Heritability and Genetic Correlation Estimates for Performance and Carcass and Body Composition Traits in a Male Broiler Line

Application of bioelectrical impedance analysis to assess body composition of male and female broiler chickens from 2 different strains throughout the growth period

Bioelectrical impedance analysis (BIA) was performed in males and females of 2 different broiler strains from 0 to 42 d of age to develop and validate equations to predict body composition (BC). A total of 528 birds, 132 birds per sex and strain (Ross 308 and Cobb 500) were used in the experiment. Birds were fed ad libitum following CVB recommendations with a common starter (0-14 d), grower (15-29 d), and finisher diet (30-42 d). Bioelectrical impedance analysis was measured weekly from 0 to 42 d. Birds were euthanized, frozen and ground for sample collection. Each sample was analyzed through proximate analysis for dry matter (DM), protein, fat, ash, and energy content. Water (%), protein and ash (% DM) decreased with age (77.5-67.5, 69.1-52.2, and 8.12-7.29, respectively; P < 0.0001); whereas fat (% DM) and energy (cal/g DM) increased with the age (20.7-36.4 and 5,421-6151, respectively; P < 0.0001). Males had significantly higher water (%) and protein (% DM) contents, and lower lipid (% DM) deposits than females (70.5, 55.5, and 32.6 vs. 69.6, 54.6, and 33.7, respectively; P < 0.0001). Cobb 500 had a higher fat and lower protein (% DM) and water (%) content than Ross (34.6, 54.0, and 69.7 vs. 31.7, 56.1, and 70.4, respectively; P < 0.0001). A multiple linear regression analysis was carried out to select the equation model to predict BC using the relative mean prediction error (RMPE, %) to evaluate the accuracy. The coefficients of determination (R2) to estimate water (%), protein, fat, ash (% DM) and energy content (cal/g DM) were 0.909, 0.825, 0.795, 0.493, and 0.838, respectively, and the RMPE were 1.26, 3.46, 7.73, 8.85, and 1.86%, respectively. A t test analysis was run, observing no differences in any of the parameters under study between the analyzed and estimated values. Based on these results, we can conclude that BIA can be used as a valid non-invasive technique to estimate in vivo BC in broilers.

A Study on the Growth and Development Characteristics of Lindian Chickens

As an excellent chicken breed found in a high-altitude zone of northern China, Lindian chickens are characterized by good egg and meat production, strong adaptability, cold tolerance, rough feeding resistance, excellent egg quality, and delicious meat quality. To facilitate the exploitation of the unique qualities of the Lindian chicken, the varying patterns and correlations of various body size and carcass traits of 3-22-week-old Lindian chickens were analyzed in this study. The optimal growth model of these traits was determined by growth curve fitting analysis. The results showed that most traits of Lindian chickens increased steadily with increasing age, and most of them increased rapidly before 10 weeks of age. In addition, the inflection point age of each trait was predicted to be between 4 and 10 weeks. Furthermore, this study revealed that body size traits were closely related to carcass traits in Lindian chickens. In summary, Lindian chickens are in a rapid growth stage before the age of 10 weeks, and better slaughter performance can be achieved through good feeding management during this stage. The reproductive traits and muscles are the main developmental focus after the age of 19 weeks, so it is important to adequately meet their energy requirements for subsequent good breeding performance.

Strategies to improve genomic predictions for 35 duck carcass traits in an F2 population

BACKGROUND

Carcass traits are crucial for broiler ducks, but carcass traits can only be measured postmortem. Genomic selection (GS) is an effective approach in animal breeding to improve selection and reduce costs. However, the performance of genomic prediction in duck carcass traits remains largely unknown.

RESULTS

In this study, we estimated the genetic parameters, performed GS using different models and marker densities, and compared the estimation performance between GS and conventional BLUP on 35 carcass traits in an F₂ population of ducks. Most of the cut weight traits and intestine length traits were estimated to be high and moderate heritabilities, respectively, while the heritabilities of percentage slaughter traits were dynamic. The reliability of genome prediction using GBLUP increased by an average of 0.06 compared to the conventional BLUP method. The Permutation studies revealed that 50K markers had achieved ideal prediction reliability, while 3K markers still achieved 90.7% predictive capability would further reduce the cost for duck carcass traits. The genomic relationship matrix normalized by our true variance method instead of the widely used [Formula: see text] could achieve an increase in prediction reliability in most traits. We detected most of the bayesian models had a better performance, especially for BayesN. Compared to GBLUP, BayesN can further improve the predictive reliability with an average of 0.06 for duck carcass traits.

CONCLUSION

This study demonstrates genomic selection for duck carcass traits is promising. The genomic prediction can be further improved by modifying the genomic relationship matrix using our proposed true variance method and several Bayesian models. Permutation study provides a theoretical basis for the fact that low-density arrays can be used to reduce genotype costs in duck genome selection.

QPCTL Affects the Daily Weight Gain of the F2 Population and Regulates Myogenic Cell Proliferation and Differentiation in Chickens

Molecular breeding can accelerate the process of animal breeding and improve the breeding efficiency. To date, many Indel molecular markers have been identified in livestock and poultry, but how Indels affect economic traits is not well understood. For molecular breeding, it is crucial to reveal the mechanism of action of Indels and to provide more accurate information. The purpose of this study was to investigate how the 52/224-bp multiallelic Indels of the chicken QPCTL promoter area affect the daily weight gain of chickens and the potential regulatory mechanism of the QPCTL gene. The analysis was conducted by association analysis, qPCR, dual-fluorescence assay and Western blotting. The results showed that Indels in the QPCTL promoter region were significantly associated with the daily weight gain in chickens and that QPCTL expression showed a decreasing trend in embryonic breast muscle tissues. Furthermore, QPCTL expression was significantly higher in breast muscle tissues of the AC genotype than in those of the AB and BB genotypes. Based on the transcriptional activity results, the pGL3-C vector produced more luciferase activity than pGL3-A and pGL3-B. In addition, overexpression of QPCTL promoted chicken primary myoblast (CPM) proliferation and inhibited differentiation. The results of this study suggest that Indels in the promoter region of the QPCTL gene may regulate the proliferation and differentiation of CPMs by affecting the expression of QPCTL, which ultimately affects the growth rate of chickens. These Indels have important value for the molecular breeding of chickens, and QPCTL can be used as a candidate gene to regulate and improve chicken growth and development.

