Genome-wide association study exploring the genetic architecture of eggshell speckles in laying hens

BACKGROUND

Eggshell speckle phenotype is an important trait in poultry production because they affect eggshell quality. However, the genetic architecture of speckled eggshells remains unclear. In this study, we determined the heritability of eggshell speckles and conducted a genome-wide association study (GWAS) on purebred Rhode Island Red (RIR) hens at 28 weeks to detect potential genomic loci and candidate genes associated with eggshell speckles.

RESULTS

The heritability of eggshell speckles was 0.35 at 28 weeks, and the speckle level is not related to other eggshell quality traits in terms of phenotypic correlation. We detected 311 SNPs (6 significantly, and 305 suggestively associated) and 39 candidate genes associated with eggshell speckles. Based on the pathway analysis, the 39 candidate genes were mainly involved in alpha-linolenic acid metabolism, linoleic acid metabolism, ether lipid metabolism, GnRH signaling pathway, vascular smooth muscle contraction, and MAPK signaling pathway. Ultimately, ten genes, LOC423226, SPTBN5, EHD4, LOC77155, TYRO3, ITPKA, DLL4, PLA2G4B, PLA2G4EL5, and PLA2G4EL6 were considered the most promising genes associated with eggshell speckles that were implicated in immunoregulation, calcium transport, and phospholipid metabolism, while its function in laying hens requires further studies.

CONCLUSIONS

This study provides new insights into understanding the genetic basis of eggshell speckles and has practical application value for the genetic improvement of eggshell quality.

Egg production in nests and nesting behaviour: genetic correlations with egg quality and BW for laying hens on the floor

In laying hen production, cage-free housing is growing rapidly to provide living conditions that meet hens' needs. Unlike cages, this housing requires nests for automatic collection of eggs, as eggs laid outside nests must be collected by hand. Selecting hens for nest-related traits, such as egg production in nests and nesting behaviour, could help meet the requirements of cage-free housing. However, genetic correlations between these traits and major traits of breeding programmes, such as egg quality or BW, are poorly known. In addition, the genetic determinism of major traits has rarely been studied under cage-free conditions. The objective of the present study was to estimate the heritability of egg quality and BW measured on the floor and their genetic correlations with nest-related traits. Egg production in nests was based on the laying rate in nests, laying rhythm (clutch number and mean oviposition time), and nest acceptance. Nesting behaviour was based on nest preference (mean distance between nests used for laying) and mean laying duration (time spent in the nest for laying). Nest-related traits were recorded from 24 to 64 weeks of age. BW and egg quality were measured at 50 and 55 weeks of age, respectively. Nest-related traits and identification of the eggs laid by each hen (for individual measurements of egg quality) were obtained using individual electronic nests used by hens raised in groups and on the floor. The phenotypes of 1 455 Rhode Island Red and 1 538 White Leghorn hens were analysed. Heritability coefficients and genetic correlations were estimated using a multi-trait animal model for each line. Heritability estimates for egg quality and BW were moderate to high for both lines (0.17-0.74). Overall, weak genetic correlations were estimated between nest-related traits and egg quality or BW for both lines. However, strong and antagonistic genetic correlations were estimated between eggshell strength and laying rate in the nests (-0.46 to -0.42) or laying rhythm (+0.46 to +0.68) for both lines. Several moderate-to-strong genetic correlations were found for White Leghorn between nest-related traits and egg weight, eggshell shape, albumen height, and BW. This study shows that nest-related traits can be used to select hens better adapted to cage-free housing without degrading overall egg quality and BW. It also shows that some traits, like the eggshell strength, must be carefully monitored if these new traits are included in breeding goals. These results must now be confirmed for other populations and larger datasets.

Genetic parameters for production, quality, and colors from eggs in Brazilian lineages of chickens

Genetic parameters were estimated for egg production, egg quality, and eggshell colors in eight lineages of Brazilian laying hens. Age at first egg (AFE), total egg production up to the 45th week (PROD), egg weight (EW), albumen height (AH), yolk color (YC), the Haugh units (HU), eggshell strength (ESS), eggshell thickness (EST), yolk weight (YW), eggshell weight (ESW), and eggshell color (L*, a*, and b*) were measured in 2030 eggs obtained from 645 laying hens. Variance components were estimated from a mixed animal model, which included the fixed effects of contemporary groups, cage location, and hen line, and the additive genetic, permanent environmental, and residual as random effects. In general, heritabilities were low to moderate (h² = 0.11 to 0.48). Genetic correlations among eggshell quality traits were moderate to high (0.36 and 0.69). High genetic correlations were obtained between the eggshell color traits [r_g = -0.90 (L* and a*); r_g = -0.64 (L* and b*); and r_g = 0.65 (a* and b*)]. Results suggest that EW is strongly correlated with ESW, but the genetic correlations between EW and ESS and between EW and EST were low. Genetic correlations between L* and eggshell quality traits were low to moderate, suggesting that L* has little or no relation with external egg quality. However, genetic correlations between a* and b* values and eggshell quality traits were high. The genetic correlations between eggshell color and eggshell quality traits were low, suggesting that the eggshell color does not influence external egg quality. Genetic correlations between PROD and egg quality traits were negative and varied between -0.42 and -0.05. This antagonistic relationship emphasizes the importance of adopting breeding schemes that allow the simultaneous genetic progress of these traits by considering their genetic correlation and economic relevance, such as the selection index.

