production environment to meet welfare needs

The balance between genetic modification and welfare may be as old as the chicken and egg debate. Meeting welfare needs of farm animals has become an integral part of animal agriculture. Until recently, environmental and management modifications have been the methods of choice for meeting welfare needs of animals. Genetic selection has improved growth, livability, and general welfare, but some aspects of welfare like metabolic disorders, susceptibility to some diseases, and skeletal problems have increased. Genetic variability in behavioral and physiological traits relating to welfare exists thus raising the possibility of selecting for welfare-related traits. Advances in molecular biology have also made it possible for the identification of QTL for behavioral and welfare traits. Identification of causal or associative genes for welfare traits and improved biotechnology tools raises the possibility of either selecting for improved welfare or genetically modifying birds to suit the commercial production environment. An integration of management, genetics, and genomic tools should be employed to genetically improve production and welfare traits with concurrent welfare risk assessments to address public and consumer concerns.

Gompertz-Laird model prediction of optimum utilization of crude protein and metabolizable energy by French guinea fowl broilers

This study was conducted to assess the influence of dietary CP and ME on growth parameters of the French guinea fowl, a meat-type variety. In a 2 x 3 x 3 factorial arrangement, 297 one-day-old French guinea keets (162 females and 135 males) were randomly assigned to experimental diets comprising 3,050, 3,100, and 3,150 kcal of ME/kg, each containing 21, 23, and 25% CP from hatch to 4 wk of age (WOA), and 3,100, 3150, and 3,200 kcal of ME/kg, each containing 19, 21, and 23% CP at 5 to 8 WOA. Using BW and G:F data from hatch to 8 WOA, the Gompertz-Laird growth model was employed to estimate growth patterns of the French guinea fowl. Mean differences in exponential growth rate, age of maximum growth, and asymptotic BW among dietary CP and ME levels were not significant. However, instantaneous growth rate and weight at inflection point were significantly higher (P < 0.05) in birds on the 25% CP diet than those on the 21% CP diet at hatch to 4 WOA (1.12 kg/wk and 0.79 kg vs. 1.04 kg/wk and 0.74 kg, respectively). The exponential growth rate was also higher (P < 0.05) in birds fed the 3,050 kcal of ME/kg diet with either 23 or 25% CP than those fed diets containing 3,050 kcal of ME/kg and 21% CP. Mean G:F was higher (P < 0.05) in birds fed diets containing 3,050 kcal of ME/kg and either 21 or 23% CP than those in other dietary treatments. Therefore, based on the Gompertz-Laird growth model estimates, feeding 21 and 23% CP and 3,100 kcal of ME/kg at hatch to 4 WOA and 19 and 21% CP with 3,150 kcal of ME/kg at 5 to 8 WOA can be recommended as adequate for growth for the French guinea fowl broilers.

A comprehensive analysis of QTL for abdominal fat and breast muscle weights on chicken chromosome 5 using a multivariate approach

Quantitative trait loci (QTL) influencing the weight of abdominal fat (AF) and of breast muscle (BM) were detected on chicken chromosome 5 (GGA5) using two successive F(2) crosses between two divergently selected 'Fat' and 'Lean' INRA broiler lines. Based on these results, the aim of the present study was to identify the number, location and effects of these putative QTL by performing multitrait and multi-QTL analyses of the whole available data set. Data concerned 1186 F(2) offspring produced by 10 F(1) sires and 85 F(1) dams. AF and BM traits were measured on F(2) animals at slaughter, at 8 (first cross) or 9 (second cross) weeks of age. The F(0), F(1) and F(2) birds were genotyped for 11 microsatellite markers evenly spaced along GGA5. Before QTL detection, phenotypes were adjusted for the fixed effects of sex, F(2) design, hatching group within the design, and for body weight as a covariable. Univariate analyses confirmed the QTL segregation for AF and BM on GGA5 in male offspring, but not in female offspring. Analyses of male offspring data using multitrait and linked-QTL models led us to conclude the presence of two QTL on the distal part of GGA5, each controlling one trait. Linked QTL models were applied after correction of phenotypic values for the effects of these distal QTL. Several QTL for AF and BM were then discovered in the central region of GGA5, splitting one large QTL region for AF into several distinct QTL. Neither the 'Fat' nor the 'Lean' line appeared to be fixed for any QTL genotype. These results have important implications for prospective fine mapping studies and for the identification of underlying genes and causal mutations.

Modeling growth characteristics of meat-type guinea fowl

This study was conducted to describe the growth pattern of the French guinea fowl, a meat-type variety. Using BW data from hatch to 9 wk, 2 nonlinear mathematical functions (Gompertz and logistic) were used to estimate growth patterns of the French guinea fowl. The French guinea fowl did not exhibit sexual dimorphism for growth characteristics. From the Gompertz model, the asymptotic BW, growth rate, and age at maximum growth were 2.05 kg, 0.25 kg/wk, and 5.74 wk in males, respectively, and 2.03 kg, 0.25 kg/wk, and 5.72 wk in females, respectively. The ages at maximum growth were 5.75 and 5.74 wk for males and females, respectively, using the logistic model. Differences in asymptotic BW between males and females were not significant in both Gompertz and logistic models. However, the average asymptotic BW of about 1.50 kg for both sexes predicted by the logistic model was below the average predicted BW from the Gompertz model (2.04 kg) at 9 wk. Also, the logistic model overestimated hatching weight (0.06 kg) more than the Gompertz model (0.03 kg), suggesting that the growth pattern of the French guinea fowl is Gompertz. The inverse relationship between the asymptotic weight and age at maximum growth of the French guinea fowl is similar to that of the pearl gray guinea fowl, chickens, quail, and ducks. Understanding the growth characteristics of French guinea fowl will contribute to the efforts of improving production efficiency of this least studied avian species.

