Multi-trait estimation of genetic parameters for body weight in a commercial broiler chicken population

The use of partially slatted floor designs as an alternative to littered systems in broiler chickens. I. The effects on the performance, slaughter and carcass traits

In this study, the effects of fully littered, slatted and their varying combinations on growth, performance, carcass and meat quality characteristics in broiler chickens were investigated. In the experiment, five treatment groups were formed as fully littered (FL), fully slatted (FS), 1/3 littered + 2/3 slatted (2/3 SF), 1/2 littered + 1/2 slatted (1/2SF), 2/3 littered + 1/3 slatted (1/3 SF). Each treatment group included 5 replicates (24 chicks in each) and a total of 600 male-female mixed fast growing broiler chicks (Ross-308) were used during 6 weeks. Weekly body weight (BW, g), feed intake (FI, g), feed conversion ratio (FCR, g.feed intake/g.weight gain), livability (%) and EPEF (European Production Efficiency Factor) were determined as performance characteristics. Carcass yield (CY, %), and the percentages of abdominal fat (AFP, %), edible internal organs (EIOP, %), gizzard (GP, %), breast (BRP, %) and thigh (TP, %) meat were the carcass characteristics. Meat quality measured by pH and color (L*: lightness, a*: redness, b*: yellowness) of breast and thigh meat, and occurrence of white striping and hemorrhaging in breast meat. The weekly BW differences among the floor treatments were significant (P < 0.01), and 1/3SF broilers were the heaviest at slaughter age (3311.6 g). The 6-week FCR in FS broilers was significantly worse than the others (1.471), but FI, livability and EPEF were similar among treatments. AFP tended to be higher in FL birds (P = 0.066), while CY, EIOP, GP, BRP and TP did not differ between groups. Breast pH was similar between treatments, with 1/2SF showing the highest (6.34) and FL the lowest (6.24) breast pH (P < 0.01). The partially slatted systems caused lighter, redder and yellower color values in breast meat (P < 0.01) than the fully littered or slatted systems, but did not change the color of the thigh meat. White striping and hemorrhaging in breast meat were not affected by the floor treatments. This study suggests that the use of partially slatted systems in broiler chickens improves meat color without compromising performance traits (body weight, feed efficiency, EPEF), litter moisture and slaughter traits and these systems could be an alternative to fully littered systems.

Sex-specific genetic parameter estimates of body weight in Mazandaran indigenous chickens

Body weight is an economically important trait in poultry that shows sexual dimorphism (SD). In the present study, variation in SD in Mazandaran native chickens was investigated in terms of the (Co) variance components and genetic parameters of body weight between males and females. Studied traits were body weights at hatch (BW1), 8 weeks (BW8) and 12 weeks of age (BW12). Also, for weight at sexual maturity (WSM) covariance components were only estimated in females. Cross-sex direct and maternal correlations were also estimated for studied traits except for WSM. For this purpose, a deep 21-generation pedigree and body weight data (57,576 BW1, 72,925 BW8, 62,727 BW12 and, 42,496 WSM) were used. Evaluation of SD of body weight was performed using six bivariate animal models with and without considering the genetic and permanent maternal environmental effects under the restricted maximum likelihood method in WOMBAT software. Model with direct additive genetic effects and maternal genetic effects without covariance between them was identified as the best model for BW1 and BW8. The Model including direct additive genetic effects and permanent maternal environmental effects was the best model for BW12 and WSM. Direct heritability (h2) estimates for BW1, BW8 and, BW12 were, respectively, 0.05 ± 0.013, 0.17 ± 0.02 and, 0.25 ± 0.03 in males and, 0.05 ± 0.012, 0.15 ± 0.01 and 0.21 ± 0.01 in females. Also, the direct heritability of WSM based on univariate analysis in females was estimated to be 0.40 ± 0.01. Maternal heritability (h m 2 ) varied from 0.39 ± 0.01 (BW1) to 0.04 ± 0.009 (BW8) in males, and 0.36 ± 0.10 (BW1) to 0.04 ± 0.006 (BW8) in females. The correlation between direct genetic effects between males and females for BW1 was not significantly different from one. The direct genetic correlation between the two sexes for BW8 and BW12 was significantly different from 1 concluding that these traits are dimorphic in terms of direct genetic effects and therefore independent selection in both sexes is possible.

Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits

Monitoring the genetic variance of traits is a key priority to ensure the sustainability of breeding programmes in populations under directional selection, since directional selection can decrease genetic variation over time. Studies monitoring changes in genetic variation have typically used long-term data from small experimental populations selected for a handful of traits. Here, we used a large dataset from a commercial breeding line spread over a period of twenty-three years. A total of 2,059,869 records and 2,062,112 animals in the pedigree were used for the estimations of variance components for the traits: body weight (BWT; 2,059,869 records) and hen-housed egg production (HHP; 45,939 records). Data were analysed with three estimation approaches: sliding overlapping windows, under frequentist (restricted maximum likelihood (REML)) and Bayesian (Gibbs sampling) methods; expected variances using coefficients of the full relationship matrix; and a "double trait covariances" analysis by computing correlations and covariances between the same trait in two distinct consecutive windows. The genetic variance showed marginal fluctuations in its estimation over time. Whereas genetic, maternal permanent environmental, and residual variances were similar for BWT in both the REML and Gibbs methods, variance components when using the Gibbs method for HHP were smaller than the variances estimated when using REML. Large data amounts were needed to estimate variance components and detect their changes. For Gibbs (REML), the changes in genetic variance from 1999-2001 to 2020-2022 were 82.29 to 93.75 (82.84 to 93.68) for BWT and 76.68 to 95.67 (98.42 to 109.04) for HHP. Heritability presented a similar pattern as the genetic variance estimation, changing from 0.32 to 0.36 (0.32 to 0.36) for BWT and 0.16 to 0.15 (0.21 to 0.18) for HHP. On the whole, genetic parameters tended slightly to increase over time. The expected variance estimates were lower than the estimates when using overlapping windows. That indicates the low effect of the drift-selection process on the genetic variance, or likely, the presence of genetic variation sources compensating for the loss. Double trait covariance analysis confirmed the maintenance of variances over time, presenting genetic correlations >0.86 for BWT and >0.82 for HHP. Monitoring genetic variance in broiler breeding programmes is important to sustain genetic progress. Although the genetic variances of both traits fluctuated over time, in some windows, particularly between 2003 and 2020, increasing trends were observed, which warrants further research on the impact of other factors, such as novel mutations, operating on the dynamics of genetic variance.

Selective genotyping strategies for a sib test scheme of a broiler breeder program

BACKGROUND

In broiler breeding, genotype-by-environment interaction is known to result in a genetic correlation between body weight measured in bio-secure and commercial environments that is substantially less than 1. Thus, measuring body weights on sibs of selection candidates in a commercial environment and genotyping them could increase genetic progress. Using real data, the aim of this study was to evaluate which genotyping strategy and which proportion of sibs placed in the commercial environment should be genotyped to optimize a sib-testing breeding program in broilers. Phenotypic body weight and genomic information were collected on all sibs raised in a commercial environment, which allowed to retrospectively analyze different sampling strategies and genotyping proportions.

RESULTS

Accuracies of genomic estimated breeding values (GEBV) obtained with the different genotyping strategies were assessed by computing their correlation with GEBV obtained when all sibs in the commercial environment were genotyped. Results showed that, compared to random sampling (RND), genotyping sibs with extreme phenotypes (EXT) resulted in higher GEBV accuracy across all genotyping proportions, especially for genotyping proportions of 12.5% or 25%, which resulted in correlations of 0.91 vs 0.88 for 12.5% and 0.94 vs 0.91 for 25% genotyped. Including pedigree on birds with phenotype in the commercial environment that were not genotyped increased accuracy at lower genotyping proportions, especially for the RND strategy (correlations of 0.88 vs 0.65 at 12.5% and 0.91 vs 0.80 at 25%), and a smaller but still substantial increase in accuracy for the EXT strategy (0.91 vs 0.79 for 12.5% and 0.94 vs 0.88 for 25% genotyped). Dispersion bias was virtually absent for RND if 25% or more birds were genotyped. However, GEBV were considerably inflated for EXT, especially when the proportion genotyped was low, which was further exacerbated if the pedigree of non-genotyped sibs was excluded.

CONCLUSIONS

When less than 75% of all animals placed in a commercial environment are genotyped, it is recommended to use the EXT strategy, because it yields the highest accuracy. However, caution should be taken when interpreting the resulting GEBV because they will be over-dispersed. When 75% or more of the animals are genotyped, random sampling is recommended because it yields virtually no bias of GEBV and results in similar accuracies as the EXT strategy.

