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.

Quantitative trait loci and transcriptome signatures associated with avian heritable resistance to Campylobacter.

Campylobacter is the leading cause of bacterial foodborne gastroenteritis worldwide. Handling or consumption of contaminated poultry meat is a key risk factor for human campylobacteriosis. One potential control strategy is to select poultry with increased resistance to Campylobacter. We associated high-density genome-wide genotypes (600K single nucleotide polymorphisms) of 3000 commercial broilers with Campylobacter load in their caeca. Trait heritability was modest but significant (h2 = 0.11 ± 0.03). Results confirmed quantitative trait loci (QTL) on chromosomes 14 and 16 previously identified in inbred chicken lines, and detected two additional QTLs on chromosomes 19 and 26. RNA-Seq analysis of broilers at the extremes of colonisation phenotype identified differentially transcribed genes within the QTL on chromosome 16 and proximal to the major histocompatibility complex (MHC) locus. We identified strong cis-QTLs located within MHC suggesting the presence of cis-acting variation in MHC class I and II and BG genes. Pathway and network analyses implicated cooperative functional pathways and networks in colonisation, including those related to antigen presentation, innate and adaptive immune responses, calcium, and renin-angiotensin signalling. While co-selection for enhanced resistance and other breeding goals is feasible, the frequency of resistance-associated alleles was high in the population studied and non-genetic factors significantly influenced Campylobacter colonisation.

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.

Deciphering the mode of action and position of genetic variants impacting on egg number in broiler breeders.

BACKGROUND: Aim of the present study was first to identify genetic variants associated with egg number (EN) in female broilers, second to describe the mode of their gene action (additive and/or dominant) and third to provide a list with implicated candidate genes for the trait. A number of 2586 female broilers genotyped with the high density (~ 600 k) SNP array and with records on EN (mean = 132.4 eggs, SD = 29.8 eggs) were used. Data were analyzed with application of additive and dominant multi-locus mixed models. RESULTS: A number of 7 additive, 4 dominant and 6 additive plus dominant marker-trait significant associations were detected. A total number of 57 positional candidate genes were detected within 50 kb downstream and upstream flanking regions of the 17 significant markers. Functional enrichment analysis pinpointed two genes (BHLHE40 and CRTC1) to be involved in the 'entrainment of circadian clock by photoperiod' biological process. Gene prioritization analysis of the positional candidate genes identified 10 top ranked genes (GDF15, BHLHE40, JUND, GDF3, COMP, ITPR1, ELF3, ELL, CRLF1 and IFI30). Seven prioritized genes (GDF15, BHLHE40, JUND, GDF3, COMP, ELF3, CRTC1) have documented functional relevance to reproduction, while two more prioritized genes (ITPR1 and ELL) are reported to be related to egg quality in chickens. CONCLUSIONS: Present results have shown that detailed exploration of phenotype-marker associations can disclose the mode of action of genetic variants and help in identifying causative genes associated with reproductive traits in the species.

Discovery and characterization of functional modules associated with body weight in broilers.

Aim of the present study was to investigate whether body weight (BW) in broilers is associated with functional modular genes. To this end, first a GWAS for BW was conducted using 6,598 broilers and the high density SNP array. The next step was to search for positional candidate genes and QTLs within strong LD genomic regions around the significant SNPs. Using all positional candidate genes, a network was then constructed and community structure analysis was performed. Finally, functional enrichment analysis was applied to infer the functional relevance of modular genes. A total number of 645 positional candidate genes were identified in strong LD genomic regions around 11 genome-wide significant markers. 428 of the positional candidate genes were located within growth related QTLs. Community structure analysis detected 5 modules while functional enrichment analysis showed that 52 modular genes participated in developmental processes such as skeletal system development. An additional number of 14 modular genes (GABRG1, NGF, APOBEC2, STAT5B, STAT3, SMAD4, MED1, CACNB1, SLAIN2, LEMD2, ZC3H18, TMEM132D, FRYL and SGCB) were also identified as related to body weight. Taken together, current results suggested a total number of 66 genes as most plausible functional candidates for the trait examined.