Growth Characteristics of Pearl Gray Guinea Fowl as Predicted by the Richards, Gompertz, and Logistic Models

This study was undertaken to describe the growth pattern of the pearl gray Guinea fowl. Using BW data from hatch to 22 wk, 3 nonlinear mathematical functions (Richards, Gompertz, and logistic) were used to estimate growth patterns of the pearl gray guinea fowl. The logistic and Gompertz models are a special case of the Richards model, which has a variable point of inflection defined by the shape or growth trajectory parameter, m. The shape parameter m was 1.08 and 0.98 in males and females, respectively, suggesting that the growth pattern of the pearl gray female guinea fowl is Gompertz. The pearl gray guinea fowl exhibited sexual dimorphism for their growth characteristics. From the Gompertz model, the asymptotic BW, growth rate, and age at maximum growth were 1.62 kg, 0.22 kg/wk, and 6.65 wk in males, respectively, and 1.70 kg, 0.19 kg/wk, and 6.70 wk in females, respectively. The ages at maximum growth were 6.65, 6.47, and 8.12 wk for the Richards, Gompertz, and logistic models, respectively. The pearl gray guinea fowl females have a higher asymptotic BW compared with the males. The average asymptotic BW of about 1.57 kg for both sexes predicted by the logistic model was below the average predicted BW from the Richards (1.66 kg) and Gompertz (1.67 kg) models, respectively, at 22 wk of age. The inverse relationship between the asymptotic weight and both relative growth and age at maximum growth of the pearl gray guinea fowl is similar to that of chickens, quail, and ducks. Success in studying the growth characteristics of guinea fowl will contribute to the efforts of genetically improving this least-studied avian species.

Genetic analysis on the direct response to divergent selection for phytate phosphorus bioavailability in a randombred chicken population

The current study was undertaken to evaluate the direct response to 3 generations of divergent selection for phytate P bioavailability (PBA) in the Athens-Canadian randombred chicken population. Cumulated divergent response (R(C)) was measured as the line difference in PBA at a given generation after adjusting for hatch and sex effects. Results showed a significant response at generation (G)1. The R(C) was unchanged from G1 to G2 and increased (1.62%) from G2 to G3 (P < 0.01) due to the application of best linear unbiased prediction (BLUP) selection in the line selected for high PBA at G2. The average BLUP estimated breeding values were used to estimate the genetic trend for the selected trait across generations. The results showed that the genetic trend was symmetric at G1 and G2 but asymmetric at G3. The application of mixed model methodology was effective in separating the environmental component from phenotypic change. When the data of the high (H) line or the low (L) line in the selected generations (G1 to G3) were combined with the data from the base population (G0), the heritability estimates for PBA were 0.07 +/- 0.02 and 0.09 +/- 0.02, respectively. The line selected for high PBA showed gain, and the line selected for low PBA showed a decrease in estimated breeding values across the generations. The results demonstrated that modest progress could be obtained by incorporating PBA into selection programs. However, other correlated traits of economic importance need to be evaluated before any decision to incorporate selection of PBA into breeding schemes be initiated.

Correlated responses to divergent selection for phytate phosphorus bioavailability in a randombred chicken population

The current study was undertaken to evaluate the correlated responses to 3 generations of divergent selection for phytate phosphorus bioavailability (PBA) in the Athens-Canadian randombred chicken population. The traits studied were BW at 4 wk of age, BW gain (BWG), feed consumption (FC), and feed conversion ratio (FCR) during a period of 3 d. The first evaluation criterion was the cumulated divergent correlated response (CR(C)), which was calculated as the line difference of the least square means of phenotypic values for each trait at a given generation after adjustment for sex and hatch effects. The results showed a consistent correlated response in BW across generations. The CR(C) at generation G3 was 26.8 g (P < 0.01). The chickens in the low PBA line (L line) had higher BW than the high PBA line (H line). The CR(C) for BWG, FC, and FCR were significant (P < 0.05) only at G3. The second evaluation criterion was the average best linear unbiased prediction estimated breeding value (EBV). The results showed asymmetric genetic trends in BW, BWG, and FC, and the correlated responses were mainly due to the genetic changes that occurred in H line because little genetic change occurred in L line across generations. At G3, the line differences of EBV were close to the CR(C) values for all the traits except FCR. This suggested that CR(C) and EBV criteria would tend to be consistent with the increase across generations. However, at G1 and G2, the line differences of the EBV actually deviated from the CR(C) values for BWG and FC. The inconsistency could be attributed to experimental errors and genetic drift that were not accounted by the fixed model for obtaining CR(C).