In vivo prediction of abdominal fat and breast muscle in broiler chicken using live body measurements based on machine learning

The purpose of this study was to predict the carcass characteristics of broilers using support vector regression (SVR) and artificial neural network (ANN) model methods. Data were obtained from 176 yellow feather broilers aged 100-day-old (90 males and 86 females). The input variables were live body measurements, including external measurements and B-ultrasound measurements. The predictors of the model were the weight of abdominal fat and breast muscle in male and female broilers, respectively. After descriptive statistics and correlation analysis, the datasets were randomly divided into train set and test set according to the ratio of 7:3 to establish the model. The results of this study demonstrated that it is feasible to use machine learning methods to predict carcass characteristics of broilers based on live body measurements. Compared with the ANN method, the SVR method achieved better prediction results, for predicting breast muscle (male: R² = 0.950; female: R² = 0.955) and abdominal fat (male: R² = 0.802; female: R² = 0.944) in the test set. Consequently, the SVR method can be considered to predict breast muscle and abdominal fat of broiler chickens, except for abdominal fat in male broilers. However, further revaluation of the SVR method is suggested.

Searching for causal relationships among latent variables concerning performance, carcass, and meat quality traits in broilers

In causal relationship studies, the latent variables may summarize the phenotypes in theoretical traits according to their phenotypic correlations, improving the understanding of causal relationships between broilers phenotypes. In this study, we aimed to investigate potential causal relationships among latent variables in broilers using a structural equation model in the context of genetic analysis. The data used in this study comprised 14 traits in broilers with 2,017 records each, and 104,154 animals in pedigree. Four latent variables (WEIGHT, LOSSES, COLOUR, and VISCERA) were defined and validated using Bayesian Confirmatory Factor Analysis. Subsequently, a search for causal linkage structures was performed, obtaining a single causal link structure between the latent variables. Then, this information was used to fit the structural equation model (SEM). The results from the SEM indicated positive causal effects of the variables WEIGHT and LOSSES on the variables VISCERA and COLOUR, respectively, with structural coefficient estimates of 1.006 and 0.040, respectively. On the other hand, an antagonist causal effect of the variable WEIGHT on the variable LOSSES was verified, with a structural coefficient estimate of -4.333. These results highlight the causal relationship between performance and meat quality traits, which may be associated with the natural processes involved in the conversion of muscle into meat and the structural changes in muscle tissues due to intense selection for high growth rates in broilers.

Accounting for genetic architecture for body weight improves accuracy of predicting breeding values in a commercial line of broilers

BLUP (best linear unbiased prediction) is the standard for predicting breeding values, where different assumptions can be made on variance–covariance structure, which may influence predictive ability. Herein, we compare accuracy of prediction of four derived‐BLUP models: (a) a pedigree relationship matrix (PBLUP), (b) a genomic relationship matrix (GBLUP), (c) a weighted genomic relationship matrix (WGBLUP) and (d) a relationship matrix based on genomic features that consisted of only a subset of SNP selected on a priori information (GFBLUP). We phenotyped a commercial population of broilers for body weight (BW) in five successive weeks and genotyped them using a 50k SNP array. We compared predictive ability of univariate models using conservative cross‐validation method, where each full‐sib group was divided into two folds. Results from cross‐validation showed, with WGBLUP model, a gain in accuracy from 2% to 7% compared with GBLUP model. Splitting the additive genetic matrix into two matrices, based on significance level of SNP (G_f: estimated with only set of SNP selected on significance level, G_r: estimated with the remaining SNP), led to a gain in accuracy from 1% to 70%, depending on the proportion of SNP used to define G_f. Thus, information from GWAS in models improves predictive ability of breeding values for BW in broilers. Increasing the power of detection of SNP effects, by acquiring more data or improving methods for GWAS, will help improve predictive ability.

Exploring the genetic architecture of feed efficiency traits in chickens

Chicken feed efficiency (FE) traits are the most important economic traits in broiler production. Several studies evaluating genetic factors affecting food consumption in chickens are available. However, most of these studies identified genomic regions containing putative quantitative trait loci for each trait separately. It is still a challenge to find common gene networks related to these traits. Therefore, here, a genome-wide association study (GWAS) was conducted to explore candidate genomic regions responsible for Feed Intake (FI), Body Weight Gain (BWG) and Feed Conversion Ratio (FCR) traits and their gene networks. A total of 1430 broilers from an experimental population was genotyped with the high density Affymetrix 600K SNP array. A total of 119 associated SNPs located in 20 chromosomes were identified, where some of them were common in more than one FE trait. In addition, novel genomic regions were prospected considering the SNPs dominance effects and sex interaction, identifying putative candidate genes only when these effects were fit in the model. Relevant candidate genes such as ATRNL1, PIK3C2A, PTPRN2, SORCS3 and gga-mir-1759 were highlighted in this study helping to elucidate the genomic architecture of feed efficiency traits. These results provide new insights on the mechanisms underlying the consumption and utilization of food in chickens.

Physiological parameter values for physiologically based pharmacokinetic models in food-producing animals. Part II: Chicken and turkey

Physiologically based pharmacokinetic (PBPK) models are growing in popularity due to human food safety concerns and for estimating drug residue distribution and estimating withdrawal intervals for veterinary products originating from livestock species. This paper focuses on the physiological and anatomical data, including cardiac output, organ weight, and blood flow values, needed for PBPK modeling applications for avian species commonly consumed in the poultry market. Experimental and field studies from 1940 to 2019 for broiler chickens (1-70 days old, 40 g - 3.2 kg), laying hens (4-15 months old, 1.1-2.0 kg), and turkeys (1 day-14 months old, 60 g -12.7 kg) were searched systematically using PubMed, Google Scholar, ProQuest, and ScienceDirect for data collection in 2019 and 2020. Relevant data were extracted from the literature with mean and standard deviation (SD) being calculated and compiled in tables of relative organ weights (% of body weight) and relative blood flows (% of cardiac output). Trends of organ or tissue weight growth during different life stages were calculated when sufficient data were available. These compiled data sets facilitate future PBPK model development and applications, especially in estimating chemical residue concentrations in edible tissues to calculate food safety withdrawal intervals for poultry.

Estimation of the genetic parameters of traits relevant to feed efficiency: result from broiler lines divergent for high or low abdominal fat content

Feed consumption represents a major cost in poultry production and improving feed efficiency is one of the important goals in breeding strategies. The present study aimed to analyze the relationship between feed efficiency and relevant traits and find the proper selection method for improving feed efficiency by using the Northeast Agricultural University High and Low Fat broiler lines that were divergently selected for abdominal fat content. A total of 899 birds were used to measure the feed intake (FI), abdominal fat weight (AFW), and body weight traits. The abdominal fat percentage (AFP), feed conversion ratio (FCR), and the residual feed intake (RFI) were calculated for each individual broiler. The differences in the AFW, AFP, and in traits relevant to feed efficiency, such as FCR and RFI, between the fat line and the lean line were analyzed, and the genetic parameters were estimated for AFW, AFP, and feed efficiency relevant traits. The results showed that AFW, AFP, body weight gain (BWG), FI, FCR, and RFI were significantly higher in the fat line compared with the lean line. The heritability of FI, BWG, FCR, RFI, AFW, and AFP were 0.45, 0.28, 0.36, 0.38, 0.33, and 0.30, respectively. Both FCR and RFI showed high positive genetic correlations with FI, AFW, and AFP and relatively low, negative genetic correlations with BWG. The RFI showed much higher positive genetic correlation with the abdominal fat traits than FCR. In addition, the FCR showed negative genetic correlation with body weight of 4 wk (BW4) and 7 wk (BW7), whereas RFI showed positive genetic correlation with BW4 and BW7. The results showed that both RFI and FCR could be used for improving feed efficiency. When selecting against RFI, the AFP could be significantly reduced, and by selecting against FCR, the body weight could be improved simultaneously.