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.

Development of a Mechatronic System for Rehabilitation of Injuries in the Radial Nerve / Desarrollo de un Sistema Mecatrónico para Rehabilitación de Lesiones del Nervio Radial

ABSTRACT This work presents the design, analysis and implementation of a mechatronic System focused on helping to improve Rehabilitation therapies to patients affected by some Radial Nerve Injuries (SYRR-NERI). The device was developed with the aim of finding simple solutions for the different subsystems that form the SYRR-NERI. The mechatronic system basically consists of two coupled four-bar mechanisms with a Proportional-Integral-Derivative (PID) controller in their respective drive motors to regulate the rotational velocity. In addition, each mechanism has touch sensors in order to limit its movement. The implementation of the control algorithm and the logic to perform the synchronized movements is performed by a microcontroller. The result is an affordable and functional prototype which needs to be tested in real situations with the help of physiotherapists and patients to obtain the necessary information to improve its performance.

RESUMEN Este trabajo presenta el diseño, análisis e implementación de un sistema mecatrónico enfocado en ayudar a mejorar las terapias de rehabilitación para pacientes afectados por algunas lesiones del nervio radial. El dispositivo fue desarrollado tratando de proponer soluciones sencillas para los diferentes subsistemas que integran el dispositivo. El sistema mecatrónico consiste básicamente en dos mecanismos acoplados de cuatro barras con un controlador Proporcional-Integral-Derivativo (PID) en sus respectivos motores impulsores para regular la velocidad angular. Además, cada mecanismo tiene sensores táctiles para limitar el movimiento. La implementación del algoritmo de control y de la lógica para realizar los movimientos sincronizados se lleva a cabo mediante un microcontrolador. El resultado es un dispositivo económicamente accesible y funcional que tiene por objetivo ser probado en situaciones reales y, con la ayuda de fisioterapeutas y pacientes, obtener la información necesaria para mejorar su desempeño.

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.

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.

Comparison of classification methods for detecting associations between SNPs and chick mortality.

Multi-category classification methods were used to detect SNP-mortality associations in broilers. The objective was to select a subset of whole genome SNPs associated with chick mortality. This was done by categorizing mortality rates and using a filter-wrapper feature selection procedure in each of the classification methods evaluated. Different numbers of categories (2, 3, 4, 5 and 10) and three classification algorithms (naïve Bayes classifiers, Bayesian networks and neural networks) were compared, using early and late chick mortality rates in low and high hygiene environments. Evaluation of SNPs selected by each classification method was done by predicted residual sum of squares and a significance test-related metric. A naïve Bayes classifier, coupled with discretization into two or three categories generated the SNP subset with greatest predictive ability. Further, an alternative categorization scheme, which used only two extreme portions of the empirical distribution of mortality rates, was considered. This scheme selected SNPs with greater predictive ability than those chosen by the methods described previously. Use of extreme samples seems to enhance the ability of feature selection procedures to select influential SNPs in genetic association studies.

Nonparametric methods for incorporating genomic information into genetic evaluations: an application to mortality in broilers.

Four approaches using single-nucleotide polymorphism (SNP) information (F(infinity)-metric model, kernel regression, reproducing kernel Hilbert spaces (RKHS) regression, and a Bayesian regression) were compared with a standard procedure of genetic evaluation (E-BLUP) of sires using mortality rates in broilers as a response variable, working in a Bayesian framework. Late mortality (14-42 days of age) records on 12,167 progeny of 200 sires were precorrected for fixed and random (nongenetic) effects used in the model for genetic evaluation and for the mate effect. The average of the corrected records was computed for each sire. Twenty-four SNPs seemingly associated with late mortality were included in three methods used for genomic assisted evaluations. One thousand SNPs were included in the Bayesian regression, to account for markers along the whole genome. The posterior mean of heritability of mortality was 0.02 in the E-BLUP approach, suggesting that genetic evaluation could be improved if suitable molecular markers were available. Estimates of posterior means and standard deviations of the residual variance were 24.38 (3.88), 29.97 (3.22), 17.07 (3.02), and 20.74 (2.87) for E-BLUP, the linear model on SNPs, RKHS regression, and the Bayesian regression, respectively, suggesting that RKHS accounted for more variance in the data. The two nonparametric methods (kernel and RKHS regression) fitted the data better, having a lower residual sum of squares. Predictive ability, assessed by cross-validation, indicated advantages of the RKHS approach, where accuracy was increased from 25 to 150%, relative to other methods.