Modeling of Parameters Affecting Phytate Phosphorus Bioavailability in Growing Birds

The current study was undertaken to establish a population from an unselected random-mating chicken population for the development of a model to predict factors that affect phytate P utilization in growing birds. A population was established from a mating of 40 male and 200 female chickens from the Athens Canadian randombred population. At 4 wk of age, birds were housed in individual metabolic cages and fed a diet containing 1.06% Ca, 0.35% total P, and 0.03% available P. After 3 d of acclimatization, feed consumption (FC) was measured and excreta produced in 3 consecutive d were collected. Individual 4-wk BW, BW gain (BWG), phytate P intake (PPI), inorganic P intake (IPI), Ca intake (CaI), N intake (NI), and energy intake (EI) during the 3 d excreta collection period were also measured. Feed conversion ratios (FCR) and relative growth rate were calculated. Phytate P bioavailability (PPB), Ca bioavailability (CaB), and N bioavailability (NB) were estimated from the disappearance of the nutrients during the passage of feed through the gastrointestinal tract. Energy bioavailability (EB) was measured by bomb calorimetry as the difference in the gross energy of the feed and the energy of the excreta. The major factors affecting PPB were CaB and EB for both sexes. In the males, BW contributed significantly to PPB. However, in the females, NB also contributed significantly to PPB. Faster growing birds tended to have a reduced retention time of feed compared with slow growing birds, and as a result utilized phytate P less. Birds that are able to utilize phytate P better are putatively able to release P for energy utilization. Therefore, the birds that were able to utilize phytate P better were also better energy utilizers.

Genetics of phytate phosphorus bioavailability: heritability and genetic correlations with growth and feed utilization traits in a randombred chicken population

The current study was undertaken to estimate variance components for phytate P bioavailability (PBA) and the genetic correlations among PBA with growth and feed utilization (or intake) traits in an unselected random mating chicken population. Pedigreed data from 901 Athens-Canadian randombred chickens hatched from 26 sires, 71 dams, and 105 grandparents were used for estimation of genetic parameters. Birds were individually housed in metabolic cages at 4 wk of age and fed a 0.35% P diet. After 3 d of acclimatization, excreta produced for 3 consecutive d were collected and feed consumed (FC) was measured. Individual 4-wk BW and BW gain (BWG) during the 3-d excreta collection period were also measured. Feed conversion ratios (FCR) were calculated. Phytate P bioavailability was estimated from the disappearance of phytate during the passage of feed through the gastrointestinal tract. The restricted maximum likelihood method with the average information matrix algorithm was used for the estimation of variance components. The heritability estimate for PBA was about 0.10. Genetic correlations between PBA and BW, BWG, and FC were moderate and negative, indicating that improving PBA utilization would moderately affect growth. The genetic correlation between PBA and FCR was negligible and suggested that selection for PBA will not adversely affect FCR. The economic implications of genetically modifying poultry to improving phytate P utilization and the subsequent elimination or reduction of the amount of phytase used in poultry diets are yet to be determined.

The dynamics of the genotype-phenotype association

The integrity of an organism is maintained by networks of interacting genes. Such networks predict that genetic variants affect phenotypes in a nonadditive fashion. That is, the effect of an allelic variation in one gene is dependent on the variations in other genes. We summarize the analyses of a series of genes in a White Leghorn strain that support the existence of such gene networks: 1) genes are pleiotropic, 2) genes affect trait correlations, 3) genes affect trait distributions in a nonadditive fashion, 4) genes interact with each other, and 5) genes are at linkage disequilibrium, even when located on different chromosomes. The latter observation indicated that certain gene combinations lead to reduced reproductive fitness. Each candidate genes we analyzed segregated for multiple alleles that affected production traits. This finding was surprising, even for a strain with a large effective population size. The shapes of trait distributions appear to be a better descriptor of gene effects than measures of central tendency. Despite this complexity, it is feasible to conduct DNA-based selection, starting from any of several different genes that affect a trait. Gene networks may be altered in many different ways to improve a particular phenotype, but networks may differ in their effects on other traits.

Systems-wide chicken DNA microarrays, gene expression profiling, and discovery of functional genes