Autosomal and Z-linked genetic evaluation for body weight in Mazandaran native chicken using different models for dosage compensation on the Z chromosome

The objectives of this study were to assess the autosomal and sex-linked genetic inheritance of growth traits and identify the effective dosage compensation on the Z chromosome in Mazandaran native chickens. The data included body weights at hatching (BW0), 8 weeks (BW8) and 12 weeks (BW12) of age, related to the first 21 generations of selection, were collected from Mazandaran native chicken breeding centre. The fixed effects included sex of birds in two classes, hatch in five classes and generation in 21 classes. The inverse of the sex-linked additive genetic relationship matrix was constructed using nadiv package in R considering different models for dosage compensation on the Z chromosome. The setup inversed matrix was then supplied externally to WOMBAT using the GIN option. Twelve univariate animal models separating participation of autosomal additive genetic, sex-linked additive genetic and maternal effects (both genetic and permanent environment effects) with considering the five different dosage compensation methods for models with sex-linked effects were analysed by WOMBAT software. BW0 was not affected by sex-linked additive genetic effects. For BW8 and BW12 the model which included autosomal, sex-linked direct additive and maternal effects with no global dosage compensation for the Z chromosome was the most appropriate model. Autosomal heritability estimates were 0.05 ± 0.02, 0.10 ± 0.01 and 0.11 ± 0.01, for BW0, BW8 and BW12, respectively. For BW8 and BW12, sex-linked heritability estimates were 0.07 and 0.27, respectively. Spearman rank correlation coefficient between autosomal and sex-linked breeding values were 0.45 and 0.12 for BW8 and BW12, respectively. Spearman rank correlation coefficient between autosomal and sex-linked breeding values were 0.45 and 0.12 for BW8 and BW12, respectively. The autosomal direct additive genetic correlations between all traits were positive. The estimate of direct sex-linked additive genetic correlation between BW8 and BW12 was high (0.88). Also, maternal genetic correlations were 0.53, 0.54 and 0.91 between BW0-BW8, BW0-BW12 and BW8-BW12, respectively. Given the importance of Z-linked genes for BW8 and BW12, it is recommended that Z-linked effects be separated from autosomal effects in order to increase the accuracy of genetic evaluation of birds for these traits.

Divergent selection for natural antibodies in poultry in the presence of a major gene

Background

Natural antibodies (NAb) are antibodies that are present in a healthy individual without requiring previous exposure to an exogenous antigen. Selection for high NAb levels might contribute to improved general disease resistance. Our aim was to analyse the genetic background of NAb based on a divergent selection experiment in poultry, and in particular the effect of a polymorphism in the TLR1A gene.

Methods

The study population consisted of a base population from a commercial pure-bred elite white leghorn layer line and seven generations of birds from a High and Low selection line. Birds were selected for total KLH-binding NAb titer (IgTotal). An enzyme-linked immunosorbent assay was performed to determine NAb titers in blood plasma for IgTotal and the antibody isotypes IgM and IgG. NAb titers were available for 10,878 birds. Genotypes for a polymorphism in TLR1A were determined for chickens in generations 5, 6 and 7. The data were analysed using mixed linear animal models.

Results

The heritability estimate for IgM was 0.30 and higher than that for IgG and IgTotal (0.12). Maternal environmental effects explained 2 to 3% of the phenotypic variation in NAb. Selection for IgTotal resulted in a genetic difference between the High and Low line of 2.4 titer points (5.1 genetic standard deviation) in generation 7. For IgM, the selection response was asymmetrical and higher in the Low than the High line. The frequency of the TLR1A C allele was 0.45 in the base population and 0.66 and 0.04 in generation 7 of the High and Low line, respectively. The TLR1A polymorphism had large and significant effects on IgTotal and IgM. Estimated genotypic effects suggest full dominance of the TLR1A C allele. Significant TLR1A by generation interactions were detected for IgM and IgTotal.

Conclusions

The effect of a polymorphism in the TLR1A gene on IgTotal and IgM NAb was confirmed. Furthermore, we provide experimental verification of changes in allele frequencies at a major gene with dominant gene action on a quantitative trait that is subjected to mass selection. TLR1A by generation interactions indicate sensitivity to environmental factors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00715-9.

Genetic parameters for production traits in F1 reciprocal crossbred Chee Fah and Fah Luang chickens

