Genetic parameters of foot-pad dermatitis and body weight in purebred broiler lines in 2 contrasting environments

Genetics of gait score in broilers: Genetic parameters of gait score in purebred broiler lines

Leg health assessment is a vital component of poultry breeding goals; it includes a range of skeletal disorders and contact dermatitis traits as well as a general assessment of a bird's walking ability in the form of gait score (GS). If trained scorers are used, GS correlates well with more objective walking assessment methods and allows for high throughput data collection from large numbers of individuals. The paper describes for the first time GS heritabilities for broilers. The Aviagen GS system (AGS) consists of an 8-class scale of 10-45 in increments of 5, whereby 10 is the best score and 45 the worst. It has sufficient variation between categories to enable a clear distinction of GS classes for selection purposes. The results of GS at 4-5 weeks of age show GS heritabilities between 0.14 and 0.24 which is higher than turkey (0.08-0.13) or duck (0.06-0.12) heritabilities. Genetic correlations with body weight and breast percentage were unfavorable but moderate. Correlations among leg health traits (AGS, long bone deformities, crooked toes, hockburn and footpad dermatitis) were generally low (-0.16-0.10) for most traits and lines. While genetic correlations between AGS and production traits were unfavorable, both AGS and other leg health and production traits can be improved simultaneously in a multi-trait selection strategy combining production and welfare characteristics. AGS has been included in the Aviagen breeding goal since 2011.

Developments in welfare of parent stock and commercial broilers

Meat poultry breeding plays a critical role at the start of the food chain. Breeding solutions are long-term - as available in the DNA of the populations. They are also cumulative - the gradual improvements add up -, and disseminated widely throughout the production chain. Poultry meat is an important animal source food, and instrumental for global food security. The contribution that poultry breeding makes to meet current and future needs can be described in terms of a Code of Good Practice for Sustainable Breeding (Code-EFABAR®), and as Five Commitments to 1) Health, Food Safety and Food Security; 2) Diversity; 3) Balanced Breeding; 4) Management and Stockmanship; and 5) Transparency, Communication and Engagement. The review describes these commitments. Understanding what future directions are foreseen in the medium and long term is the basis for change. The dialogue and close cooperation with stakeholders in society is crucial to anticipate developments, by investigating and implementing them in steady and careful balanced selection leading to better welfare, productivity and sustainability outcomes.

A walk through the broiler breeder life: how do footpad dermatitis and gait scores develop from rearing to slaughter?

The two most common animal-based indicators used to evaluate leg health in broiler chickens are footpad dermatitis (FPD) and gait scoring, but these indicators are less explored in broiler breeders. This study is the first to investigate FPD and gait scoring in broiler breeders during their lifespan from rearing to end of life. In total, eight flocks were monitored (four Ross and four Hubbard) at five different timepoints, in rearing (5 and 15 weeks of age), during the production period (25 and 45 weeks of age) and at the end of the production period (approximately 60 weeks of age). At each visit, 50 hens and 25 roosters were gait scored (six-point scale) and footpads from another 50 hens and 25 roosters were evaluated (five-point scale) (total n = 3000 breeders, 2000 hens and 1000 roosters). Litter quality and air quality were measured at each visit. The results showed that the overall prevalence of FPD in rearing was low and that it increased towards the end of the production, with a mean FPD score of 2 out of a maximum 4 in the hens, indicating moderate lesions and 1.5 in the roosters. In all houses, the litter was dry and loose. FPD was not related to the litter quality, but to air quality, especially the ammonia concentration (P < 0.001). Overall, the gait score were good, and increased with age in both hens (P < 0.001) and roosters of both hybrids (P < 0.001).

Animal board invited review: The purebred-crossbred genetic correlation in poultry

The purebred-crossbred genetic correlation (rpc) is a key parameter to determine whether the optimal selection of purebred animals to improve crossbred performance should rely on crossbred phenotypes, purebred phenotypes, or both. We reviewed published estimates of the rpc in poultry. In total, 19 studies were included, of which four were on broilers and 15 on laying hens, with 150 rpc estimates for nine different trait categories. Average reported rpc estimates were highest for egg weight, egg quality and egg colour (0.74-0.82), intermediate for BW, maturity and mortality (0.61-0.70) and egg number (0.58), and low for resilience (0.40) and body conformation (0.14). Most studies were based on measuring purebred and crossbred phenotypes in the same environment and thus did not capture the contribution of genotype by environment interactions to the rpc, suggesting that the presented average estimates may be higher than values that apply in practice. Nearly all studies were based on two-way crossbred animals. We hypothesised that rpc values for a two-way cross are good proxies for rpc of a four-way cross. Only eight out of 19 studies were published in the last 25 years, and only two of those used genomic data. We expect that more studies using genomic data may be published in the coming years, as the required data may be generated when implementing genomic selection for crossbred performance, which will lead to more accurate rpc estimates. Future studies that aim to estimate rpc are encouraged to capture the genotype by environment interaction component by housing purebred and crossbred animals differently as is done in practice. Moreover, there is a need for further studies that enable to explicitly estimate the magnitude of genotype by environment versus genotype by genotype interactions for multiple trait categories. Further, studies are advised to report: the specific housing conditions of the animals, any differences between measurements of purebred versus crossbred performance, and the heritabilities of purebred and crossbred performance.

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.