The goal of our current consortium project is to launch a new era--functional genomics of poultry--by providing genomic resources [expressed sequence tags (EST) and DNA microarrays] and by examining global gene expression in target tissues of chickens. DNA microarray analysis has been a fruitful strategy for the identification of functional genes in several model organisms (i.e., human, rodents, fruit fly, etc.). We have constructed and normalized five tissue-specific or multiple-tissue chicken cDNA libraries [liver, fat, breast, and leg muscle/epiphyseal growth plate, pituitary/hypothalamus/pineal, and reproductive tract (oviduct/ovary/testes)] for high-throughput DNA sequencing of EST. DNA sequence clustering was used to build contigs of overlapping sequence and to identify unique, non-redundant EST clones (unigenes), which permitted printing of systems-wide chicken DNA microarrays. One of the most promising genetic resources for gene exploration and functional gene mapping is provided by two sets of experimental lines of broiler-type chickens developed at INRA, France, by divergent selection for extremes in growth traits (fast-growing versus slow-growing; fatness versus leanness at a similar growth rate). We are using DNA microarrays for global gene expression profiling to identify candidate genes and to map growth, metabolic, and regulatory pathways that control important production traits. Candidate genes will be used for functional gene mapping and QTL analysis of F2 progeny from intercrosses made between divergent genetic lines (fat x lean lines; fast-growing x slow-growing lines). Using our first chicken liver microarray, we have already identified several interesting differentially expressed genes in commercial broilers and in divergently selected broiler lines. Many of these candidate genes are involved in the lipogenic pathway and are controlled in part by the thyrotropic axis. Thus, genome-wide transcriptional profiling is a powerful tool used to visualize the cascade of genetic circuits that govern complex biological responses. Global gene expression profiling and QTL scans should enable us to functionally map the genetic pathways that control growth, development, and metabolism of chickens. This emerging technology will have broad applications for poultry breeding programs (i.e., use of molecular markers) and for future production systems (i.e., the health and welfare of birds and the quality of poultry products).

Effect of long-term divergent selection on growth characteristics in Japanese quail

The current study was undertaken to examine the effect of long-term selection for 4-wk BW on growth characteristics in divergent lines of Japanese quail and their control. Growth rate was significantly higher in males than females in all the lines. There was a significant increase in growth rate of the females selected for increased 4-wk BW over the control females, as well as a significant decline in growth rate of males selected for decreased 4-wk BW compared to their control counterparts. It appeared that selection for increased 4-wk BW did not alter the rate of growth in the males compared to the control males; however, in the females, selection for increased 4-wk BW resulted in an increase in growth rate. On the other hand, selection for decreased 4-wk BW resulted in a decline in growth rate in males but not in the females. The dynamics of the growth curve parameters indicate that selection for decreased 4-wk BW shifted the growth curve for females as well as altering the trajectories of growth in both sexes. However, selection for increased 4-wk BW only resulted in altering the trajectory of growth in the males. Long-term selection resulted in asymmetry of response in the low and high lines. In addition, different genes may respond differently to the same selection pressure in opposite directions. The use of the 4-parameter Richards model to analyze growth data from such an experiment provided a better understanding of how selection can alter the rate and trajectory of growth to affect the genetically determined growth potential of quail. Consequently selection for increased or decreased 4-wk BW affected the sexes differently.

Power of two methods for the estimation of bone ash of broilers

An experiment was conducted to compare two common methods of estimating bone ash from growing broiler chicks (A = autoclaving; B = boiling/extracting). Ross x Ross 1-d-old broiler chicks were fed a corn-soy, phosphorus-deficient diet (22.7% CP, 1% calcium, 0.22% non-phytate phosphorus), with 0, 750, 1,500, 3,000, or 6,000 units of phytase (FTU) to produce bones with a range of ash. The methods were compared with bones from chicks at 7, 14, and 21 d of age. Left legs were used for method B, and right legs were used for method A. Data was analyzed by the general linear models procedure of SAS software, and differences between means were detected using the Duncan's new multiple range test at the 0.05 level. Variance estimates were the mean square errors (from SAS outputs). Sample sizes needed to detect a 2% difference in bone ash were calculated using the method of Zar. The addition of 6,000 FTU/kg increased tibia ash from 26 to 37%, 29 to 41%, and 33 to 43% on Days 7, 14 and 21, respectively (method B). With bones from 7-d-old chicks, the same number of samples was necessary to detect a 2% difference using methods A and B. With bones from 14- and 21-d-old chicks, approximately 50 and 150% more samples were necessary, respectively, using method A. The autoclaving method is less labor-intensive and requires no toxic solvents, but for older birds, many more samples or replications are needed to detect the same treatment differences.

Comparison of three nonlinear and spline regression models for describing chicken growth curves

This study compared three non-linear growth models (Richards, Gompertz, and logistic) and the spline linear regression model using BW measurements from an unselected, randombred chicken population. Based on the goodness of fit criteria, the nonlinear models (NLM) fitted the data better than the spline regression model. The four-parameter Richards model was expected to have the best overall fit; however, because the shape parameter predicted was close to 1.0, which corresponded with the Gompertz curve, there were no differences between the Richards and Gompertz models for the data used. The growth parameters predicted with the logistic model were different from those predicted by the Richards and Gompertz models. It was concluded that growth parameters predicted with different models with fixed inflection points are not directly comparable. The spline linear regression model is a compound function consisting of a series of linear models. It can be used to compartmentalize growth into segments and also substitute as an alternative to asymptotic models when the data are truncated before the asymptote is attained. The relationship between the growth trajectory (m) and carcass composition measurements were also investigated. Carcass yields among the different growth trajectories (m) were similar within sexes. However, the proportions of the major breast muscle and abdominal fat differed according to the m a bird followed.