Effects of different levels of arginine and methionine in a high-lysine diet on the immune status, performance, and carcass traits of turkeys

We postulated that the use of appropriate levels and proportions of arginine (Arg) and methionine (Met) in compound feed with high lysine content (Lys) would make it possible to fully exploit the growth potential of modern fattening turkey crossbreds, without compromising their immune system. The aim of this study was to determine the effect of different ratios of Arg and Met in diets with high Lys content on the performance and immune status of turkeys. The turkeys were assigned to 6 groups with 8 replicates per group and 18 birds per replicate. Six feeding programs, with 3 dietary Arg levels (90, 100, and 110%) and 2 dietary Met levels (30 and 45%) relative to dietary Lys content, were compared. During each of 4 feeding phases (weeks 0–4, 5–8, 9–12, and 13–16), birds were fed ad libitum isocaloric diets containing high level of Lys, approximately 1.83, 1.67, 1.49, and 1.20%, respectively. The dietary treatments had no effect on daily feed intake or body weight at any stage of the study. The protein content of the breast meat was higher in the treatments with the highest Arg level (110%) compared with the lowest Arg level (90%). Similarly, protein content was higher in the treatments with the higher Met level compared with the lower Met level. Higher plasma levels of tumor necrosis factor, interleukin 6 (IL-6), and immunoglobulin Y were found in turkeys fed diets with the lowest Arg content. An increase in Met content resulted in a decrease in plasma content of IL-6. In growing turkeys fed diets high in Lys, an Arg level of 90% relative to Lys can be used without negatively affecting production results and immune system. Regardless of dietary Arg levels, an increase in Met content does not stimulate the immune defense system and shows no effect on growth performance of turkeys in current trial.

Processing evaluation of random bred broiler populations and a common ancestor at 55 days under chronic heat stress conditions

As a result of genetic selection, the modern broiler is more efficient, higher yielding, and faster growing than the bird of the 1950s. Unfortunately, as a result of improvement in growth rate, the modern broiler has the potential to struggle under heat stress conditions. The present study evaluates 3 different random bred populations and a common ancestor under both a thermal neutral and heat stress conditions after a 54-D grow-out period. The lines used in this study included the Athens Canadian Random Bred (ACRB), a 1995 Random Bred (95RAN), a 2015 Random Bred (MRB), and a Junglefowl (JF). Male chicks (n = 150/line) were placed by line in environmentally controlled chambers. An 8-h daily cyclic heat stress (36°C) was applied to half of the chambers beginning on day 28 (HS) and lasting until processing at day 55, while the remaining chambers remained thermal neutral (TN) at 26°C. Dock weights and carcass weights were lower in the HS-95RAN and HS-MRB, compared to their TN counterparts, while the ACRB and JF had no difference in dock and carcass weights regardless of environmental condition. The MRB line had the highest breast yield (27.79%) while the JF (12.79%) and ACRB (12.42%) had the lowest. The 95RAN line had the highest abdominal fat percentage (2.83%) while the MRB line had the lowest moisture uptake during chill. The HS exposure lowered overall breast yield and breast pH at 15 min and 4 h postmortem but did not have an impact on color (L∗) or 24 h breast drip loss. The MRB was scored for both woody breast and white striping. The TN-MRB group had a higher incidence of moderate and severe woody breast and white striping than the HS-MRB group. Based on the results of this study, it appears that HS has a greater negative impact on the higher yielding lines (MRB and 95RAN) than the ACRB and JF and that clear line differences exist between the random bred lines and their common ancestor.

An in vivo evaluation of the effects of feed restriction regimens on wooden breast using ultrasound images as a predictive tool

1. Gradual feed restriction was applied to broilers in order to reduce growth rate and, as a consequence, gradually impacts wooden breast myopathy occurrence. Ultrasound (US) images of breast muscle in live birds were correlated with breast fillets presenting wooden breast characteristics (WB). 2. A total of 1800 Cobb × Cobb 500 slow-feathering male chicks were fed one of the six feed restriction treatments with 12 replicates of 25 birds each, in a completely randomised design. Birds were fed ad libitum or were pair-fed to 50%, 60%, 70%, 80% or 90% of normal ad libitum intakes from 8 to 49 d to provide a gradual reduction in growth rate. Ultrasound images were obtained weekly from all birds and, in parallel, one bird per pen was weekly slaughtered and the major breast muscle was weighed and WB graded as 0 (normal), 1 (mild hardening in the upper), 2 (moderate hardening in the upper and/or lower), 3 (severe hardening) and 4 (severe hardening with haemorrhagic lesions and yellow fluid). Blood was taken for analysis of enzymes related to muscle cell breakdown. 3. Feed restriction applied at 50%, 60%, 70%, 80% and 90% of the ad libitum feed intake (FI) resulted in decreased body weight gain (BWG; P ≤ 0.05). 4. From 21 to 49 d, the increasing feed restriction led to linear increases (P ≤ 0.05) in WB scores, fibre density as well as breast depth and breast echogenicity. Creatine kinase, lactate dehydrogenase and aspartate aminotransferase concentration decreased linearly when broilers were feed restricted (P ≤ 0.05). 5. Wooden breast was positively correlated with echogenicity at 21 d (r = 0.510), 28 (r = 0.531), 35 (r = 0.470), 42 (r = 0.430) and 49 d (r = 0.548) (P ≤ 0.001). The use of breast echogenicity can be an additional tool to early detect alterations related to wooden breast.

A 51 bp indel polymorphism within the PTH1R gene is significantly associated with chicken growth and carcass traits

Parathyroid hormone (PTH) is a crucial regulator of calcium homeostasis and bone remodeling, and the parathyroid hormone 1 receptor (PTH1R) belongs to a class II G-protein-coupled receptor. PTH activates PTH1R, which mediates catabolic and anabolic processes in the skeleton. However, the functional mechanism of PTH1R has not been thoroughly elucidated in organisms. This study identified a 51 bp indel mutation in the first intron of the PTH1R gene and elucidated the effect of this gene mutation on the growth and carcass traits in chickens. The results indicated that the 51 bp indel was significantly associated with subcutaneous fat thickness, abdominal fat weight, body weight and daily gain over 4-8 weeks. Furthermore, we found that PTH1R gene expression was highest in the kidney and liver tissues, and it showed a trend of decreasing in leg and breast muscle tissues at different embryonic stages. In addition, we examined the expression of the three genotypes of the PTH1R gene in the liver, breast muscle and abdominal fat and found that the II genotype was significantly higher than the DD and ID genotypes. In summary, these findings suggest that the PTH1R gene can serve as a potential molecular marker for chicken breeding.