Linkage disequilibrium in related breeding lines of chickens.

High-density genotyping of single-nucleotide polymorphisms (SNPs) enables detection of quantitative trait loci (QTL) by linkage disequilibrium (LD) mapping using LD between markers and QTL and the subsequent use of this information for marker-assisted selection (MAS). The success of LD mapping and MAS depends on the extent of LD in the populations of interest and the use of associations across populations requires LD between loci to be consistent across populations. To assess the extent and consistency of LD in commercial broiler breeding populations, we used genotype data for 959 and 398 SNPs on chromosomes 1 and 4 on 179-244 individuals from each of nine commercial broiler chicken breeding lines. Results show that LD measured by r(2) extends over shorter distances than reported previously in other livestock breeding populations. The LD at short distance (within 1 cM) tended to be consistent across related populations; correlations of LD measured by r for pairs of lines ranged from 0.17 to 0.94 and closely matched the line relationships based on marker allele frequencies. In conclusion, LD-based correlations are good estimates of line relationships and the relationship between a pair of lines a good predictor of LD consistency between the lines.

Genetic heterogeneity of residual variance in broiler chickens.

Aims were to estimate the extent of genetic heterogeneity in environmental variance. Data comprised 99 535 records of 35-day body weights from broiler chickens reared in a controlled environment. Residual variance within dam families was estimated using ASREML, after fitting fixed effects such as genetic groups and hatches, for each of 377 genetically contemporary sires with a large number of progeny (>100 males or females each). Residual variance was computed separately for male and female offspring, and after correction for sampling, strong evidence for heterogeneity was found, the standard deviation between sires in within variance amounting to 15-18% of its mean. Reanalysis using log-transformed data gave similar results, and elimination of 2-3% of outlier data reduced the heterogeneity but it was still over 10%. The correlation between estimates for males and females was low, however. The correlation between sire effects on progeny mean and residual variance for body weight was small and negative (-0.1). Using a data set bigger than any yet presented and on a trait measurable in both sexes, this study has shown evidence for heterogeneity in the residual variance, which could not be explained by segregation of major genes unless very few determined the trait.

Prediction of genetic gain from quadratic optimisation with constrained rates of inbreeding.

There are selection methods available that allow the optimisation of genetic contributions of selection candidates for maximising the rate of genetic gain while restricting the rate of inbreeding. These methods imply selection on quadratic indices as the selection merit of a particular individual is a quadratic function of its estimated breeding value. This study provides deterministic predictions of genetic gain from selection on quadratic indices for a given set of resources (the number of candidates), heritability, and target rate of inbreeding. The rate of gain was obtained as a function of the accuracy of the Mendelian sampling term at the time of convergence of long-term contributions of selected candidates and the theoretical ideal rate of gain for a given rate of inbreeding after an exact allocation of long-term contributions to Mendelian sampling terms. The expected benefits from quadratic indices over traditional linear indices (i.e. truncation selection), both using BLUP breeding values, were quantified. The results clearly indicate higher gains from quadratic optimisation than from truncation selection. With constant rate of inbreeding and number of candidates, the benefits were generally largest for intermediate heritabilities but evident over the entire range. The advantage of quadratic indices was not highly sensitive to the rate of inbreeding for the constraints considered.