Analysis of censored survival data in Japanese quail divergently selected for growth and their control

The aim of the current study was to characterize and quantify risk factors involved in juvenile mortality in divergently selected and control lines of Japanese quail. Survival analysis and Cox proportional hazards regression were used to describe mortality in the three experimental lines with hatch weight and posthatch BW evaluated as risk factors. Survival function distribution indicated that the proportional mortality was highest in the line selected for high 4-wk BW compared to the low and control lines. In all the experimental lines mortality declined when posthatch BW increased; however, the magnitude of reduction was highest in the control line compared to the divergently selected lines (57 vs. 22%). Any factor that influences growth after hatching may likely have a direct impact on mortality. Lack of accessibility to water, feed, warmth, and potential negative social interaction are factors that could affect mortality immediately after hatch. The posthatch BW at time of mortality used as a risk factor indicated that the divergently selected lines have about the same risk and are less sensitive to reduced BW compared to the control population. Through survival analysis, the present study has demonstrated that factors causing reduction in posthatch BW are likely risk factors for mortality in growing birds.

Monitoring Mycoplasma gallisepticum and Mycoplasma synoviae infection in breeder chickens after treatment with enrofloxacin

Three experimental strains of breeder chickens were accidentally exposed to Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS), presumably from a newly introduced group of leghorn-type pullets. The experimental strains subsequently became infected and were diagnosed positive for MG and MS by the serum plate agglutination (SPA) test and confirmed by the hemagglutination inhibition (HI) test and the polymerase chain reaction (PCR) of tracheal swabs. Treatment with 10 mg/kg enrofloxacin via drinking water for 14 days was elected. Before and after initiation of treatment, MG and MS were monitored for changes by SPA, HI, PCR, and culture, with sampling intervals ranging from 1 wk to 7 wk. MG and MS SPA, HI, PCR, and culture were performed at each sampling period, with the exception of weeks 1.0 and 6.5. Week 1.0 included SPA and His for MG and MS. Week 6.5 included PCR and culture for MG and MS. The MG and MS SPA results were positive throughout the 29-wk trial period. MG HI titers declined until the last sampling, whereas the MS HI titers did not decline significantly. PCR for MG yielded only one positive result, which occurred before treatment. MS PCR remained positive throughout the trial period. MG was never isolated from any sample; however, one MS organism was isolated during treatment. The treatment regimen was effective for MG on the basis of PCR results. Treatment with enrofloxacin did not eliminate SPA reactions during the 29-wk trial period. MG HI titers remained in the suspicious range throughout the remainder of the trial period. Four weeks after the treatment ended, MG HIs were reduced by approximately 40%, with MS HIs remaining high throughout the 29-wk period. PCR appeared to be a sensitive and specific test on the basis of correlation with HIs. On the basis of the isolation of MS during treatment and continued subsequent PCR positive reactions, the treatment for MS with enrofloxacin was not as efficacious as for MG.

Trait association of a genetic marker near the IGF-I gene in egg-laying chickens

The insulin-like growth factor I (IGF-I) gene was screened for genetic variants associated with trait means and trait correlations. Analysis of an unselected randomly mated White Leghorn population revealed a PstI restriction fragment length polymorphism (RFLP) in the 5' region of the gene which segregated at a frequency of 0.83 for the PstI(+) allele (presence of a PstI restriction site). A comparison of the three genotypic classes revealed that the PstI(-/-) genotype was associated with a significantly lower egg weight measured in three different time periods, while the PstI(+/-) genotype was significantly associated with a higher eggshell weight estimated from the egg weight and egg specific gravity. For eggshell weight, the effect was age dependent and significant only for the last two periods of egg laying. No genotype associations were found for body weight, feed consumption, and egg laying rates. Significant dominance effects of the IGF-I genotype were observed for two of the egg weight measurements and three of the eggshell weight estimates. Partial correlation analyses in the two most frequent genotypic classes, PstI(+/+) and PstI(+/-), revealed the presence of a regulatory loop between feed consumption, body weight, egg weight, and the rate of egg laying. Several aspects of this regulatory loop were different between the two genotypic classes. In particular, for the PstI(+/+) genotype, feed consumption was positively associated with egg weight, while there was no significant association for the PstI(+/-) genotype. Further, the degree of association of body weight with egg weight decreased with age in the genotypic class PstI(+/-), while it was constant for the PstI(+/+) genotype. The results indicated that the marker in the IGF-I gene was not only associated with changes in some trait means, but also with changes in the stability of the coordination between feed intake, body weight, and egg production traits.

Markers within the regulatory region of the growth hormone receptor gene and their association with milk-related traits in Holsteins

We studied sequence variations in the regulatory region of the bovine growth hormone receptor gene. A polymerase chain reaction (PCR)-based method for detecting AluI, AccI, and StuI restriction fragment length polymorphisms (RFLPs) in the 5' flanking region of the bovine growth hormone receptor gene was developed and tested for association with milk-related traits in Holstein bulls. Allele frequencies of the polymorphisms in two groups of Holstein progeny-tested bulls born from 1950 to 1970 and in the 1980s, respectively, were estimated. The allele frequency of the AluI(-) allele was 0.63 and 0.42 in the bulls from 1950 to 1970 and in the 1980s, respectively. The frequency of the StuI(-) allele was 0.14 and 0.07 in the two respective bull groups. Allele frequency for AccI(-) allele was about 0.22 in both bull groups. The differences in allele frequencies for the AluI polymorphism in the two bull groups were significantly different (P < or = .005). The AluI(+/+) bulls had a higher estimated breeding value (EBV) for fat (P < or = .016) than AluI(-/-) bulls. The average effect of allele substitution for the AluI polymorphism was +/- 8 for fat EBV. The AluI polymorphism could be further evaluated for use in marker-assisted selection in dairy cattle.