Genetic parameters for performance and carcass traits in a paternal 1 lineage of broiler

The objective of this study was to estimate variance components for performance and carcass traits in a paternal broiler line. The (co)variance components were estimated by the restricted maximum likelihood method applied to the animal model, including the fixed effect of group (sex and hatch) and additive genetic and residual as random effects. Estimated heritability for performance traits ranged from 0.09 to 0.42. The genetic correlations between traits ranged from -0.50 to 0.97. The heritability estimates of feed intake, weight gain, and feed conversion from 35 to 41 days of age were of low magnitude. The genetic correlations among them were favorable to genetic selection. These results suggest that moderate genetic gain can be obtained to the feed intake and weight gain when the selection criterion is the body weight and prime cuts traits. The feed conversion that had low heritability estimation and low genetic correlation with the body weight and prime cut traits needs to pay greater attention due to the economic importance in the high-meat production lineage breeding programs.

Detection of CNV in the SH3RF2 gene and its effects on growth and carcass traits in chickens

BACKGROUND

The SH3RF2 gene is a protein-coding gene located in a quantitative trait locus associated with body weight, and its deletion has been shown to be positively associated with body weight in chickens.

RESULTS

In the present study, CNV in the SH3RF2 gene was detected in 4079 individuals from 17 populations, including the "Gushi ×Anka" F2 resource population and populations of Chinese native chickens, commercial layers, and commercial broilers. The F2 resource population was then used to investigate the genetic effects of the chicken SH3RF2 gene. The results showed that the local chickens and commercial layers were all homozygous for the wild-type allele. Deletion mutation individuals were detected in all of the commercial broiler breeds except Hubbard broiler. A total of, 798 individuals in the F2 resource group were used to analyze the effects of genotype (DD/ID/II) on chicken production traits. The results showed that CNV was associated with 2-, 6-, 10-, and 12-week body weight (P = 0.026, 0.042, 0.021 and 0.039 respectively) and significantly associated with 8-week breast bone length (P = 0.045). The mutation was significantly associated with 8-week body weight (P = 0.007) and 4-week breast bone length (P = 0.010). CNV was significantly associated with evisceration weight, leg muscle weight, carcass weight, breast muscle weight and gizzard weight (P = 0.032, 0.033, 0.045, 0.004 and 0.000, respectively).

CONCLUSIONS

CNV of the SH3RF2 gene contributed to variation in the growth and weight gain of chickens.

Association of a new 99-bp indel of the CEL gene promoter region with phenotypic traits in chickens

Carboxyl ester lipase (CEL) encodes a cholesterol ester hydrolase that is secreted into the duodenum as a component of pancreatic juice. The objective of this study was to characterize the CEL gene, investigate the association between the CEL promoter variants and chicken phenotypic traits, and explore the CEL gene regulatory mechanism. An insertion/deletion (indel) caused by a 99-bp insertion fragment was shown for the first time in the chicken CEL promoter, and large differences in allelic frequency were found among commercial breeds, indigenous and feral birds. Association analysis demonstrated that this indel site had significant effects on shank length, shank girth, chest breadth at 8 weeks (p < 0.01), evisceration weight, sebum weight, breast muscle weight, and leg weight (p < 0.05). Tissue expression profiles showed extremely high levels of the CEL gene in pancreatic tissue. Moreover, the expression levels of the genes APOB, MTTP, APOV1 and SREBF1, which are involved in lipid transport, were significantly reduced by adding a 4% oxidized soybean oil diet treatment at the individual level and transfecting the embryonic primary hepatocytes with a CEL-overexpression vector. Interestingly, the results showed that the expression level of the II homozygous genotype was significantly higher than that of the ID and DD genotypes, while individuals with DD genotypes had higher phenotypic values. Therefore, these data suggested that the CEL gene might affect body growth by participating in hepatic lipoprotein metabolism and that the 99-bp indel polymorphism could be a potentially useful genetic marker for improving the economically important traits of chickens.

Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach

Background

Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F₂ Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations.

Results

Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F₂ population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1–4, 6–7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens.

Conclusions

The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.

Genetic evaluation for latent variables derived from factor analysis in broilers

1. The aim of this study was to investigate the associations between several carcass, performance and meat quality traits in broilers through factor analysis and use the latent variables (i.e. factors) as pseudo-phenotypes in genetic evaluations.2. Factors were extracted using the principal components method and varimax rotation algorithm. Genetic parameters were estimated via Bayesian inference under a multiple-trait animal model.3. All factors taken together explained 71% of the original variance of the data. The first factor, denominated as 'weight', was associated with carcass and body weight traits; and the second factor, defined as 'tenderness', represented traits related to water-holding capacity and shear force. The third factor, 'colour', was associated with traits related to meat colour, whereas the fourth, referenced as 'viscera', was related to heart, liver and abdominal fat.4. The four biological factors presented moderate to high heritability (ranging from 0.35 to 0.75), which may confer genetic gains in this population.5. In conclusion, it seems possible to reduce the number of traits in the genetic evaluation of broilers using latent variables derived from factor analysis.

Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens

Background

Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes in internal organ weights and increased incidence of metabolic disorders. These disorders can affect feed efficiency or even cause death. We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, and identify genomic regions and positional candidate genes (PCGs) associated with internal organ traits in an F2 chicken population. We integrated knowledge of haplotype blocks, selection signature regions and sequencing data to refine the list of PCGs.

Results

Estimated genomic heritability for internal organ traits in chickens ranged from low (LUNGWT, 0.06) to high (GIZZWT, 0.45). A total of 20 unique 1 Mb windows identified on GGA1, 2, 4, 7, 12, 15, 18, 19, 21, 27 and 28 were significantly associated with intestine length, and weights or percentages of liver, gizzard or lungs. Within these windows, 14 PCGs were identified based on their biological functions: TNFSF11, GTF2F2, SPERT, KCTD4, HTR2A, RB1, PCDH7, LCORL, LDB2, NR4A2, GPD2, PTPN11, ITGB4 and SLC6A4. From those genes, two were located within haplotype blocks and three overlapped with selection signature regions. A total of 13,748 annotated sequence SNPs were in the 14 PCGs, including 156 SNPs in coding regions (124 synonymous, 26 non-synonymous, and 6 splice variants). Seven deleterious SNPs were identified in TNFSF11, NR4A2 or ITGB4 genes.

