Layer breeding strategies: an overview

Host genetics and gut microbiota synergistically regulate feed utilization in egg-type chickens

BACKGROUND

Feed efficiency is a crucial economic trait in poultry industry. Both host genetics and gut microbiota influence feed efficiency. However, the associations between gut microbiota and host genetics, as well as their combined contributions to feed efficiency in laying hens during the late laying period, remain largely unclear.

METHODS

In total, 686 laying hens were used for whole-genome resequencing and liver transcriptome sequencing. 16S rRNA gene sequencing was conducted on gut chyme (duodenum, jejunum, ileum, and cecum) and fecal samples from 705 individuals. Bioinformatic analysis was performed by integrating the genome, transcriptome, and microbiome to screen for key genetic variations, genes, and gut microbiota associated with feed efficiency.

RESULTS

The heritability of feed conversion ratio (FCR) and residual feed intake (RFI) was determined to be 0.28 and 0.48, respectively. The ileal and fecal microbiota accounted for 15% and 10% of the FCR variance, while the jejunal, cecal, and fecal microbiota accounted for 20%, 11%, and 10% of the RFI variance. Through SMR analysis based on summary data from liver eQTL mapping and GWAS, we further identified four protein-coding genes, SUCLA2, TNFSF13B, SERTM1, and MARVELD3, that influence feed efficiency in laying hens. The SUCLA2 and TNFSF13B genes were significantly associated with SNP 1:25664581 and SNP rs312433097, respectively. SERTM1 showed significant associations with rs730958360 and 1:33542680 and is a potential causal gene associated with the abundance of Corynebacteriaceae in feces. MARVELD3 was significantly associated with the 1:135348198 and was significantly correlated with the abundance of Enterococcus in ileum. Specifically, a lower abundance of Enterococcus in ileum and a higher abundance of Corynebacteriaceae in feces were associated with better feed efficiency.

CONCLUSIONS

This study confirms that both host genetics and gut microbiota can drive variations in feed efficiency. A small portion of the gut microbiota often interacts with host genes, collectively enhancing feed efficiency. Therefore, targeting both the gut microbiota and host genetic variation by supporting more efficient taxa and selective breeding could improve feed efficiency in laying hens during the late laying period.

Towards genetic improvement of social behaviours in livestock using large-scale sensor data: data simulation and genetic analysis

BACKGROUND

Harmful social behaviours, such as injurious feather pecking in poultry and tail biting in swine, reduce animal welfare and production efficiency. While these behaviours are heritable, selective breeding is still limited due to a lack of individual phenotyping methods for large groups and proper genetic models. In the near future, large-scale longitudinal data on social behaviours will become available, e.g. through computer vision techniques, and appropriate genetic models will be needed to analyse such data. In this paper, we investigated prospects for genetic improvement of social traits recorded in large groups by (1) developing models to simulate and analyse large-scale longitudinal data on social behaviours, and (2) investigating required sample sizes to obtain reasonable accuracies of estimated genetic parameters and breeding values (EBV).

RESULTS

Latent traits were defined as representing tendencies of individuals to be engaged in social interactions by distinguishing between performer and recipient effects. Animal movement was assumed random and without genetic variation, and performer and recipient interaction effects were assumed constant over time. Based on the literature, observed-scale heritabilities ([Formula: see text]) of performer and recipient effects were both set to 0.05, 0.1, or 0.2, and the genetic correlation ([Formula: see text]) between those effects was set to - 0.5, 0, or 0.5. Using agent-based modelling, we simulated ~ 200,000 interactions for 2000 animals (~ 1000 interactions per animal) with a half-sib family structure. Variance components and breeding values were estimated with a general linear mixed model. The estimated genetic parameters did not differ significantly from the true values. When all individuals and interactions were included in the analysis, the accuracy of EBV was 0.61, 0.70, and 0.76 for [Formula: see text] = 0.05, 0.1, and 0.2, respectively (for [Formula: see text]= 0). Including 2000 individuals each with only ~ 100 interactions, already yielded promising accuracies of 0.47, 0.60, and 0.71 for [Formula: see text] = 0.05, 0.1, and 0.2, respectively (with [Formula: see text] = 0). Similar results were found with [Formula: see text] of - 0.5 or 0.5.

CONCLUSIONS

We developed models to simulate and genetically analyse social behaviours for animals that are kept in large groups, anticipating the availability of large-scale longitudinal data in the near future. We obtained promising accuracies of EBV with ~ 100 interactions per individual, which would correspond to a few weeks of recording. Therefore, we conclude that animal breeding can be a promising strategy to improve social behaviours in livestock.