Mitochondrial PEPCK: a highly polymorphic gene with alleles co-selected with Marek's disease resistance in chickens

The gene coding for the mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M), a pivotal component in gluconeogenesis from lactate via the Cori cycle, was highly polymorphic in strains of egg-type chickens (White Leghorn) of different origins. Based on MspI restriction fragment polymorphisms a total of seven alleles could be distinguished. The allele frequencies were determined in six pairs of strains derived from different genetic base populations. Each pair consisted of two strains which differed in their susceptibility to Marek's disease (MD), a virus-induced neoplastic disease. The frequency of the most common haplotype (M2) was consistently higher in the susceptible strains than in the corresponding resistant strains (P < 0.05, Wilcoxon signed-ranks test), indicating that the observed differences were not due to random genetic drift. This result suggests that PEPCK-M may be a candidate gene which contains genetic variants affecting MD susceptibility. Variations in gluconeogenesis may affect the interplay between proliferation of neoplasia and host metabolism.

A genetic marker in the growth hormone receptor gene associated with body weight in chickens

A genomic clone spanning 16 kb of the GH receptor gene was mapped and used as a probe for identifying restriction fragment length polymorphisms (RFLPs) in chickens. Several strains of meat-type and egg laying chickens were found to segregate for an HindIII RFLP located in the intron preceding exon 4. The polymorphic HindIII site overlapped with a poly(A) signal. Association of the HindIII RFLP with traits was analyzed in a random-bred White Leghorn strain in three generations using either selective or random genotyping. Both methods revealed significant association of the HindIII+ allele (presence of the poly(A) signal) with an increased juvenile body weight (130 days of age). In two meat-type strains divergently selected for size of the abdominal fat pad, the HindIII+ allele was coselected with leanness. The results indicate the presence of a genetic variant of the GH receptor gene which affects growth and abdominal fat deposition and which is relatively frequent in egg laying as well as in meat-type chickens.

Evidence for a genetic variation in the mitochondrial genome affecting traits in White Leghorn chickens

A mitochondrial Mspl RFLP which was coselected with Marek's disease (MD) resistance in White Leghorn chickens was mapped to the NADH subunit IV. The RFLP was due to a transition, resulting in the change of the low-usage threonine triplet ACT (Mspl- allele) to the high usage triplet ACC (Mspl+ allele). Trait association studies within an unselected strain revealed that the Mspl- allele whose frequency was reduced in MD resistant strains was associated with high body weight and high egg specific gravity (a measure of eggshell thickness). Analysis at three different time points indicated a significant interaction between the mitochondrial genotype and the growth hormone genotype in early but not in late adulthood. The analysis indicates that mitochondrial variants may contribute to phenotypic variation in chickens and that such contributions may be dependent on the genetic background.

Restriction fragment length polymorphisms at the ornithine decarboxylase locus associated with milk protein yield in Holsteins

Marker-assisted selection may provide the opportunity to make significant genetic gains in the improvement of economically important traits in livestock (Soller & Beckmann, 1983; Smith & Simpson, 1986). Implementation of this approach will first require identification of candidate genes or anonymous gene markers associated with the traits of interest. Candidate genes are those with a known relationship between physiological or biochemical processes and an economically important trait. In dairy cattle, genes associated with mammary gland growth, development and function are excellent candidate genes for milk production traits.

The polyamines are low molecular mass polycations that influence cell proliferation and growth (Tabor & Tabor, 1984; Pegg, 1986). Ornithine decarboxylase (ODC, EC 4.1.1.17) catalyses the conversion of ornithine to putrescine, the rate-limiting step in polyamine biosynthesis (Pegg, 1986). The level of ODC is induced in quiescent cells exposed to a wide variety of stimuli such as growth hormone, corticosteroids, testosterone and growth factors (Tabor & Tabor, 1984). There is ample evidence that growth factors influence morphogenesis and differentiation of the mammary gland (Imagawa et al. 1994). Trophic hormones that are associated with lactation, such as prolactin and growth hormone, are also required to induce differentiation of bovine mammary epithelial cells (Huynh et al. 1991; Flint & Gardner, 1994), and both mitogenic and lactogenic effects of prolactin, insulin and hydrocortisone appear to be mediated through the polyamine pathway (Rillema et al. 1977; Bedford & Zadworny, 1990; Golden & Rillema, 1993). Strange et al. (1992) have shown that ODC is involved in synthesis of a milk component; ODC has elevated expression in the lactating mammary gland, which declines sharply after weaning. It is therefore possible that particular variants of ODC could be associated with increased mammary gland function and thus influence milk related traits.