Conclusions

The results from this study provide novel insights to understand the genetic architecture of internal organ traits in chickens. The QTL detection performed using a high density SNP array covered the whole genome allowing the discovery of novel QTL associated with organ traits. We identified PCGs within the QTL involved in biological processes that may regulate internal organ growth and development. Potential functional genetic variations were identified generating crucial information that, after validation, might be used in poultry breeding programs to reduce the occurrence of metabolic disorders.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6040-3) contains supplementary material, which is available to authorized users.

Molecular characterization and an 80-bp indel polymorphism within the prolactin receptor (PRLR) gene and its associations with chicken growth and carcass traits

The prolactin receptor (PRLR), a type I cytokine receptor, must bind prolactin (PRL) to act on target cells to mediate various physiological functions, including reproduction and lactation. This study identified an 80-bp insertion/deletion (indel) polymorphism in the 3'-untranslated region (3'-UTR) of the chicken PRLR gene in 3736 individuals from 15 breeds and analyzed its associations with growth and carcass traits in an F₂ resource population. The results of the association analysis indicated that the 80-bp indel polymorphism was significantly (P < 0.05) or very significantly (P < 0.01) associated with multiple growth and carcass traits, such as body weight, leg weight, and shank length. In addition, we found that during the breeding process of commercial laying hens and commercial broilers, the 80-bp indel locus was artificially selected for the II genotype. Together, our findings reveal that this 80-bp indel polymorphism has potential as a new molecular marker for marker-assisted selection of chicken growth and carcass traits.

The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens

The gut microbiota has an important role in animal health and performance, but its contribution is difficult to determine, in particular given the effects of host genetic factors. Here, whole-genome sequencing of the hosts and 16S rRNA gene sequencing of the microbiota were performed to separate the effects between host genetics and the microbiota in the duodenum, jejunum, ileum, caecum and faeces on fat deposition in 206 yellow broilers reared under identical conditions. Despite the notable spatial variation in the diversity, composition and potential function of the gut microbiota, host genetics exerted limited effects on the gut microbial community. The duodenal and caecal microbiota made greater contributions to fat deposition and could separately account for 24% and 21% of the variance in the abdominal fat mass after correcting for host genetic effects. We further identified two caecal microbial taxa, Methanobrevibacter and Mucispirillum schaedleri, which were significantly correlated with fat deposition. Chickens with a lower Methanobrevibacter abundance had significantly lower abdominal fat content than those with a higher abundance of Methanobrevibacter (35.51 vs. 55.59 g), and the body weights of these chickens did not notably differ. Chickens with a higher M. schaedleri abundance exhibited lower abdominal fat accumulation (39.88 vs. 55.06 g) and body weight (2.23 vs. 2.41 kg) than those with a lower abundance of this species. These findings may aid the development of strategies for altering the gut microbiota to control fat deposition during broiler production.

A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Background

Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken’s carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds.

Results

ABF and SKIN are moderately heritable traits in our broiler population with estimates ranging from 0.23 to 0.33. Using a high density SNP panel (355,027 informative SNPs), we detected nine unique QTLs that were associated with these fat traits. Among these, four QTL were novel, while five have been previously reported in the literature. Thirteen PCGs were identified that might regulate fat deposition in these QTL regions: JDP2, PLCG1, HNF4A, FITM2, ADIPOR1, PTPN11, MVK, APOA1, APOA4, APOA5, ENSGALG00000000477, ENSGALG00000000483, and ENSGALG00000005043. We used sequence information from founder animals to detect 4843 SNPs in the 13 PCGs. Among those, two were classified as potentially deleterious and two as high impact SNPs.

Conclusions

This study generated novel results that can contribute to a better understanding of fat deposition in chickens. The use of high density array of SNPs increases genome coverage and improves QTL resolution than would have been achieved with low density. The identified PCGs were involved in many biological processes that regulate lipid storage. The SNPs identified in the PCGs, especially those predicted as potentially deleterious and high impact, may affect fat deposition. Validation should be undertaken before using these SNPs for selection against carcass fat accumulation and to improve feed efficiency in broiler chicken production.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4779-6) contains supplementary material, which is available to authorized users.

Selection response and estimation of the genetic parameters for multidimensional measured breast meat yield related traits in a long-term breeding Pekin duck line

Objective

This study was conducted to estimate the genetic parameters and breeding values of breast meat related traits of Pekin ducks. Selection response was also determined by using ultrasound breast muscle thickness (BMT) measurements in combination with bosom breadth (BB) and keel length (KL) values.

Methods

The traits analyzed were breast meat weight (BMW), body weight (BW), breast meat percentage (BMP) and the three parameters of breast meat (BB, KL, and BMT). These measurements were derived from studying 15,781 Pekin ducks selected from 10 generations based on breast meat weight. Genetic parameters and breeding value were estimated for the analysis of the breeding process.

Results

Estimated heritability of BMW and BMP were moderate (0.23 and 0.16, respectively), and heritability of BW was high (0.48). Other traits such as BB, KL, and BMT indicated moderate heritability ranging between 0.11 and 0.28. Significant phenotypic correlations of BMW with BW and BMP were discovered (p<0.05), and genetic correlations of BMW with BW and BMP were positive and high (0.83 and 0.66, respectively). It was noted that BMW had positive correlations with all the other traits. Generational average estimated breeding values of all traits increased substantially over the course of selection, which demonstrated that the ducks responded efficiently to increased breast meat yield after 10 generations of breeding.

Conclusion

The results indicated that duck BMW had the potential to be increased through genetic selection with positive effects on BW and BMP. The ultrasound BMT, in combination with the measurement of BB and KL, is shown to be essential and effective in the process of high breast meat yield duck breeding.

Artificial selection for improved energy efficiency is reaching its limits in broiler chickens

Modern broiler chickens are a major animal husbandry success story, both in terms of efficient resource utilisation and environmental sustainability. However, continuing artificial selection for both efficiency and rapid growth will be subject to both biological limits and animal welfare concerns. Using a novel analytical energy flow modelling approach, we predict how far such selection can go, given the biological limits of bird energy intake and partitioning of energy. We find that the biological potential for further improvements in efficiency, and hence environmental impact reduction, is minimal relative to past progress already made via artificial selection. An alternative breeding strategy to produce slower-growing birds to meet new welfare standards increases environmental burdens, compared to current birds. This unique analytic approach provides biologically sound guidelines for strategic planning of sustainable broiler production.