Evaluation of reciprocal F1 crosses of Fayoumi with two exotic chicken breeds 1: additive and non-additive effects on egg production traits

The present study estimates additive and non-additive effects on egg production traits in genotypes generated through pure mating and reciprocal crossing of Fayoumi (FM) with Koekoek (KK) and White Leghorn (WL). Age at first egg (AFE) and body weight at first egg (BWAFE) were determined when the first bird in the pen laid its first egg, and egg weight at first egg (EWAFE) was the average weight of eggs laid consecutively during the first 10 days. Egg number (EN) and egg weight (EW) were recorded daily from AFE to 40 weeks of age. Egg mass (EM) was the product of EN and EW. EN of hens initially housed and hens alive during the experiment were used to calculate hen-housed egg production (HHEP) and hen-day egg production (HDEP), respectively. All the traits showed statistically significant differences among the genotypes. The results revealed the importance of additive and non-additive effects, where purebred effect (PE), general combining ability (GCA), maternal effect (ME), specific combining ability (SCA), and residual reciprocal effect (RRE) significantly affected most of the traits. The KK and WL had a higher PE, and GCA was highest in KK, with FM and WL showing a higher ME. The FM x WL had higher SCA and RRE. The KK x FM and FM x WL outperformed their main and reciprocal crosses, respectively, and purebred contemporaries. Therefore, a synthetic breeding program involving KK as a sire and FM, WL, FM x WL, and KK x FM as a dam would be feasible.

Fear, anxiety, and production in laying hens with healed keel bone fractures

For laying hens, the immediate aftermath and healing period of a keel fracture (KF) is characterized by reduced ability to perform species-specific behavior, access resources, and pain. However, the longer-term impacts, once the fracture is completely healed, are less clear. As well as acute pain and behavioral changes, a negative experience can shape future responses to putatively threatening stimuli, raising future fear, and anxiety levels during husbandry-related events. We aimed to determine whether hens that had previously sustained keel bone fractures, but were now outside of the peak age range for new fractures, showed higher fear and anxiety levels compared to intact hens. We also determined if healed keel bone fractures were associated with reduced production, changes in behavior and resource use. One hundred and fifty hens with a palpation score of 1 ( "KF") and 150 hens with a palpation score of 0 (keel fracture free, "KFF") were selected from a commercial farm at 63 wk of age and housed in 6 groups (3 × KF and 3 × KFF). We compared production (hen weight and feed consumption, egg quantity, quality and weight, floor eggs, shell thickness, and weight) and home pen behavior (behaviors and transitional movements) in both groups. Finally, we measured the responses of KF (n = 75) and KFF (n = 75) during tonic immobility, novel arena, and novel object tests. KF and KFF hens did not differ in their responses to the tonic immobility, novel arena, and novel object tests, nor were there differences between the 2 groups in home pen behavior and transitional movements. KFF birds were lighter and laid eggs with less eggshell membrane compared KF birds, but no differences were found between KF and KFF in any other production measures. We found no evidence that healed KFs were associated with detrimental welfare effects in laying hens, but further work is required to determine the mechanisms and implications of the lower body weight and egg shell membrane.

Effects of Selenium Yeast on Egg Quality, Plasma Antioxidants, Selenium Deposition and Eggshell Formation in Aged Laying Hens

Internal egg and eggshell quality are often deteriorated in aging laying hens, which causes huge economic losses in the poultry industry. Selenium yeast (SY), as an organic food additive, is utilized to enhance laying performance and egg quality. To extend the egg production cycle, effects of selenium yeast supplementation on egg quality, plasma antioxidants and selenium deposition in aged laying hens were evaluated. In this study, five hundred and twenty-five 76-week-old Jing Hong laying hens were fed a selenium-deficient (SD) diet for 6 weeks. After Se depletion, the hens were randomly divided into seven treatments, which included an SD diet, and dietary supplementation of SY and sodium selenite (SS) at 0.15, 0.30, and 0.45 mg/kg to investigate the effect on egg quality, plasma antioxidant capacity, and selenium content in reproductive organs. After 12 weeks of feeding, dietary SY supplementation resulted in higher eggshell strength (SY0.45) (p < 0.05) and lower shell translucence. Moreover, organs Se levels and plasma antioxidant capacity (T-AOC, T-SOD, and GSH-Px activity) were significantly higher with Se supplementation (p < 0.05). Transcriptomic analysis identified some key candidate genes including cell migration inducing hyaluronidase 1 (CEMIP), ovalbumin (OVAL), solute carrier family 6 member 17 (SLC6A17), proopiomelanocortin (POMC), and proenkephalin (PENK), and potential molecular processes (eggshell mineralization, ion transport, and eggshell formation) involved in selenium yeast's effects on eggshell formation. In conclusion, SY has beneficial functions for eggshell and we recommend the supplementation of 0.45 mg/kg SY to alleviate the decrease in eggshell quality in aged laying hens.