The objectives of the present study were to estimate allelic frequencies of ODC polymorphisms in Holstein bulls and to evaluate further the genotypic effects of ODC variants on milk production traits.

Association of endogenous viral genes with quantitative traits in chickens selected for high egg production and susceptibility or resistance to Marek's disease

1. The association of endogenous viral (ev) genes with quantitative traits in 2 genetically distinct sets of White Leghorn strains were investigated. Strain S had been selected for susceptibility to Marek's disease (MD) whereas strain K had been selected for resistance to MD and high egg production and egg weight. 2. In all, 8 ev genes were typed. Ev10, ev19 and 'newB' occurred exclusively in strain S, 'newA' occurred only in strain K, and ev1, ev3, ev6 and ev8 occurred in both strains. 3. Whereas ev6 and ev8 were associated with reduction in egg production rate in strain S, in strain K, the presence of ev3 was associated with increased group specific antigen. 4. The genetic background of the chicken strain may play a role in the way certain ev genes affect traits. 5. It was thought that the position of ev genes on the chromosome may be important and their association with traits of economic importance make them potential genetic markers for uncovering quantitative trait loci.

Bovine ornithine decarboxylase gene: cloning, structure and polymorphisms

Bovine ornithine decarboxylase (ODC) genomic clones were isolated from a bacteriophage lambda DASH genomic library. A total of 9452 bp sequence was determined which covers the entire sequence of the bovine ODC gene. Sequence analysis showed that the bovine ODC gene consisted of 12 exons which encode a protein identical to that inferred from a bovine ODC cDNA. Comparison of the structure and nucleotide sequence of the bovine, human and mouse ODC genes revealed that the gene was highly conserved. Primer extension analysis demonstrated that the transcription start point of bovine ODC mRNA was located 378 bp upstream from the A residue in the translation initiation codon. The 5'-untranslated region (UTR) of ODC mRNA was highly G + C rich, particularly in its 5'-most portion, and computer predictions suggested a very stable secondary structure for this region, with an overall free energy of formation of -134.4 kcal/mol. Conserved sequences and potential promoter elements including a TATA box, a possible CCAAT element, SP1 ranscription factor binding sites (GC boxes) and cAMP response elements (CRE) were identified in the 5'-flanking region of the gene. Two polymorphic restriction sites, a TaqI and a MspI, were mapped to the ODC gene and PCR-based methods for detection of the 2 polymorphisms were developed.

Trait association of genetic markers in the growth hormone and the growth hormone receptor gene in a White Leghorn strain

Alleles of the growth hormone (GH) gene and GH receptor (GHR) gene were analyzed for association with juvenile body weight (HBWT), age at first egg (AFE), the hen-day rate of egg production (HDR), egg specific gravity (SPG), and egg weight (EWT) in a strain of White Leghorns. The particular strain segregated at near equal frequencies for two GH alleles defined by differences at three restriction fragment length polymorphisms (RFLP) and for two GHR alleles defined by a single RFLP. The GH genotype was significantly associated with AFE (P < or = 0.04) as well as HDR from 274 to 385 d (P < or = 0.04) and 386 to 497 d (P < or = 0.0003). The GHR genotype (haploid in female chickens) had trends for association with HBW (P < or = 0.06) and HDR from AFE to 273 d (P < or = 0.07). The effects on the egg quality traits SPG and EWT were not significant. Regression analysis revealed that HDR was associated negatively with AFE and positively with HBWT. The slope of the regression line of HDR on AFE varied with the GH genotype, with the effect that the differences in HDR between GH genotypes was relatively small in chickens with early AFE and large in chickens with late AFE. Similarly, the slope of the regression of HDR on HBWT varied between GHR genotypes, with the result that the effect of the GHR genotype on HDR in chickens with low HBWT was opposite to its effect in chickens with high HBWT. The complex relationship between genotypes and traits may reflect gene interaction and indicates that simple models based on additive gene effects may not be adequate for the dissection of the genetic architecture of quantitative traits.

Antioxidant enzymes and atherosclerosis in Japanese quail: heritability and genetic correlation estimates

OBJECTIVES

To estimate, in male quail susceptible to atherosclerotic plaque formation (SUS) fed a regular diet and an atherogenic diet, the genetic and phenotypic parameters associated with antioxidant enzymes and atherogenesis.

DESIGN

Genetic parameters were estimated from variance components of the analysis of variance on 70 males from 13 full-sib families.

MAIN RESULTS

Under the regular diet, seven of 35 males developed mild atherosclerosis. Heritability was zero for atherosclerotic plaque score and plasma cholesterol level. Plaque score was highly correlated to plasma triglyceride level (rp = 0.96) and liver fattiness (rp = 0.97), but only moderately to plasma cholesterol level (rp = 0.39). With the high cholesterol diet, plasma cholesterol level increased sixfold and became heritable (h2 = 0.4). Many males developed severe atherosclerosis. Plaque score became associated more with plasma and aortic cholesterol levels (rp = 0.56) and 0.76, respectively) than with plasma triglyceride level (rp = 0.54). Aortic glutathione reductase activity was negatively correlated with plaque score (rp = -0.42; rg = -0.51) and aortic cholesterol level (rp = -0.39; rg = -0.62).