Use and optimization of different sources of information for genomic prediction

Background

Molecular data is now commonly used to predict breeding values (BV). Various methods to calculate genomic relationship matrices (GRM) have been developed, with some studies proposing regression of coefficients back to the reference matrix of pedigree-based relationship coefficients (A). The objective was to compare the utility of two GRM: a matrix based on linkage analysis (LA) and anchored to the pedigree, i.e. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}_{{{\mathbf{LA}}}} ,$$\end{document}GLA, and a matrix based on linkage disequilibrium (LD), i.e. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}_{{{\mathbf{LD}}}}$$\end{document}GLD, using genomic and phenotypic data collected on 5416 broiler chickens. Furthermore, the effects of regressing the coefficients of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}_{{{\mathbf{LD}}}}$$\end{document}GLD back to A (LDA) and to \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}_{{{\mathbf{LA}}}}$$\end{document}GLA (LDLA) were evaluated, using a range of weighting factors. The performance of the matrices and their composite products was assessed by the fit of the models to the data, and the empirical accuracy and bias of the BV that they predicted. The sensitivity to marker choice was examined by using two chips of equal density but including different single nucleotide polymorphisms (SNPs).

Results

The likelihood of models using GRM and composite matrices exceeded the likelihood of models based on pedigree alone and was highest with intermediate weighting factors for both the LDA and LDLA approaches. For these data, empirical accuracies were not strongly affected by the weighting factors, although they were highest when different sources of information were combined. The optimum weighting factors depended on the type of matrices used, as well as on the choice of SNPs from which the GRM were constructed. Prediction bias was strongly affected by the chip used and less by the form of the GRM.

Conclusions

Our findings provide an empirical comparison of the efficacy of pedigree and genomic predictions in broiler chickens and examine the effects of fitting GRM with coefficients regressed back to a reference anchored to the pedigree, either A or \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}_{{{\mathbf{LA}}}}$$\end{document}GLA. For the analysed dataset, the best results were obtained when \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}_{{{\mathbf{LD}}}}$$\end{document}GLD was combined with relationships in A or \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}_{{{\mathbf{LA}}}}$$\end{document}GLA, with optimum weighting factors that depended on the choice of SNPs used. The optimum weighting factor for broiler body weight differed from weighting factors that were based on the density of SNPs and theoretically derived using generalised assumptions.

Genetic aspects of feed efficiency and reduction of environmental footprint in broilers: a review

Currently, optimization of feed efficiency is one of the main challenges in improvement programs of livestock and poultry genetics. The objective of this review is to present the genetic aspects of feed efficiency related traits in meat-type chicken and possible ways to reduce the environmental impact of poultry meat production with effective breeding. Basic measures of feed efficiency are defined and the genetic background of these traits, including a review of heritabilities is described. Moreover, a number of genomic regions and candidate genes determining feed efficiency traits of broilers that were detected over the past decades are described. Classical and genomic selection strategies for feed efficiency in the context of its relationships with other performance traits are discussed as well. Finally, future strategies to improve feed digestibility are described as it is expected that they will decrease wastes and greenhouse gas emission. Further genetic improvement of feed efficiency, should be examined jointly with appropriate feeding strategies in broilers.

Evaluation of fatty acid metabolism and innate immunity interactions between commercial broiler, F1 layer × broiler cross and commercial layer strains selected for different growth potentials

Background

The broiler industry has undergone intense genetic selection over the past 50 yr. resulting in improvements for growth and feed efficiency, however, significant variation remains for performance and growth traits. Production improvements have been coupled with unfavourable metabolic consequences, including immunological trade-offs for growth, and excess fat deposition. To determine whether interactions between fatty acid (FA) metabolism and innate immunity may be associated with performance variations commonly seen within commercial broiler flocks, total carcass lipid %, carcass and blood FA composition, as well as genes involved with FA metabolism, immunity and cellular stress were investigated in male birds of a broiler strain, layer strain and F1 layer × broiler cross at d 14 post hatch. Heterophil: lymphocyte ratios, relative organ weights and bodyweight data were also compared.

Results

Broiler bodyweight (n = 12) was four times that of layers (n = 12) by d 14 and had significantly higher carcass fat percentage compared to the cross (n = 6; P = 0.002) and layers (P = 0.017) which were not significantly different from each other (P = 0.523). The carcass and whole blood FA analysis revealed differences in the FA composition between the three groups indicating altered FA metabolism, despite all being raised on the same diet. Genes associated with FA synthesis and β-oxidation were upregulated in the broilers compared to the layers indicating a net overall increase in FA metabolism, which may be driven by the larger relative liver size as a percentage of bodyweight in the broilers. Genes involved in innate immunity such as TLR2 and TLR4, as well as organelle stress indicators ERN1 and XBP1 were found to be non-significant, with the exception of high expression levels of XBP1 in layers compared to the cross and broilers. Additionally there was no difference in heterophil: lymphocytes between any of the birds.

Conclusions

The results provide evidence that genetic selection may be associated with altered metabolic processes between broilers, layers and their F1 cross. Whilst there is no evidence of interactions between FA metabolism, innate immunity or cellular stress, further investigations at later time points as growth and fat deposition increase would provide useful information as to the effects of divergent selection on key metabolic and immunological processes.

Genome-wide association study for performance traits in chickens using genotype by sequencing approach

Performance traits are economically important and are targets for selection in breeding programs, especially in the poultry industry. To identify regions on the chicken genome associated with performance traits, different genomic approaches have been applied in the last years. The aim of this study was the application of CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) on Genome-Wide Association Studies (GWAS) in an outbred F₂ chicken population. We have validated 91.7% of these 134,528 SNPs after imputation of missed genotypes. Out of those, 20 SNPs were associated with feed conversion, one was associated with body weight at 35 days of age (P < 7.86E-07) and 93 were suggestively associated with a variety of performance traits (P < 1.57E-05). The majority of these SNPs (86.2%) overlapped with previously mapped QTL for the same performance traits and some of the SNPs also showed novel potential QTL regions. The results obtained in this study suggests future searches for candidate genes and QTL refinements as well as potential use of the SNPs described here in breeding programs.

Effect of housing environment on laying hen meat quality: Assessing Pectoralis major pH, colour and tenderness in three strains of 80-81 week-old layers housed in conventional and furnished cages

1. Meat quality is affected by factors such as stress, genetic strain and activity and is determined in part by measures of pH, colour and tenderness. In conventional laying hen cages (CC), lack of physical space and inability to perform highly motivated behaviours leads to stress and inactivity. Furnished cages (FCs) permit expression of highly motivated behaviours, but typically house larger group sizes than CC, thereby contributing to social stress. The objective of this study was to evaluate the effects of CC and FC laying hen housing environments and strain differences on meat quality of 80-81-week-old birds. 2. Pectoralis major meat quality was assessed for two flocks of Shaver White (SH), Lohmann Lite (LL) and Lohmann Brown (LB) hens housed in either 5-hen CC or 40-hen FC. Between 80 and 81 weeks, muscle samples were collected from randomly selected hens and analysed for muscle pH, colour and shear force (SF) using established methods. 3. In both flocks, the combined treatment body weights (BWs) were higher for CC than FC hens and the combined strain BWs were higher for LB than LL and SH hens. Flock 1 LB had lower initial and ultimate pH than SH and LL, and greater pH decline than SH. Muscle redness (a*) was higher for CC SH than FC SH in both flocks. Muscle a* was higher for LL than SH and LB in Flock 1, and higher than SH in Flock 2. Housing differences in muscle SF were absent. In CC, SF was higher for SH than LL and LB in Flock 1, and higher than LB in Flock 2. 4. Lack of housing differences suggests that environmental stressors present in both housing systems similarly affected meat quality. Strain differences for muscle pH, a* and SF indicate increased stress experienced by SH and LL hens. The absence of Flock 2 strain differences is consistent with the cannibalism outbreak that occurred in this flock and most severely impacted LB hens.