Evolutions in Commercial Meat Poultry Breeding

This paper provides a comprehensive overview of the history of commercial poultry breeding, from domestication to the development of science and commercial breeding structures. The development of breeding goals over time, from mainly focusing on production to broad goals, including bird welfare and health, robustness, environmental impact, biological efficiency and reproduction, is detailed. The paper outlines current breeding goals, including traits (e.g., on foot and leg health, contact dermatitis, gait, cardiovascular health, robustness and livability), recording techniques, their genetic basis and how trait these antagonisms, for example, between welfare and production, are managed. Novel areas like genomic selection and gut health research and their current and potential impact on breeding are highlighted. The environmental impact differences of various genotypes are explained. A future outlook shows that balanced, holistic breeding will continue to enable affordable lean animal protein to feed the world, with a focus on the welfare of the birds and a diversity of choice for the various preferences and cultures across the world.

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.

Reliability of a White Striping Scoring System and Description of White Striping Prevalence in Purebred Turkey Lines

Simple Summary

A relatively recent issue in the turkey industry is white striping (presence of white striations on the surface of the breast fillets). This defect influences consumer acceptance and the nutritional value of the meat and, therefore, is of economic importance to the industry. This study is aimed to test the reliability of a white striping scoring system used by several observers and estimate the prevalence of this defect in modern turkeys. After a few training sessions, the scoring system was found to be moderately reliable within and between the six participating observers. We found that 88% of turkeys in the studied population had some degree of white striping, with most scores being of moderate-severe severity (Score 1 or 2). Furthermore, white striping severity was found to be associated with higher slaughter weight, breast weight, and breast meat yield. Future research is needed to evaluate the use of white striping information in turkey genetic selection programs, as a balanced approach is needed to avoid slowing gains in economically favorable traits, such as growth.

Abstract

To efficiently meet consumer demands for high-quality lean meat, turkeys are selected for increased meat yield, mainly by increasing breast muscle size and growth efficiency. Over time, this has altered muscle morphology and development rates, which are believed to contribute to the prevalence of myopathies. White striping is a myopathy of economic importance which presents as varying degrees of white striations on the surface of skinless breast muscle and can negatively affect consumer acceptance at the point of sale. Breeding for improved meat quality may be a novel strategy for mitigating the development of white striping in turkey meat; however, it is crucial to have a reliable assessment tool before it can be considered as a phenotype. Six observers used a four-category scoring system (0–3) to score severity in several controlled rounds and evaluate intra- and inter-observer reliability of the scoring system. After sufficient inter-observer reliability (Kendall’s W > 0.6) was achieved, 12,321 turkey breasts, from four different purebred lines, were scored to assess prevalence of the condition and analyze its relationship with important growth traits. Overall, the prevalence of white striping (Score > 0) was approximately 88% across all genetic lines studied, with most scores being of moderate-severe severity (Score 1 or 2). As was expected, increased white striping severity was associated with higher slaughter weight, breast weight, and breast meat yield (BMY) within each genetic line. This study highlights the importance of training to improve the reliability of a scoring system for white striping in turkeys and was required to provide an updated account on white striping prevalence in modern turkeys. Furthermore, we showed that white striping is an important breast muscle myopathy in turkeys linked to heavily selected traits such as body weight and BMY. White striping should be investigated further as a novel phenotype in future domestic turkey selection through use of a balanced selection index.

Genome-wide association studies for growth traits in broilers

BACKGROUND

The identification of markers and genes for growth traits may not only benefit for marker assist selection /genomic selection but also provide important information for understanding the genetic foundation of growth traits in broilers.

RESULTS

In the current study, we estimated the genetic parameters of eight growth traits in broilers and carried out the genome-wide association studies for these growth traits. A total of 113 QTNs discovered by multiple methods together, and some genes, including ACTA1, IGF2BP1, TAPT1, LDB2, PRKCA, TGFBR2, GLI3, SLC16A7, INHBA, BAMBI, APCDD1, GPR39, and GATA4, were identified as important candidate genes for rapid growth in broilers.

CONCLUSIONS

The results of this study will provide important information for understanding the genetic foundation of growth traits in broilers.

In pursuit of a better broiler: growth, efficiency, and mortality of 16 strains of broiler chickens

To meet the growing consumer demand for chicken meat, the poultry industry has selected broiler chickens for increasing efficiency and breast yield. While this high productivity means affordable and consistent product, it has come at a cost to broiler welfare. There has been increasing advocacy and consumer pressure on primary breeders, producers, processors, and retailers to improve the welfare of the billions of chickens processed annually. Several small-scale studies have reported better welfare outcomes for slower-growing strains compared to fast-growing, conventional strains. However, these studies often housed birds with range access or used strains with vastly different growth rates. Additionally, there may be traits other than growth, such as body conformation, that influence welfare. As the global poultry industries consider the implications of using slower growing strains, there was a need for a comprehensive, multidisciplinary examination of broiler chickens with a wide range of genotypes differing in growth rate and other phenotypic traits. To meet this need, our team designed a study to benchmark data on conventional and slower-growing strains of broiler chickens reared in standardized laboratory conditions. Over a 2-year period, we studied 7,528 broilers from 16 different genetic strains. In this paper, we compare the growth, efficiency, and mortality of broilers to one of two target weights (TW): 2.1 kg (TW1) and 3.2 kg (TW2). We categorized strains by their growth rate to TW2 as conventional (CONV), fastest-slow strains (FAST), moderate-slow strains (MOD), and slowest-slow strains (SLOW). When incubated, hatched, housed, managed, and fed the same, the categories of strains differed in body weights, growth rates, feed intake, and feed efficiency. At 48 d of age, strains in the CONV category were 835 to 1,264 g heavier than strains in the other categories. By TW2, differences in body weights and feed intake resulted in a 22 to 43-point difference in feed conversion ratios. Categories of strains did not differ in their overall mortality rates.