Genetic and microbiome analysis of feed efficiency in laying hens

Improving feed efficiency is an important target for poultry breeding. Feed efficiency is affected by host genetics and the gut microbiota, but many of the mechanisms remain elusive in laying hens, especially in the late laying period. In this study, we measured feed intake, body weight, and egg mass of 714 hens from a pedigreed line from 69 to 72 wk of age and calculated the residual feed intake (RFI) and feed conversion ratio (FCR). In addition, fecal samples were also collected for 16S ribosomal RNA gene sequencing (V4 region). Genetic analysis was then conducted in DMU packages by using AI-REML with animal model. Moderate heritability estimates for FCR (h² = 0.31) and RFI (h² = 0.52) were observed, suggesting that proper selection programs can directly improve feed efficiency. Genetically, RFI was less correlated with body weight and egg mass than that of FCR. The phenotypic variance explained by gut microbial variance is defined as the microbiability (m²). The microbiability estimates for FCR (m² = 0.03) and RFI (m² = 0.16) suggested the gut microbiota was also involved in the regulation of feed efficiency. In addition, our results showed that the effect of host genetics on fecal microbiota was minor in three aspects: 1) microbial diversity indexes had low heritability estimates, and genera with heritability estimates more than 0.1 accounted for only 1.07% of the tested fecal microbiota; 2) the genetic relationship correlations between host genetics and different microbial distance were very weak, ranging from -0.0057 to -0.0003; 3) the microbial distance between different kinships showed no significant difference. Since the RFI has the highest microbiability, we further screened out three genera, including Anaerosporobacter, Candidatus Stoquefichus, and Fournierella, which were negatively correlated with RFI and played positive roles in improving the feed efficiency. These findings contribute to a great understanding of the genetic background and microbial influences on feed efficiency.

Inheritance of the duration of fertility in chickens and its correlation with laying performance

Background

Duration of fertility (DF) is an important economic trait in poultry production because it has a strong effect on chick output. Various criteria or traits to assess DF on individual hens have been reported but they are affected by many nongenetic factors. Thus, a reliable definition and associated genetic parameters are needed. Because egg production is also vital in chicken breeding, knowledge of the relationship between DF and laying performance is needed for designing selection programs.

Methods

We used five traits that consider both fertility and embryonic livability to delineate DF. Phenotypic and genetic analyses were completed for 2094 hens, with measurements of DF at 35 and 60 weeks of age and hatching egg production at 400 days of age (HEP400). The selection differentials for DF and HEP400 were evaluated.

Results

DF is largely independent of the number of oviposited eggs in the peak laying period but both egg production and DF naturally decline with age. The heritability of the five DF traits ranged from 0.11 to 0.13 at 35 weeks of age and increased slightly in the later laying period, ranging from 0.14 to 0.17 (except for efficient duration, time between insemination and the first unhatched egg). Estimates of the genetic correlation for a given trait measured at the two ages were moderate (0.37–0.44), except for efficient duration. However, number of viable embryos depends strongly on egg production. Estimates of genetic correlations of fertility duration day (FDD) at both ages with HEP were weak. Selection for FDD improved DF but without a significant change in laying performance. Selection for increased HEP400 did not contribute to DF improvement.

Conclusions

Although estimates of heritability of the five traits related to DF were low, selection to improve DF based on any one of them is possible. Among these, FDD is an effective selection criterion when the eggs are collected for approximately two weeks after insemination. The best selection procedure for DF improvement would involve multiple measurements at various ages. FDD is independent of laying performance and can be incorporated into a breeding program with egg production to improve reproductive efficiency.

The effects of the breeder index value on the microscopic structure of egg shells, hatching results, and hybrid performance