A short insertion mutation disrupts genesis of miR-16 and causes increased body weight in domesticated chicken

Body weight is one of the most important quantitative traits with high heritability in chicken. We previously mapped a quantitative trait locus (QTL) for body weight by genome-wide association study (GWAS) in an F2 chicken resource population. To identify the causal mutations linked to this QTL, expression profiles were determined on livers of high-weight and low-weight chicken lines by microarray. Combining the expression pattern with SNP effects by GWAS, miR-16 was identified as the most likely potential candidate with a 3.8-fold decrease in high-weight lines. Re-sequencing revealed that a 54-bp insertion mutation in the upstream region of miR-15a-16 displayed high allele frequencies in high-weight commercial broiler line. This mutation resulted in lower miR-16 expression by introducing three novel splicing sites instead of the missing 5′ terminal splicing of mature miR-16. Elevating miR-16 significantly inhibited DF-1 chicken embryo cell proliferation, consistent with a role in suppression of cellular growth. The 54-bp insertion was significantly associated with increased body weight, bone size and muscle mass. Also, the insertion mutation tended towards fixation in commercial broilers (Fst > 0.4). Our findings revealed a novel causative mutation for body weight regulation that aids our basic understanding of growth regulation in birds.

Genetic parameters for growth characteristics of free-range chickens under univariate random regression models

Repeated measures from the same individual have been analyzed by using repeatability and finite dimension models under univariate or multivariate analyses. However, in the last decade, the use of random regression models for genetic studies with longitudinal data have become more common. Thus, the aim of this research was to estimate genetic parameters for body weight of four experimental chicken lines by using univariate random regression models. Body weight data from hatching to 84 days of age (n = 34,730) from four experimental free-range chicken lines (7P, Caipirão da ESALQ, Caipirinha da ESALQ and Carijó Barbado) were used. The analysis model included the fixed effects of contemporary group (gender and rearing system), fixed regression coefficients for age at measurement, and random regression coefficients for permanent environmental effects and additive genetic effects. Heterogeneous variances for residual effects were considered, and one residual variance was assigned for each of six subclasses of age at measurement. Random regression curves were modeled by using Legendre polynomials of the second and third orders, with the best model chosen based on the Akaike Information Criterion, Bayesian Information Criterion, and restricted maximum likelihood. Multivariate analyses under the same animal mixed model were also performed for the validation of the random regression models. The Legendre polynomials of second order were better for describing the growth curves of the lines studied. Moderate to high heritabilities (h(2) = 0.15 to 0.98) were estimated for body weight between one and 84 days of age, suggesting that selection for body weight at all ages can be used as a selection criteria. Genetic correlations among body weight records obtained through multivariate analyses ranged from 0.18 to 0.96, 0.12 to 0.89, 0.06 to 0.96, and 0.28 to 0.96 in 7P, Caipirão da ESALQ, Caipirinha da ESALQ, and Carijó Barbado chicken lines, respectively. Results indicate that genetic gain for body weight can be achieved by selection. Also, selection for body weight at 42 days of age can be maintained as a selection criterion.

Differential expression of feeding-related hypothalamic neuropeptides in the first generation of quails divergently selected for low or high feed efficiency

Livestock and poultry sectors are facing a combination of challenges, including a substantial increase in global demand for high quality animal protein, general droughts and steady rise in animal feed cost. Thus feed efficiency (FE), which defines the animal's ability to convert feed into body weight, is a vital economic and agricultural trait. Genetic selection for FE has been largely used in chickens and has been applied without knowledge of the underlying molecular mechanisms. Although it has made tremendous progress (breast yield, growth rate, egg production), there have been a number of undesirable changes such as metabolic disorders. In the present study we divergently selected male and female quail for high and low FE and we aimed to characterize the molecular basis of these differences at the central level, with the long-term goal of maximizing FE and avoiding the unfavorable consequences. The FE phenotype in first generation quails seemed to be achieved by reduced feed intake in female and increased body weight gain in males. At the molecular level, we found that the expression of feeding-related hypothalamic genes is gender- and line-dependent. Indeed, the expression of NPY, POMC, CART, CRH, melanocortin system (MC1R, MC2R, MC4R, MC5R), ORX, mTOR and ACCα was significantly decreased, however ORXR1/2, AMPKα1, S6K1 and STAT1, 5 and 6 were increased in high compared to low FE males (P<0.05). These genes did not differ between the two female lines. ADPN gene expression was higher and its receptor Adip-R1 was lower in LFE compared to HFE females (P<0.05). In male however, although there was no difference in ADPN gene expression between the genotypes, Adip-R1 and Adip-R2 mRNA abundances were higher in the LFE compared to HFE line (P<0.05). This study identified several key central feeding-related genes that are differentially expressed between low and high FE male and female quails which might explain the differences in feed intake/body weight gain observed between the two lines. Of particular interest, we provided novel insights into central AMPK-mTOR-ACC transcriptional differences between low and high FE quail which may open new research avenues on their roles in the regulation of energy balance and FE in poultry and livestock species.

Genetic parameters of feed efficiency traits in laying period of chickens

Laying records on 1,534 F₂ hens, derived from a reciprocal cross between White Leghorns and Dongxiang blue-shelled chickens, were used to estimate genetic parameters for residual feed intake (RFI), feed conversion ratio (FCR), daily feed intake (FI), metabolic BW (MBW), BW gain (BWG), and daily egg mass (EM) at 37 to 40 (T1) and 57 to 60 wk age (T2), respectively. Genetic analysis was subsequently conducted with the AI-REML method using an animal model. Estimates for heritability of RFI, FCR, and FI were 0.21, 0.19, and 0.20 in T1, and 0.29, 0.13, and 0.26 in T2, respectively. In T1 and T2, RFI showed high and positive genetic correlations with FCR (0.51, 0.43) and FI (0.72, 0.84), whereas the genetic correlation between FI and FCR was very low (−0.09, 0.11). Genetically, negative correlations were found between RFI and its component traits (−0.01 to −0.47). In addition, high genetic correlations, from 0.76 to 0.94, were observed between T1 and T2 for RFI, FCR, and FI, suggesting that feed efficiency traits in the 2 stages had a similar genetic background. The results indicate that selection for low RFI could reduce FI without significant changes in EM, while selection on FCR will increase EM. The present study lays the foundation for genetic improvement of feed efficiency during the laying period of chickens.