Modeling genetic components of hatch of fertile in broiler breeders

Reproductive efficiency such as fertility and hatch of fertile (HoF) are of economic importance and concern to breeding companies becaue of their effects on chick output. Similar to other traits of economic importance in poultry breeding, the rate of response for HoF is largely dependent on the use of an appropriate model for evaluating the trait. Therefore, the objectives of this study were to estimate genetic parameters from cumulative, repeatability, fixed regression, random regression, and multitrait models for HoF from a pure-line broiler breeder. The data available for this study consisted of weekly HoF records from 11,729 hens with a total pedigree record of 38,260. Estimates of heritability from the various models ranged from 0.04 to 0.22 with the highest estimate obtained from the cumulative model and the lowest from the repeatability model. Responses to selection estimated for the different models ranged from 0.03 to 0.08% gain per year of the phenotypic mean. In general, the cumulative and the repeatability models underestimated response to selection. The multitrait and random regression models gave similar results for response to selection at 0.08 percentage change in phenotypic mean. In conclusion, the cumulative model is not optimal for modeling HoF, and likewise, the repeatability model. The random regression and multitrait models should be considered instead as they offered a higher response to selection. However, if a multitrait analysis is to be considered, it is recommended to split up the production period in such a way as to avoid computational constraints due to overparameterization.

Bird Health, Housing and Management Routines on Swedish Organic Broiler Chicken Farms

Slower-growing broilers on organic farms have replaced fast-growing hybrids to increase bird welfare. Due to limited knowledge of broiler welfare and management on organic farms in Sweden, the study aim was to gather information regarding health, housing and management routines, in order to describe the current situation on these. Farm visits performed in 2018 included 8 out of 12 established organic farms, on which either Rowan Ranger or HubbardJA57/HubbardJA87 were reared. Chickens in the observed flocks were 55 ± 6 (44-62) days of age. Observations included farmer interviews, indoor environment assessments, clinical examinations and gait scoring. Clinical examinations revealed no severe remarks, however minor to moderate plumage dirtiness, food pad dermatitis and hock burns were found in 47%, 21% and 13% of the birds, respectively. Although no severe walking impairments were observed, minor to moderate gait abnormalities were seen in two-thirds of the birds. Gait in birds assessed outdoors was significantly better than in birds observed indoors. Body weight uniformity was low in all flocks. This study provides increased knowledge of certain chicken health and welfare aspects, housing and management on Swedish organic farms. Future research should further investigate important aspects related to bird welfare, such as the high mortality rates observed.

Characterising the Influence of Genetics on Breast Muscle Myopathies in Broiler Chickens

This report provides the first estimates of the genetic basis of all key breast muscle myopathies (BMM) in broiler chickens [Deep pectoral myopathy, wooden breast, white striping and spaghetti breast] and their relationship with body weight and breast yield. Data from a pure bred high yielding commercial broiler line were analysed to estimate the genetic parameters using a multivariate animal model with the appropriate fixed effects and permanent environmental effect of the dam. Heritabilities of the BMM ranged from 0.04 to 0.25 and the genetic correlation of the BMM with body weight and breast yield ranged from -0.06 to 0.41. Here we highlight that the genetic variance of BMM accounts for a low proportion of the phenotypic variance and the BMM have a low genetic relationship with performance traits. The large contribution of residual variance to the phenotypic variance for the BBM was >71.5% which indicates the importance of the non-genetic effects on BMM. The data presented also show that the moderate to low genetic influence for the development of BMM can be used, through balanced selection, to reduce the myopathy incidence in the long term. The impact of genetic selection against BMM was tested empirically by comparing the incidence of WB and % breast yield of a commercial broiler with a high generation (HG) broiler. The HG broiler used represents 2 years of genetic improvement compared to the commercial broiler; the HG broiler had an 18.4% relative decrease in WB and a 1.02% relative increase in breast yield compared to the commercial broiler. This paper describes the relationship between the genetic and non-genetic factors influencing BMM highlighting the importance of understanding the non-genetic effects on myopathy incidence. It also shows that the genetic component of BMM can be reduced whilst at the same time improving breast yield as part of balanced breeding goals.

Evaluation of dietary supplementation of a novel microbial muramidase on gastrointestinal functionality and growth performance in broiler chickens

This study was conducted to assess the effect of dietary supplementation of Muramidase 007 to broiler chickens on gastrointestinal functionality, evaluating growth performance, apparent ileal digestibility, intestinal histomorphology, vitamin A in plasma and cecal microbiota. A total of 480 one-day male chicks (Ross 308) were distributed in 16 pens allocated in 2 experimental diets: the control diet (CTR) without feed enzymes, coccidiostat or growth promoters, and the experimental diet (MUR): CTR supplemented with 35,000 units (LSU(F))/kg of the Muramidase 007. Digesta and tissue samples were obtained on days 9 and 36 of the study. A lower feed conversion ratio was observed in the MUR treatment. Apparent ileal digestibility of DM, organic matter and energy were improved by Muramidase 007. It was also observed that MUR improved digestibility of total fatty acids, mono-unsaturated fatty acids and poly-unsaturated fatty acids, and content of vitamin A in plasma at day 9 (P < 0.05). Histomorphological analysis of jejunum samples revealed no differences in the villus height or crypt depth; but a higher number of goblet cells and intraepithelial lymphocytes at day 36 with MUR. No differences were observed in plate counts of enterobacteria or Lactobacillus along the gastrointestinal tract, neither on the cecal short-chain fatty acids. An statistical trend was observed for reduction of cecal clostridia at day 9 for MUR. Analysis of cecal microbiota structure by 16S rRNA gene sequencing revealed relevant changes correlated to age. At day 9, broilers receiving MUR showed decreased alpha diversity compared to CTR that was not detected at day 36. Changes in specific taxonomic groups with an increase in Lactobacillus genus were identified. In conclusion, evaluation of the variables in this study indicates that dietary Muramidase 007 contributes to improve feed conversation ratio and gastrointestinal function in broiler chickens. Effects could have been mediated by slight shifts observed in the intestinal microbiota. More studies are guaranteed to fully understand the mechanisms involved.

Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses

To address the need for sensitive high-throughput assays to analyse avian innate and adaptive immune responses, we developed and validated a highly multiplexed qPCR 96.96 Fluidigm Dynamic Array to analyse the transcription of chicken immune-related genes. This microfluidic system permits the simultaneous analysis of expression of 96 transcripts in 96 samples in 6 nanolitre reactions and the 9,216 reactions are ready for interpretation immediately. A panel of 89 genes was selected from an RNA-seq analysis of the transcriptional response of chicken macrophages, dendritic cells and heterophils to agonists of innate immunity and from published transcriptome data. Assays were confirmed to be highly specific by amplicon sequencing and melting curve analysis and the reverse transcription and preamplification steps were optimised. The array was applied to RNA of various tissues from a commercial line of broiler chickens housed at two different levels of biosecurity. Gut-associated lymphoid tissues, bursa, spleen and peripheral blood leukocytes were isolated and transcript levels for immune-related genes were defined. The results identified blood cells as a potentially reliable indicator of immune responses among all the tissues tested with the highest number of genes significantly differentially transcribed between birds housed under varying biosecurity levels. Conventional qPCR analysis of three differentially transcribed genes confirmed the results from the multiplex qPCR array. A highly multiplexed qPCR-based platform for evaluation of chicken immune responses has been optimised and validated using samples from commercial chickens. Apart from applications in selective breeding programmes, the array could be used to analyse the complex interplay between the avian immune system and pathogens by including pathogen-specific probes, to screen vaccine responses, and as a predictive tool for immune robustness.

Femur and tibia development in meat-type chickens with different growth potential for 56 days of rearing period

We studied the changes in morphological, geometric, densitometric, and mechanical parameters of the femur and tibia during 56 D of rearing chickens with different growth rates. Ten femur and tibia were collected from fast-growing chickens (FG) and 2 types of medium-growing chickens (MGH and MGGP) immediately after hatching (0 D) and on 7, 14, 21, 35, 42, 49, and 56 D of life. The bone parameters of chickens across all genetic groups were found to be similar on 0 D, with exceptions of lower percentage contribution of bone weight (BW) in FG chickens (P < 0.05), lower total bone volume in MGGP chickens (P < 0.05), and lower maximum elastic strength in MGH chickens (P < 0.05). The bones developed in FG chickens were longer and wider; however, an increase in bone mineral density (BMD) between 42 and 49 D was not observed. The BMD value in FG chickens on 56 D was comparable to that in MGH chickens (P = 0.089) and significantly lower than that in MGGP chickens (P = 0.021). Mean relative wall thickness, despite longer and thicker bones in FG chickens, was comparable and often lower than that of MGH and MGGP chickens. In conclusion, the results showed that medium-growing chickens could be reared for up to 56 D without the risk of any growth impairment due to problems associated with deterioration of pelvic limb bone quality.

Genetic analysis on body weight at different ages in broiler chicken raised in commercial environment

A multivariate model was developed and used to estimate genetic parameters of body weight (BW) at 1-6 weeks of age of broilers raised in a commercial environment. The development of model was based on the predictive ability of breeding values evaluated from a cross-validation procedure that relied on half-sib correlation. The multivariate model accounted for heterogeneous variances between sexes through standardization applied to male and female BWs differently. It was found that the direct additive genetic, permanent environmental maternal and residual variances for BW increased drastically as broilers aged. The drastic increase in variances over weeks of age was mainly due to scaling effects. The ratio of the permanent environmental maternal variance to phenotypic variance decreased gradually with increasing age. Heritability of BW traits ranged from 0.28 to 0.33 at different weeks of age. The direct genetic effects on consecutive weekly BWs had high genetic correlations (0.85-0.99), but the genetic correlations between early and late BWs were low (0.32-0.57). The difference in variance components between sexes increased with increasing age. In conclusion, the permanent environmental maternal effect on broiler chicken BW decreased with increasing age from weeks 1 to 6. Potential bias of the model that considered identical variances for sexes could be reduced when heterogeneous variances between sexes are accounted for in the model.

Use of genomic information to exploit genotype-by-environment interactions for body weight of broiler chicken in bio-secure and production environments

BACKGROUND

The increase in accuracy of prediction by using genomic information has been well-documented. However, benefits of the use of genomic information and methodology for genetic evaluations are missing when genotype-by-environment interactions (G × E) exist between bio-secure breeding (B) environments and commercial production (C) environments. In this study, we explored (1) G × E interactions for broiler body weight (BW) at weeks 5 and 6, and (2) the benefits of using genomic information for prediction of BW traits when selection candidates were raised and tested in a B environment and close relatives were tested in a C environment.

METHODS

A pedigree-based best linear unbiased prediction (BLUP) multivariate model was used to estimate variance components and predict breeding values (EBV) of BW traits at weeks 5 and 6 measured in B and C environments. A single-step genomic BLUP (ssGBLUP) model that combined pedigree and genomic information was used to predict EBV. Cross-validations were based on correlation, mean difference and regression slope statistics for EBV that were estimated from full and reduced datasets. These statistics are indicators of population accuracy, bias and dispersion of prediction for EBV of traits measured in B and C environments. Validation animals were genotyped and non-genotyped birds in the B environment only.