The quality of egg shell and bone properties of hen are important for hen welfare, consumers, and producers. Parameters of the genetic selection have both desirable and undesirable effects among themselves. Until recently, it has been stated that the concept of shell quality is not only about breaking strength, thickness, and weight of shell, but also microscopic properties of the shell. In this study, the effect of index selection including age and weight at sexual maturity, number of eggs and egg weight on eggshell structures, hatching results, and hybrid performance was determined. Ninety Barred Rock 1 (BAR-1) and ninety Rhode Island Red 1 (RIR-1) hens and twenty RIR-1 cocks (46 weeks old) were used. BAR-1 and RIR-1 were classified according to the breeder index value as low and high. Egg quality characteristics, embryo development and hatching results were examined in eggs obtained from these lines. In the hybrid eggs with high breeder index, the thickness of the palisade layer, breaking strength, ash, and Ca level of the shell were lower and cone similarity and egg weight were higher than that with low breeder index. The breaking strength of the egg shell had a significantly positive correlation with the palisade layer thickness of the shell. In addition, the tibia weight of the high breeder index group was lower than that of the low breeder index group. Differences in femur and tibia weights in hybrids with low and high breeder index increased with age. A negative correlation was observed between hatchability and the thickness of the palisade layer. Further studies are needed to determine which selection programs positively affect the thickness of the palisade layer, the Ca level and the breaking strength of the shell, the number of broken eggs, and the tibia weight in layer hybrids.

Egg Production and Bone Stability of Local Chicken Breeds and Their Crosses Fed with Faba Beans

Poultry production is raising concerns within the public regarding the practice of culling day-old chicks and the importation of soy from overseas for feedstuff. Therefore, an alternative approach to poultry production was tested. In two consecutive experiments, two traditional chicken breeds, Vorwerkhuhn and Bresse Gauloise, and White Rock as a commercial layer genotype as well as crossbreds thereof were fed diets containing either 20% vicin-rich or vicin-poor faba beans, though addressing both subjects of debate. Hen performance traits and bone stability were recorded. All parameters were considerably influenced by the genotype with White Rock showing the significantly highest (p < 0.05) laying performance (99.4% peak production) and mean egg weights (56.6 g) of the purebreds, but the lowest bone breaking strength (tibiotarsus 197.2 N, humerus 230.2 N). Regarding crossbreds, the Bresse Gauloise × White Rock cross performed best (peak production 98.1%, mean egg weight 58.0 g). However, only limited dietary effects were found as only the feeding of 20% vicin-rich faba beans led to a significant reduction of egg weights of at most 1.1 g (p < 0.05) and to a significant reduction of the shell stability in the crossbred genotypes. In terms of dual-purpose usage, crossing of Bresse Gauloise with White Rock seems to be the most promising variant studied here.

Relationship between Bone Stability and Egg Production in Genetically Divergent Chicken Layer Lines

Impaired animal welfare due to skeletal disorders is likely one of the greatest issues currently facing the egg production industry. Reduced bone stability in laying hens is frequently attributed to long-term selection for increased egg production. The present study sought to analyse the relationship between bone stability traits and egg production. The study comprised four purebred layer lines, differing in their phylogenetic origin and performance level, providing extended insight into the phenotypic variability in bone characteristics in laying hens. Data collection included basic production parameters, bone morphometry, bone mineral density (BMD) and bone breaking strength (BBS) of the tibiotarsus and humerus. Using a multifactorial model and regression analyses, BMD proved to be of outstanding importance for bone stability. Only for the tibiotarsus were morphometric parameters and the bone weight associated with BBS. Within the chicken lines, no effect of total eggshell production on BBS or BMD could be detected, suggesting that a high egg yield itself is not necessarily a risk for poor bone health. Considering the complexity of osteoporosis, the estimated genetic parameters confirmed the importance of genetics in addressing the challenge of improving bone strength in layers.

Keel bone fractures affect egg laying performance but not egg quality in laying hens housed in a commercial aviary system

The aim of this study was to investigate the effect of keel bone fracture (KBF) severity and healing activity on individual productivity of laying hens. Focal hens (75 Lohmann Selected Leghorn (LSL), 75 Lohmann Brown (LB)) were housed alongside non-focal hens in 10 identical pens containing a commercial aviary system (15 focal hens per pen). Eggs of focal hens were identified by orally administering a dye on 3 consecutive days, resulting in a hen-specific color pattern in the yolk. Eggs were collected at 7 time points (37 to 61 weeks of age; WOA) for 5 d to determine individual laying performance and to assess egg quality. Radiographs were performed to score KBF severity on a continuous scale. Healing activity was scored as inactive, healing, or fresh. Linear mixed effects models were used for statistical analyses. We found an association between KBF severity and reduced egg laying performance with increasing age (P = 0.005). At 37 WOA, egg laying performance was similar across KBF severities, whereas at 61 WOA, performance in hens with the highest observed KBF severity was 16.2% lower than in hens without fractures. Hens with fresh fractures had a lower performance than hens with healing and inactive fractures at 37 WOA but higher performance at 61 WOA (P = 0.02). Egg quality parameters were not affected by fractures but were associated with an age × hybrid interaction (egg mass: P = 0.039, shell breaking strength: P = 0.03, shell width: P = 0.001). In conclusion, hens could maintain high performance irrespective of fracture severity until shortly after peak of lay, but seemed to redirect available resources towards fracture healing if a fresh fracture was present. At the end of lay, the negative effect of KBF fracture severity on individual production amplified indicating that hens were no longer able to cope with the physiological challenge of a fracture.