Genetic evaluation of carcass traits in Japanese quail using ultrasonic and morphological measurements

1. A study was conducted to evaluate the carcass composition of 1083 live birds using ultrasonic and morphological measurements and to estimate the genetic relationship between predicted and dissected carcass composition in Japanese quail. 2. Birds were reared for 35 d, and morphological measurements consisting of the length and width of breast muscle were recorded for all birds using a digital caliper. After slaughtering, the weight and percentage of carcass traits were measured on chilled carcasses. The dimensions of breast muscle were measured in 638 birds with an ultrasound scanner before slaughter at 35 d of age. 3. Genetic parameters from univariate and bivariate analyses were obtained by restricted maximum likelihood using ASREML software. 4. Genetic correlations between body weight at 35 d (BW35) and the percentage of carcass traits were low. Therefore, selection for BW35 may not effectively improve the yield of carcass components in Japanese quail. 5. High genetic correlations between carcass traits and ultrasonic measurements compared to morphological measurements suggest that the ultrasonic technique is a better method to improve breast weight and yield in Japanese quail.

Correlated responses and genetic parameters for performance and carcass traits in a broiler line

The growth rate of broilers has triplicated in the last decades. The body weight is used as one of the selection criteria whereas the carcass traits are valuable market requirements. Thus, the meat industry like animals with high weights at slaughter and better carcass traits. However, the genetic relation of carcass traits with several body weights is unknown. Therefore, we established genetic associations among performance and carcass traits in a broiler chicken line and estimated genetic gain and trends. We also evaluated what age of selection would lead to a more efficient indirect selection of carcass traits. The data set with information of weights in different ages and carcass traits of 128,459 chickens was used. The pedigree data used contained 132,442 chickens. Genetic analysis were realized using ASREML® software applied a restricted maximum likelihood method. Heritability estimates ranged from moderate to high, which indicates that these traits can have high selection response. Genetic correlations between performance and carcass traits varied from moderate to high, which indicates the presence of a genetic association whereas genetic trends indicated that direct selection is occurring for body weight at different ages. Theselection at 30 and 38 days should be considered instead of the slaughter weight, as it anticipates selection in around 12 days.

Genetic variability of metabolic characteristics in chickens selected for their ability to digest wheat

Improving feed efficiency remains crucial for poultry production. Birds have previously been selected on their ability to digest their diet, as assessed by AMEn (Apparent ME corrected for 0 nitrogen). Such selection, for either a high (D+) or a low AMEn (D-), affects energy, nitrogen, lipid, and starch digestibility. The aim of this study was to establish whether selection on the digestive ability of birds modified metabolic traits. A total of 630 broiler chickens of the eighth generation of a divergent selection experiment on AMEn were used for this purpose. A balance trial was performed to determine energy, nitrogen, and phosphorus retention. Growth performance was recorded and body protein and lipid deposition assessed by breast and abdominal fat yields. Tibia development and mineralization were also studied and heat production was indirectly assessed through the measurement of body temperature during fasting and feeding. Phenotypic correlations estimated within line showed that an increased efficiency was associated to fatter birds and more solid bones in D- but not in D+ line, whereas increased consumption was associated with more solid bones in D+ but not in D- line. The heritability estimates for metabolic traits were relatively high, except for temperature traits (from 0.08 to 0.12), ranging from 0.28 to 0.56 for body composition, and from 0.38 to 0.77 for bone characteristics. Breast meat yield did not differ between the 2 lines whereas a slight increase in abdominal fat yield was observed in the high-digestion line (D+). The relative dry tibia weights and ash weights were greater in D+ birds (+6.56 and +8.06%, respectively) but the lengths and the diameters of the tibia were lower (-7.89 and -3.77%, respectively). Finally, AMEn was poorly correlated with almost all metabolic traits (ranging from -0.10 to 0.20), indicating that the ability of the animal to digest its diet is genetically independent of post-digestion metabolic traits.

Identification and association of polymorphisms in CAPN1 and CAPN3 candidate genes related to performance and meat quality traits in chickens

Meat quality is an important feature for the poultry industry and is associated with consumer satisfaction. The calpain 1 (CAPN1) gene is related to the tenderness process of meat post- mortem, and the calpain 3 (CAPN3) gene plays an important role in myofibrillar organization and growth. The objective of the present study was to identify polymorphisms in these genes and to determine the association between these polymorphisms and traits of economic interest in poultry. Eleven animals (F₁) from an experimental poultry population at Embrapa Swine and Poultry were used to identify the polymorphisms. Four single nucleotide polymorphisms (SNPs) were found in the CAPN1 gene, and one SNP was found in the CAPN3 gene. A polymorphism from each gene was selected for genotyping in 152 chickens from the Embrapa F₂ experimental population and 311 chickens from a commercial population. Polymorphism g.2554T>C (CAPN1) was associated with body weight at 35 to 42 days, thigh weight, breast weight, carcass weight, and meat lightness content. SNP g.15486C>T (CAPN3) was associated with thigh yield, thawing-cooking loss, and shear force. Results suggest the possibility of using molecular markers in CAPN1 and CAPN3 genes as a tool for performance and meat quality traits in poultry breeding programs.

Polymorphisms in FGFBP1 and FGFBP2 genes associated with carcass and meat quality traits in chickens

In the past, the focus of broiler breeding programs on yield and carcass traits improvement led to problems related to meat quality. Awareness of public concern for quality resulted in inclusion of meat quality traits in the evaluation process. Nevertheless, few genes associated with meat quality attributes are known. Previous studies mapped quantitative trait loci for weight at 35 and 42 days in a region of GGA4 flanked by the microsatellite markers, MCW0240 and LEI0063. In this region, there are 2 fibroblast growth factor binding protein (FGFBP) genes that play an important role in embryogenesis, cellular differentiation, and proliferation in chickens. The objective of this study was to identify and associate single nucleotide polymorphisms (SNPs) in FGFBP1 and FGFBP2 with performance, carcass, and meat quality in experimental and commercial chicken populations. In the commercial population, SNP g.2014G>A in FGFBP1 was associated with decreased carcass weight (P < 0.05), and SNP g.651G>A in FGFBP2 was associated with thawing loss and meat redness content (P < 0.05). Four haplotypes were constructed based on 2 SNPs and were associated with breast weight, thawing loss, and meat redness content. The diplotypes were associated with thawing loss, lightness, and redness content. The SNPs evaluated in the present study may be used as markers in poultry breeding programs to aid in improving growth and meat quality traits.