RESULTS

Several indications of G × E interactions due to environmental differences were found for BW traits including significant re-ranking, heterogeneous variances and different heritabilities for BW measured in environments B and C. The genetic correlations between BW traits measured in environments B and C ranged from 0.48 to 0.54. The use of combined pedigree and genomic information increased population accuracy of EBV, and reduced bias of EBV prediction for genotyped birds compared to the use of pedigree information only. A slight increase in accuracy of EBV was also observed for non-genotyped birds, but the bias of EBV prediction increased for non-genotyped birds.

CONCLUSIONS

The G × E interaction was strong for BW traits of broilers measured in environments B and C. The use of combined pedigree and genomic information increased population accuracy of EBV substantially for genotyped birds in the B environment compared to the use of pedigree information only.

Estimating the purebred-crossbred genetic correlation of body weight in broiler chickens with pedigree or genomic relationships

Background

In pig and poultry breeding programs, the breeding goal is to improve crossbred (CB) performance, whereas selection in the purebred (PB) lines is often based on PB performance. Thus, response to selection may be suboptimal, because the genetic correlation between PB and CB performance (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc) is generally lower than 1. Accurate estimates of the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc are needed, so that breeders can decide if they should collect data from CB animals. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc can be estimated either from pedigree or genomic relationships, which may produce different results. With genomic relationships, the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc estimate could be improved when relationships between purebred and crossbred animals are based only on the alleles that originate from the PB line of interest. This work presents the first comparison of estimated \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc and variance components of body weight in broilers, using pedigree-based or genotype-based models, where the breed-of-origin of alleles was either ignored or considered. We used genotypes and body weight measurements of PB and CB animals that have a common sire line.

Results

Our results showed that the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc estimates depended on the relationship matrix used. Estimates were 5 to 25% larger with genotype-based models than with pedigree-based models. Moreover, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc estimates were similar (max. 7% difference) regardless of whether the model considered breed-of-origin of alleles or not. Standard errors of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc estimates were smaller with genotype-based than with pedigree-based methods, and smaller with models that ignored breed-of-origin than with models that considered breed-of-origin.

Conclusions

We conclude that genotype-based models can be useful for estimating \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc, even when the PB and CB animals that have phenotypes are closely related. Considering breed-of-origin of alleles did not yield different estimates of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{pc}$$\end{document}rpc, probably because the parental breeds of the CB animals were distantly related.

Electronic supplementary material

The online version of this article (10.1186/s12711-019-0447-9) contains supplementary material, which is available to authorized users.

Colonization of a commercial broiler line by Campylobacter is under limited genetic control and does not significantly impair performance or intestinal health

Campylobacter is the leading bacterial cause of foodborne diarrheal illness in humans and source attribution studies unequivocally identify handling or consumption of poultry meat as a key risk factor. Campylobacter colonizes the avian intestines in high numbers and rapidly spreads within flocks. A need therefore exists to devise strategies to reduce Campylobacter populations in poultry flocks. There has been a great deal of research aiming to understand the epidemiology and transmission characteristics of Campylobacter in poultry as a means to reduce carriage rates in poultry and reduce infection in humans. One potential strategy for control is the genetic selection of poultry for increased resistance to colonization by Campylobacter. The potential for genetic control of colonization has been demonstrated in inbred populations following experimental challenge with Campylobacter where quantitative trait loci associated with resistance have been identified. Currently in the literature there is no information of the genetic basis of Campylobacter colonization in commercial broiler lines and it is unknown whether these QTL are found in commercial broiler lines. The aim of this study was to estimate genetic parameters associated with Campylobacter load and genetic correlations with gut health and production traits following natural exposure of broiler chickens to Campylobacter.The results from the analysis show a low but significant heritability estimate (0.095 ± 0.037) for Campylobacter load which indicates a limited genetic basis and that non-genetic factors have a greater influence on the level of Campylobacter found in the broiler chicken.Furthermore, through examination of macroscopic intestinal health and absorptive capacity, our study indicated that Campylobacter has no detrimental effects on intestinal health and bird growth following natural exposure in the broiler line under study. These data indicate that whilst there is a genetic component to Campylobacter colonization worthy of further investigation, there is a large proportion of phenotypic variance under the influence of non-genetic effects. As such the control of Campylobacter will require understanding and manipulation of non-genetic host and environmental factors.

Benefits of testing in both bio-secure and production environments in genomic selection breeding programs for commercial broiler chicken

Background

A breeding program for commercial broiler chicken that is carried out under strict biosecure conditions can show reduced genetic gain due to genotype by environment interactions (G × E) between bio-secure (B) and commercial production (C) environments. Accuracy of phenotype-based best linear unbiased prediction of breeding values of selection candidates using sib-testing in C is low. Genomic prediction based on dense genetic markers may improve accuracy of selection. Stochastic simulation was used to explore the benefits of genomic selection in breeding schemes for broiler chicken that include birds in both B and C for assessment of phenotype.

Results

When genetic correlations (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{g}$$\end{document}rg) between traits measured in B and C were equal to 0.5 and 0.7, breeding schemes with 15, 30 and 45% of birds assessed in C resulted in higher genetic gain for performance in C compared to those without birds in C. The optimal proportion of birds phenotyped in C for genetic gain was 30%. When the proportion of birds in C was optimal and genotyping effort was limited, allocating 30% of the genotyping effort to birds in C was also the optimal genotyping strategy for genetic gain. When \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{g}$$\end{document}rg was equal to 0.9, genetic gain for performance in C was not improved with birds in C compared to schemes without birds in C. Increasing the heritability of traits assessed in C increased genetic gain significantly. Rates of inbreeding decreased when the proportion of birds in C increased because of a lower selection intensity among birds retained in B and a reduction in the probability of co-selecting close relatives.