ContextRecently, Chee Fah and Fah Luang chickens have been registered as a black-bone native chicken in Thailand. Only a few studies revealed genetic information about them. No publication has reported any data related to their cross-mating, particularly, genetic parameters.AimsThis study aimed to estimate genetic parameters for production traits of F1 generation of reciprocal crossbred Chee Fah and Fah Luang chickens.MethodsA dataset of production traits of two crossbred groups was used in the present study. Effects of breed, month-day of incubation and sex were tested at P&lt;0.05. Genetic parameters were estimated using the restricted maximum likelihood method with multi-trait animal model.Key resultsThe crossbred Chee Fah×Fah Luang was significantly heavier and consumed more feed than Fah Luang×Chee Fah (P&lt;0.05). Male chickens had significantly better 20-week-old bodyweight, feed conversion ratio and average daily gain compared with females for both crossbred groups (P&lt;0.05). The effect of month-day of incubation had a significant influence on production traits (P&lt;0.05), except for day-old bodyweight. Heritabilities for production traits of crossbred chickens were low to high. The highest estimate was observed for day-old bodyweight (0.97), followed by feed intake (0.40), 20-week-old bodyweight (0.06), average daily gain (0.05) and feed conversion ratio (0.03), respectively. Both positive and negative genetic correlations were found among their production traits. Favourable relationships were found between average daily gain versus bodyweight and versus feed conversion ratio (rgg=0.99 and −0.90, respectively). Similarly, production traits showed phenotypic correlations in both directions, which ranged from −0.95 to 0.99.ConclusionsHeritability estimations for production traits were found in low to high magnitude. The desirable genetic relationships were found between feed conversion ratio and day-old bodyweight, 20-week-old bodyweight and average daily gain, and between 20-week-old bodyweight and average daily gain.ImplicationsThese findings could be considered as a source of genetic data for enhancing production traits of crossbred black-bone native chickens.

Analysis of (co) variance components and estimation of breeding value of growth and production traits in Dahlem Red chicken using pedigree relationship in an animal model

Variance and covariance components of growth and production traits were analyzed employing REML animal model to assess the Dahlem Red (PD-3) chicken population for direct additive genetic, maternal effects and to estimate the estimated breeding value (EBV), genetic parameters, genetic trends and rate of inbreeding (ΔF) utilizing seven generation’s data. The generation and hatch had significant (P≤0.01) effect on the body weight at 0 day (BW0), 2 (BW2), 4 (BW4) and 6 weeks (BW6) and shank length at six weeks of age (SL6). The average least squares means (LSM) for BW6 and SL6 were 273.93±0.62 g and 53.97±0.05 mm, respectively. All the production traits were significantly (P≤0.01) influenced by generation and hatch. The average LSM for age at sexual maturity (ASM), egg production up to 40 weeks (EP40) and egg mass up to 40 weeks (EM40) were 168.82±0.25 d, 72.60±0.41 eggs and 4.21±0.07 kg, respectively. Model 5 with additive direct, maternal genetic, maternal permanent environmental and residual variance components was the best for BW0, BW2 and BW4 based on the AIC values obtained in WOMBAT. Model 4 was the best model for BW6, SL6, ASM, EP40 and EM40 with additive direct, maternal permanent environmental and residual variance components. Maternal effects were higher during early age, decreased with age, and remained present until 20 weeks of age. The heritability (h²) estimates were low to moderate in magnitude for all the growth traits and ranged from 0.02±0.03 to 0.19±0.03. The maternal heritability was high at hatch (0.35±0.06), decreased gradually until 4^th week (0.02±0.01) and ceased afterwards. The heritabilities of EP40 (0.11±0.03) and EM40 (0.12±0.04) were low. The direct additive genetic correlations (r_a) between BW2, BW4, BW6 and SL6 were high and positive (P≤ 0.05). The additive genetic and maternal permanent environmental correlation between EP40 and EM40 were high and positive (P≤ 0.05). The EBV of EM40 was significant (P≤ 0.05) with 0.48 kg/generation in PD-3 chicken at the end of the seventh generation. The EBV of EP40 showed an increasing trend with a genetic gain of 1.87 eggs per generation. The average inbreeding coefficient of the population was 0.019 and average ΔF was 0.007 over the last seven generations of selection. The EBV trends for primary and associated traits showed linear trends in the desired direction and negligible inbreeding.

Identification of QTL regions and candidate genes for growth and feed efficiency in broilers

BACKGROUND

Feed accounts for about 70% of the total cost of poultry meat production. Residual feed intake (RFI) has become the preferred measure of feed efficiency because it is phenotypically independent of growth rate and body weight. In this study, our aim was to estimate genetic parameters and identify quantitative trait loci (QTL) for feed efficiency in 3314 purebred broilers using a genome-wide association study. Broilers were genotyped using a custom 55 K single nucleotide polymorphism (SNP) array.

RESULTS

Estimates of genomic heritability for seven growth and feed efficiency traits, including body weight at 28 days of age (BW28), BW42, average daily feed intake (ADFI), RFI, and RFI adjusted for weight of abdominal fat (RFIa), ranged from 0.12 to 0.26. Eleven genome-wide significant SNPs and 15 suggestively significant SNPs were detected, of which 19 clustered around two genomic regions. A region on chromosome 16 (2.34-2.66 Mb) was associated with both BW28 and BW42, and the most significant SNP in this region, AX_101003762, accounted for 7.6% of the genetic variance of BW28. The other region, on chromosome 1 (91.27-92.43 Mb) was associated with RFI and ADFI, and contains the NSUN3 and EPHA6 as candidate genes. The most significant SNP in this region, AX_172588157, accounted for 4.4% of the genetic variance of RFI. In addition, a genomic region containing the gene AGK on chromosome 1 was found to be associated with RFIa. The NSUN3 and AGK genes were found to be differentially expressed in breast muscle, thigh muscle, and abdominal fat between male broilers with high and low RFI.