Susceptibility to keel bone fractures in laying hens and the role of genetic variation

Keel bone fractures are a well-known welfare problem in modern commercial laying hen systems. The present study sought to identify genetic variation in relation to keel bone fracture susceptibility of 4 distinct crossbred and one pure line, and by extension, possible breeding traits. Susceptibility to fractures were assessed using an ex vivo impact testing protocol in combination with a study design that minimized environmental variation to focus on genetic differences. The 5 crossbred/pure lines differed in their susceptibility to keel bone fractures with the greatest likelihood of fracture in one of the 3 commercial lines and the lowest susceptibility to fractures in one of the experimental lines. Egg production at the hen-level did not differ between the crossbred/pure lines (P > 0.05), though an increased susceptibility to keel bone fractures was associated with thinner eggshells and reduced egg breaking strength, a pattern consistent among all tested crossbred/pure lines. Our findings suggest an association between egg quality and bone strength which appeared to be independent of crossbred/pure line. The findings indicate the benefit of the impact methodology to identify potential breeding characteristics to reduce incidence of keel fracture as well as the potential relationship with eggshell quality.

Detection of genomic signatures of recent selection in commercial broiler chickens

Background

Identification of the genomic signatures of recent selection may help uncover causal polymorphisms controlling traits relevant to recent decades of selective breeding in livestock. In this study, we aimed at detecting signatures of recent selection in commercial broiler chickens using genotype information from single nucleotide polymorphisms (SNPs). A total of 565 chickens from five commercial purebred lines, including three broiler sire (male) lines and two broiler dam (female) lines, were genotyped using the 60K SNP Illumina iSelect chicken array. To detect genomic signatures of recent selection, we applied two methods based on population comparison, cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR), and further analyzed the results to find genomic regions under recent selection in multiple purebred lines.

Results

A total of 321 candidate selection regions spanning approximately 1.45 % of the chicken genome in each line were detected by consensus of results of both XP-EHH and XP-CLR methods. To minimize false discovery due to genetic drift, only 42 of the candidate selection regions that were shared by 2 or more purebred lines were considered as high-confidence selection regions in the study. Of these 42 regions, 20 were 50 kb or less while 4 regions were larger than 0.5 Mb. In total, 91 genes could be found in the 42 regions, among which 19 regions contained only 1 or 2 genes, and 9 regions were located at gene deserts.

Conclusions

Our results provide a genome-wide scan of recent selection signatures in five purebred lines of commercial broiler chickens. We found several candidate genes for recent selection in multiple lines, such as SOX6 (Sex Determining Region Y-Box 6) and cTR (Thyroid hormone receptor beta). These genes may have been under recent selection due to their essential roles in growth, development and reproduction in chickens. Furthermore, our results suggest that in some candidate regions, the same or opposite alleles have been under recent selection in multiple lines. Most of the candidate genes in the selection regions are novel, and as such they should be of great interest for future research into the genetic architecture of traits relevant to modern broiler breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0430-1) contains supplementary material, which is available to authorized users.

Long-term selection using a single trait criterion, non-destructive deformation, in White Leghorns: Effect over time on genetic parameters for traits related to egg production

Although non-destructive deformation is relevant for assessing eggshell strength, few long-term selection experiments are documented which use non-destructive deformation as a selection criterion. This study used restricted maximum likelihood-based methods with a four-trait animal model to analyze the effect of non-destructive deformation on egg production, egg weight and sexual maturity in a two-way selection experiment involving 17 generations of White Leghorns. In the strong shell line, corresponding to the line selected for low non-destructive deformation values, the heritability estimates were 0.496 for non-destructive deformation, 0.253 for egg production, 0.660 for egg weight and 0.446 for sexual maturity. In the weak shell line, corresponding to the line selected for high non-destructive deformation values, the heritabilities were 0.372, 0.162, 0.703 and 0.404, respectively. An asymmetric response to selection was observed for non-destructive deformation, egg production and sexual maturity, whereas egg weight decreased for both lines. Using non-destructive deformation to select for stronger eggshell had a small negative effect on egg production and sexual maturity, suggesting the need for breeding programs to balance selection between eggshell traits and egg production traits. However, the analysis of the genetic correlation between non-destructive deformation and egg weight revealed that large eggs are not associated with poor eggshell quality.