Conclusions

If G × E interactions (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{g}$$\end{document}rg of 0.5 and 0.7) are strong, a genomic selection scheme in which 30% of the birds hatched are phenotyped in C has larger genetic gain for performance in C compared to phenotyping all birds in B. Rates of inbreeding decreased as the proportion of birds moved to C increased from 15 to 45%.

A comparative study of acute-phase protein concentrations in historical and modern broiler breeding lines

Acute-phase proteins (APP) are secreted from the liver as a result of inflammation or infection and are measurable in serum and plasma. To determine whether the constitutive APP serum amyloid A (SAA), alpha-1-acid glycoprotein (AGP), ceruloplasmin (Cp), and ovotransferrin (Ovt) have changed as a result of selection for improved production and growth characteristics over the last 40 yr two historical broilers lines were compared to a modern line of the same lineage. Serum was harvested from blood samples taken from the 3 broiler lines on days 10, 17, and 20, and the APP concentrations were determined using immunoassay methods. Most of the significant changes observed were age related, with SAA and Cp having significantly lower concentrations at day 20 than days 10 and 17 in all lines. The only significant difference between lines was observed at day 20 on which both Cp (P = 0.01) and AGP (P = 0.03) were significantly higher in the modern line than the 90s line, though no significant differences were noted between the modern and 70s line. When evaluating the difference in APP concentrations between males (Cx) and females (Px) across all 3 lines, females had a higher SAA at day 17 and lower SAA at day 20, P = 0.0078 and 0.0327 respectively, and males had a significantly higher Ovt on days 17 and 20 (P = 0.0002 and P = 0.003 respectively). These results reveal that APP concentrations fluctuate over this early period of growth and that the changes in APP serum concentration appear uniform between 3 lines with very contrasting selection history, suggesting the improvements made in meat production efficiency since the 1970s have not affected the circulating concentrations of these constitutively expressed APP.

Does selection for growth rate in broilers affect their resistance and tolerance to Eimeria maxima?

Chickens exhibit varied responses to infection with Eimeria parasites. We hypothesise that broilers selected for increased growth rate will show lower resistance and tolerance to a coccidian challenge. 288 chickens of fast (F) or slow (S) growing lines were inoculated with 0 (control), 2500 (low-dose), or 7000 (high-dose) sporulated E. maxima oocysts at 13 days of age in two consecutive rounds. Gain and Intake were measured daily and their values relative to BW at the point of infection were calculated over the pre-patent (days 1-4 post-infection), acute (d5-8 pi), and recovery (d9-12 pi) phases of infection to assess the impact of infection. Levels of plasma carotenoids, vitamins E and A, long bone mineralisation, caecal microbiota diversity indices, and histological measurements were assessed at the acute (d6 pi) and recovery stage (d13 pi). In addition, we measured the levels of nitric oxide metabolites and the number of parasite genome copies in the jejunumat d6pi. In absolute terms F birds grew 1.42 times faster than S birds when not infected. Infection significantly reduced relative daily gain and intake (P < 0.001), with the effects being most pronounced during the acute phase (P < 0.001). Levels of all metabolites were significantly decreased, apart from NO which increased (P < 0.001) in response to infection on d6pi, and were accompanied by changes in histomorphometric features and the presence of E. maxima genome copies in infected birds, which persisted to d13pi. Furthermore, infection reduced tibia and femur mineralisation, which also persisted to d13pi. Reductions in measured variables were mostly independent of dose size, as was the level of parasite replication. The impact of infection was similar for S and F-line birds for all measured parameters, and there were no significant interactions between line x dose size on any of these parameters. In conclusion, our results suggest that line differences in productive performance do not influence host responses to coccidiosis when offered nutrient adequate diets.

Genetic basis of leg health and its relationship with body weight in purebred turkey lines

The aims of this study were to estimate the genetic parameters for leg and foot health and mobility in purebred turkey lines and their genetic correlations with BW. Traits were gait score (GS) as an overall measure of leg health, footpad dermatitis (FPD), and 2 skeletal leg health traits, namely, valgus and varus deformities (VVD) and tibial dyschondroplasia (TD). Data from 4 different lines, comprising 3 yr of phenotypic records and 4 yr of pedigree information per line, were used. The sex average BW for the lines at 18 wk ranged from 19.1 kg (line A) to 12.4 kg (line D). The prevalence of VVD ranged from 5.2 to 14.6% and for TD from 4.1 to 23.2%. The average score for FPD on a scale of 0 to 100 ranged from 48.5 to 61.1. Gait Score was scored on a scale of 1 to 5, standardized to a mean of 3 and SD of 1. Heritabilities were estimated at 0.08 to 0.13 for GS, 0.01 to 0.07 for VVD, 0.06 to 0.12 for TD, and 0.10 to 0.15 for FPD (all SE ≤ 0.02). Estimates of the genetic correlations between VVD and TD ranged from 0.03 to 0.21 (all SE ≤ 0.08), and estimates of these with GS ranged from 0.07 to 0.87 (all SE ≤ 0.09). The genetic correlations of FPD with GS ranged from 0.00 to 0.34 (all SE ≤ 0.04), and with the skeletal leg health traits from -0.06 to 0.33 (all SE ≤ 0.06). Body weight showed estimated genetic correlations ranging from 0.28 to 0.51 (all SE ≤ 0.06) with GS, -0.06 to 0.50 (all SE ≤ 0.13) with VVD/TD and 0.05 to 0.34 (all SE ≤ 0.05) with FPD. The results suggest that selection for improved leg health can be incorporated effectively in a commercial turkey breeding program using balanced breeding goals, in which production traits and leg health traits are considered simultaneously.