CONCLUSIONS

We identified QTL regions for BW28 and BW42 (spanning 0.32 Mb) and RFI (spanning 1.16 Mb). The NSUN3, EPHA6, and AGK were identified as the most likely candidate genes for these QTL. These genes are involved in mitochondrial function and behavioral regulation. These results contribute to the identification of candidate genes and variants for growth and feed efficiency in poultry.

Estimation of breeding value, genetic parameters and maternal effects of economic traits in rural male parent line chicken using pedigree relationships in an animal model

Breeding value (BV), genetic parameters and additive genetic, and maternal effects were evaluated on growth and production traits utilizing data from eight generations employing animal model in a rural male parent line (PD-6) chicken at ICAR-Directorate of Poultry Research, Hyderabad, India. The least squares means (LSM) for body weight (BW) and shank length (SL) up to 6 weeks of age varied significantly (p ≤ .01) among the generations and hatches. BW increased significantly (p ≤ .01) over the generations and decreased with the hatches. Sex also had a significant effect on BW and shank length except for BW at 0 day (BW0). LSM for BW (BW6) and Shank length (SL6) at 6 weeks of age were 598.84 ± 0.79 g and 74.57 ± 0.04 mm, respectively. Males recorded significantly (p ≤ .01) higher BWs and shank length. All the production traits were significantly (p ≤ .01) influenced by the generation effect. The overall LSM for age at sexual maturity (ASM), egg production at 40 weeks (EP40) and egg weight at 40 weeks (EW40) were 164.93 ± 0.23 days, 74.66 ± 0.40 eggs and 54.79 ± 0.08 g, respectively. Model 3 with additive, maternal permanent environmental and residual effects was the appropriate model for BW2, BW4, BW6, SL4 and SL6, whereas Model 4 with maternal effects was the best for BW0. The heritability estimates for BW6 and SL6 were 0.22 ± 0.02 and 0.18 ± 0.02, respectively. Model 1 with additive direct and residual effects was the best appropriate model for all the production traits. The heritability estimates of EP40 and EW40 were 0.16 ± 0.04 and 0.34 ± 0.05, respectively. BW and shank length were highly correlated with significant (p ≤ .05) positive association from different components. The correlation coefficient from direct additive component between egg production and BW40 was negative, while it was positive with less magnitude between egg production and BW20. The egg production and egg weights had a negative association at different ages. BV of SL6, the primary trait of selection, was significant (p ≤ .05) across the generations and increased linearly with an average genetic gain of 1.05 mm per generation. BV of BW6 was also significant (p ≤ .05) and increased linearly as correlated response with an average genetic response of 22.34 g per generation. BV of EP40 showed an increasing trend with a genetic gain of 0.02 eggs per generation. The EW 40 also increased linearly with an average genetic gain of 0.06 g. The average inbreeding coefficient of the population was 0.015. The study concluded that the population was in ideal status with a linearly increasing trend of average BV with negligible inbreeding over the eight generations of selection.

A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight

Background

The important property of the quantitative traits of model organisms is time-dependent. However, the methodology for investigating the genetic interaction network over time is still lacking. Our study aims to provide insights into the mechanistic basis of epistatic interactions affecting the phenotypes of model organisms.

Results

We performed an exhaustive genome-wide search for significant SNP-SNP interactions associated with male birds’ body weight (BW) (n = 475) at multiple time points (day of hatch (BW0) and 1, 3, 5, and 7 weeks (BW1, BW3, BW5, and BW7)). Statistical analysis detected 67, four, and two significant SNP pairs associated with BW0, BW1, and BW3, respectively, with a significance threshold at 8.67 × 10^− 12 (Bonferroni-adjusted: 1%). Meanwhile, no significant SNP pairs associated with BW5 and BW7 were found. The SNP-SNP interaction networks of BW0, BW1, and BW3 were built and annotated.

Conclusions

With strong annotated information and a strict significant threshold, SNP-SNP interactions underpinned the gene-gene interactions that might occur between chromosomes or within the same chromosome. Comparing and combing the networks, the results indicated that the genetic network for chicken body weight was dynamic and time-dependent.