CONCLUSIONS

Plasma triglyceride level was an important factor affecting the development of fatty streaks and the early progression of atherosclerotic plaques. Without high levels of dietary cholesterol in the plasma and aorta, any early atherosclerotic plaques that developed did not progress further within the time-frame of the experiment. Aortic cholesterol concentration and glutathione reductase activity were important factors in the advancement of severe plaque formation. Heritability of plaque score was high in the SUS line, and further selective breeding should increase the susceptibility of these quail to cholesterol-induced atherosclerosis.

Sequence variations in the bovine growth hormone gene characterized by single-strand conformation polymorphism (SSCP) analysis and their association with milk production traits in Holsteins

Sequence variations in the bovine growth hormone (GH) gene were investigated by single strand conformation polymorphism (SSCP) analysis of seven amplified fragments covering almost the entire gene (2.7 kb). SSCPs were detected in four of these fragments and a total of six polymorphisms were found in a sample of 128 Holstein bulls. Two polymorphisms, a T-->C transition in the third intron (designated GH4.1) and an A-->C transversion in the fifth exon (designated GH6.2), were shown to be associated with milk production traits. GH4.1c/GH4.1c bulls had higher milk yield than GH4.1c/GH4.1t (P < or = 0.005) and GH4.1t/GH4.1t (P < or = 0.0022) bulls. GH4.1c/GH4.1c bulls had higher kg fat (P < or = 0.0076) and protein (P < or = 0.0018) than GH4.1c/GH4.1t bulls. Similar effects on milk production traits with the GH6.2 polymorphism were observed with the GH6.2a allele being the favorable allele. The average effects of the gene substitution for GH4.1 and GH6.2 are similar, with +/-300 kg for milk yield, +/-8 kg for fat content and +/-7 kg for protein content per lactation. The positive association of GH4.1c and GH6.2a with milk production traits may be useful for improving milk performance in dairy cattle.

A MspI polymorphism in the bovine ornithine decarboxylase gene and its possible association with selection for milk production in Holstein bulls

A polymerase chain reaction (PCR)-based method for detection of a MspI-restriction fragment length polymorphism (RFLP) in the bovine ornithine decarboxylase gene was developed, and the allele frequencies of the polymorphism in two groups of Holstein bulls representing progeny-tested bulls during the 1950s-1960s and 1980s, respectively, were estimated. The frequencies of the MspI(-) allele ere 0.229 and 0.077 and that of MspI(+) were 0.771 and 0.923 in the progeny-tested bulls of the 1950s-1960s and 1980s, respectively. The difference in allele frequencies between the two groups was statistically significant (P < 0.005). Genetic drift could be responsible for the changes in allele frequencies; however, it could also be possible that selection for milk production was associated with the changes of the allele frequencies in the two bull populations.

Size of breeding populations required for selection programs

The minimum population size required for selection in order to reduce the effect of genetic drift to a particular level has been considered. The model of Nicholas was extended to include the measurement-error variance in the response variance. Situations where the sex ratios among scored and breeding individuals are unequal are also considered. When the duration of a selection experiment is relatively long, Nicholas' approximation (i.e., assuming that measurement error is negligible relative to drift) is useful in determining the minimum effective population size required. However, the measurement-error variance becomes an important source of variation in short-term (≤ 5 generations) selection experiments, and should not be ignored.

Animal model analysis of genetic (co)variances for growth traits in Japanese quail

Records of 1,530 Japanese quail were used to estimate heritabilities and genetic correlations based on a derivative-free restricted maximum likelihood (REML) method with an animal model and ANOVA. The animal model included fixed effects of hatch and sex, random effects of additive genetic value of the bird, and common environmental effect of the dam. Heritabilities estimated from REML for body weights at hatch, 7, 14, 21, and 28 d of age were .38, .12, .31, .12, and .44, respectively. Heritabilities estimates from the sire component of variance for the same traits were .57, .08, .28, .15, and .47. These values indicate that genetic progress can be made by selecting for either 14-d or 28-d body weight. Genetic correlation (REML) of .76 between body weights at 14 and 28 d of age indicates the possibility of improving body weight at 28 d of age by selecting for body weight at 14 d of age.

Multiphasic analysis of egg production in Japanese quail

A multiphasic function that considers egg production of individual hens to result from more than one phase was used to describe egg production for Japanese quail. Each phase is determined by number of eggs within a clutch, including internally laid eggs, and pause between clutches. Cumulative egg production was fitted by using a function (Koops and Grossman, 1992) expressing time in terms of cumulative egg number. Data from nine hens over a 31-day period were analyzed to estimate parameters for lag and delay. The data were preadjusted for internal laying. Lag ranged from -1.14 to .19 h. Unlike chickens, there was no clear relationship between lag and average clutch length in Japanese quail. Average delay was about 21.6 h and seemed to be longer than that in the chicken. Furthermore, the residual standard error for delay was higher in Japanese quail than in the chicken.