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.

AvBD1 nucleotide polymorphisms, peptide antimicrobial activities and microbial colonisation of the broiler chicken gut

BACKGROUND

The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs affecting host peptides involved in the innate defences tend to be rare, but three non-synonymous SNPs in the avian β-defensin (AvBD1) gene encoding the variant peptides NYH, SSY and NYY were identified that segregated specifically to three lines of commercial broiler chickens Line X (LX), Line Y(LY) and Line Z. The impacts of such amino acid changes on peptide antimicrobial properties were analysed in vitro and described in relation to the caecal microbiota and gut health of LX and LY birds.

RESULTS

Time-kill and radial immune diffusion assays indicated all three peptides to have antimicrobial properties against gram negative and positive bacteria with a hierarchy of NYH > SSY > NYY. Calcein leakage assays supported AvBD1 NYH as the most potent membrane permeabilising agent although no significant differences in secondary structure were identified to explain this. However, distinct claw regions, identified by 3D modelling and proposed to play a key role in microbial membrane attachment, and permeation, were more distinct in the NYH model. In vivo AvBD1 synthesis was detected in the bird gut epithelia. Analyses of the caecal gut microbiota of young day 4 birds suggested trends in Lactobacilli sp. colonisation at days 4 (9% LX vs × 30% LY) and 28 (20% LX vs 12% LY) respectively, but these were not statistically significant (P > 0.05).

CONCLUSION

Amino acid changes altering the killing capacity of the AvBD1 peptide were associated with two different bird lines, but such changes did not impact significantly on caecal gut microbiota.

A predictive assessment of genetic correlations between traits in chickens using markers

Background

Genomic selection has been successfully implemented in plant and animal breeding programs to shorten generation intervals and accelerate genetic progress per unit of time. In practice, genomic selection can be used to improve several correlated traits simultaneously via multiple-trait prediction, which exploits correlations between traits. However, few studies have explored multiple-trait genomic selection. Our aim was to infer genetic correlations between three traits measured in broiler chickens by exploring kinship matrices based on a linear combination of measures of pedigree and marker-based relatedness. A predictive assessment was used to gauge genetic correlations.

Methods

A multivariate genomic best linear unbiased prediction model was designed to combine information from pedigree and genome-wide markers in order to assess genetic correlations between three complex traits in chickens, i.e. body weight at 35 days of age (BW), ultrasound area of breast meat (BM) and hen-house egg production (HHP). A dataset with 1351 birds that were genotyped with the 600 K Affymetrix platform was used. A kinship kernel (K) was constructed as K = λG + (1 − λ)A, where A is the numerator relationship matrix, measuring pedigree-based relatedness, and G is a genomic relationship matrix. The weight (λ) assigned to each source of information varied over the grid λ = (0, 0.2, 0.4, 0.6, 0.8, 1). Maximum likelihood estimates of heritability and genetic correlations were obtained at each λ, and the “optimum” λ was determined using cross-validation.

Results

Estimates of genetic correlations were affected by the weight placed on the source of information used to build K. For example, the genetic correlation between BW–HHP and BM–HHP changed markedly when λ varied from 0 (only A used for measuring relatedness) to 1 (only genomic information used). As λ increased, predictive correlations (correlation between observed phenotypes and predicted breeding values) increased and mean-squared predictive error decreased. However, the improvement in predictive ability was not monotonic, with an optimum found at some 0 < λ < 1, i.e., when both sources of information were used together.

Conclusions

Our findings indicate that multiple-trait prediction may benefit from combining pedigree and marker information. Also, it appeared that expected correlated responses to selection computed from standard theory may differ from realized responses. The predictive assessment provided a metric for performance evaluation as well as a means for expressing uncertainty of outcomes of multiple-trait selection.

The genetic basis of pectoralis major myopathies in modern broiler chicken lines

This is the first report providing estimates of the genetic basis of breast muscle myopathies (BMM) and their relationship with growth and yield in broiler chickens. In addition, this paper addresses the hypothesis that genetic selection for increase breast yield has contributed to the onset of BMM. Data were analyzed from ongoing recording of BMM within the Aviagen breeding program. This study focused on three BMM: deep pectoral myopathy (DPM; binary trait), white striping (WS; 4 categories) and wooden breast (WB; 3 categories). Data from two purebred commercial broiler lines (A and B) were utilized providing greater than 40,000 meat quality records per line. The difference in selection history between these two lines has resulted in contrasting breast yield (BY): 29% for Line A and 21% for Line B. Data were analyzed to estimate genetic parameters using a multivariate animal model including six traits: body weight (BW), processing body weight (PW), BY, DPM, WB, and WS, in addition to the appropriate fixed effects and permanent environmental effect of the dam. Results indicate similar patterns of heritability and genetic correlations for the two lines. Heritabilities (h²) of BW, PW and BY ranged from 0.271–0.418; for DPM and WB h² <0.1; and for WS h² ≤0.338. Genetic correlations between the BMM and BW, PW, or BY were ≤0.132 in Line A and ≤0.248 in Line B. This paper demonstrates the polygenic nature of these traits and the low genetic relationships with BW, PW, and BY, which facilitates genetic improvement across all traits in a balanced breeding program. It also highlights the importance of understanding the environmental and/or management factors that contribute greater than 65% of the variance in the incidence of white striping of breast muscle and more than 90% of the variance of the incidence of wooden breast and deep pectoral myopathy in broiler chickens.

Unexpected consequences of genetic selection in broilers and turkeys: problems and solutions

1. Genetic theory leads to the expectation that unexpected consequences of genetic selection for production traits will inevitably occur and that these changes are likely to be undesirable. 2. Both artificial selection for production efficiency and "natural" selection for adaptation to the production environment result in selection sweeps that increase the frequencies of rare recessive alleles that have a negative effect on fitness. 3. Fitness is broadly defined as any trait that affects the ability to survive, reproduce and contribute to the next generation, such as musculoskeletal disease in growing broiler chickens and multiple ovulation in adult broiler parents. 4. Welfare concerns about the negative effects of genetic selection on bird welfare are sometimes exaggerated but are nevertheless real. Breeders have paid increasing attention to these traits over several decades and have demonstrated improvement in pedigree flocks. There is an urgent need to monitor changes in commercial flocks to ensure that genetic change is accompanied by improvements in that target population. 5. New technologies for trait measurement, whole genome selection and targeted genetic modification hold out the promise of efficient and rapid improvement of welfare traits in future breeding of broiler chickens and turkeys. The potential of targeted genetic modification for enhancing welfare traits is considerable, but the goal of achieving public acceptability for the progeny of transgenic poultry will be politically challenging.

Campylobacter colonization and proliferation in the broiler chicken upon natural field challenge is not affected by the bird growth rate or breed

The zoonotic association between Campylobacter bacteria in poultry and humans has been characterized by decades of research which has attempted to elucidate the epidemiology of this complex relationship and to reduce carriage within poultry. While much work has focused on the mechanisms facilitating its success in contaminating chicken flocks (and other animal hosts), it remains difficult to consistently exclude Campylobacter under field conditions. Within the United Kingdom poultry industry, various bird genotypes with widely varying growth rates are available to meet market needs and consumer preferences. However, little is known about whether any differences in Campylobacter carriage exist across this modern broiler range. The aim of this study was to establish if a relationship exists between growth rate or breed and cecal Campylobacter concentration after natural commercial flock Campylobacter challenge. In one investigation, four pure line genotypes of various growth rates were grown together, while in the second, eight different commercial broiler genotypes were grown individually. In both studies, the Campylobacter concentration was measured in the ceca at 42 days of age, revealing no significant difference in cecal load between birds of different genotypes both in mixed- and single-genotype pens. This is important from a public health perspective and suggests that other underlying reasons beyond genotype are likely to control and affect Campylobacter colonization within chickens. Further studies to gain a better understanding of colonization dynamics and subsequent proliferation are needed, as are novel approaches to reduce the burden in poultry.

Traditional and commercial turkeys show similar susceptibility to foot pad dermatitis and behavioural evidence of pain

1. An experiment was conducted to compare the development and clinical significance of foot pad dermatitis (FPD) in 4 lines of turkey poults kept on wet or dry litter for 6 d. 2. Turkeys kept on wet litter were less active and expressed fewer unique sequences of behaviour than poults kept on dry litter, suggesting that high FPD scores are associated with pain during movement. 3. Heavier lines of turkeys had higher mean foot scores that developed earlier, than those in a traditional line, but the effect was relatively small and not statistically significant after 6 d, whereas there were large differences between individuals within line. 4. Body weight gains were greater, and feed intake was lower in the commercial lines kept on dry litter compared with wet litter. There were no differences in water intake between poults kept on wet or dry litter.

Twenty-five years of selection for improved leg health in purebred broiler lines and underlying genetic parameters

Leg health is an important component of broiler welfare and the economics of broiler production. This study presents the development of leg health in 3 purebred commercial broiler lines during 25 yr of selection and investigates the genetic background of leg health traits in current populations of these lines. The leg health traits were deformities of the long bones (LD) and crooked toes (CT), recorded since 1985, and tibial dyschondroplasia (TD) and hock burn (HB), recorded since 1990. The prevalence of CT and HB decreased mainly in the first decade (range among lines -1.2 to -2.3% and -1.3 to -1.5% per year, respectively), after which it stabilized at low levels. The prevalence of LD and TD decreased by -0.6 to -0.9% and -0.4 to -1.2% per year, respectively. Genetic parameters were estimated using data from 4 recent generations. The BW ranged from 2.0 to 2.4 kg at 5 wk of age; the prevalences of LD, CT, TD, and HB from 8.6 to 12.9%, 0.6 to 2.6%, 4.6 to 8.0%, and 4.0 to 12.2%, respectively. Estimates of heritability were 0.04 to 0.07 for LD, 0.01 to 0.10 for CT, 0.10 to 0.27 for TD, and 0.06 to 0.09 for HB (all SE ≤0.01). Estimates of the genetic correlations between LD and CT were 0.11 to 0.43 (all SE ≤0.09), between these traits and HB were negligible, and of TD with LD, CT, and HB were -0.26 to 0.16 (all SE ≤0.11). Estimates of genetic correlations between the leg health traits and BW were lowly to moderately unfavorable, ranging from 0.09 to 0.37 (all SE ≤0.06). The differences between the lines suggest that strategies for simultaneous improvement of all traits tailored for each line individually have been effective. This research demonstrates the long-term effectiveness of selection for improving leg health in broilers and highlights that, despite somewhat unfavorable genetic correlations with BW, these traits can be improved simultaneously in a balanced breeding program.