The structure of the eggshell and eggshell membranes of Crocodylus niloticus

The macro- and microstructure, elemental composition, and crystallographic characteristics of the eggshell and eggshell membranes of the Crocodylus niloticus egg was investigated using optical and electron microscopy, energy-dispersive X-ray spectroscopy (EDS), electron backscatter diffraction (EBSD) and computerised tomography. The translucent ellipsoid egg is composed of two basic layers, the outer calcified layer referred to as the shell and an inner organic fibre layer, referred to as the shell membrane. The outer inorganic calcite shell is further divided into an external, palisade and mammillary layers with pore channels traversing the shell. The external layer is a thin layer of amorphous calcium and phosphorus, the underlying palisade layer consist of irregular wedge-shaped crystals composed calcite with traces of magnesium, sodium, sulphur and phosphorus. The crystals are mostly elongated, orientated perpendicular to the shell surface ending in cone-shaped knobs, which forms the inner mammillary layer. The elemental composition of the mammillae is like that of the palisade layer, but the crystal structure is much smaller and orientated randomly. The highest number of mammillae and shell pores are found at the equator of the egg, becoming fewer towards the egg poles. The shell thickness follows the same pattern, with the thickest area located at the equator. The eggshell membrane located right beneath and embedded in the mammillary layer of the shell; it is made up of unorganised fibre sheets roughly orientated at right angles to one another. Individual fibres consist of numerous smaller fibrils forming open channels that run longitudinally through the fibre.

Effect of Fermented Corn By-products on Production Performance, Blood Biochemistry, and Egg Quality Indices of Laying Hens

Residual wastes can be fermented by using probiotics to formulate a well-balanced diet for poultry. The current study was conducted to investigate the effect of fermented feed (FF) formulated by the supplementation of probiotics into corn by-products, on the production performance of laying hens. A total of 468 49-week-old Hy-Line Brown chickens were randomly allocated into four treatments with three replicates, control group (basal diet), group Ⅰ (4% FF, w/w), group Ⅱ (8% FF, w/w), and antibiotic group (flavomycin, 50mg/kg). Laying hens were housed in three-tier cages (28 × 48 cm x 48 cm) and the temperature was maintained at 21ºC. The birds were fed 4.56 kg of feed to each group twice a day. Compared to the control group, the egg production and feed intake (FI) in the FF groups increased significantly. Egg weight (EW) in group Ⅰ was higher than that of group Ⅱ and antibiotic (p<0.01) while that in group Ⅱ was lower than control (p<0.05). The feed to egg ratio of FF groups compared to control was decreased (p<0.05). Eggshell strength (ESS) and egg shape index (ESI) in group Ⅱ were decreased significantly as compared to the control group (p<0.05). Yolk color (YC) albumen height (AH) and Haugh unit (HU) in FF groups were improved compared to the control group and antibiotic group (p<0.01). Yolk triglyceride (TG) level was significantly reduced in group II, compared to group I. These results indicated that the FF has no adverse effects and has beneficial effects on production performance and egg quality parameters of laying hens.

Effect of a targeted treatment strategy against Ascaridia galli on egg production, egg quality and bird health in a laying hen farm

Worm control is an important aspect of the successful management of the egg production industry. Of particular concern is Ascaridia galli, which at high parasite loads affect health and production in layers. Application of a targeted treatment strategy (TT) to control A. galli has shown promise. The purpose of this study was to explore the effect of such a strategy on welfare indicators and production performance of layers. Six flocks (F1-6) on a commercial farm were allocated to three treatment groups. Flocks F1 and F4 were treated (TT) with fenbendazole at 22, 27 and 36 weeks post-placement (WPP). Flocks F2 and F5 were treated at 27 WPP (conventional treatment, CT) and hens in flocks F3 and F6 served as untreated (UT) control groups. At 19, 35 and 45 WPP twenty-five hens plus thirty eggs per flock were randomly selected. Hens were weighed and their plumage conditions (PC) were assessed. The eggs were subjected to various external and interior quality analyses. Production data such as number of eggs/hen/week, egg mass and feed conversion ratio (FCR) were calculated from raw data obtained from all flocks on a weekly basis. The number of eggs/hen/week, egg mass and FCR were higher (P < 0.05) in the TT flocks and hens had better PC both at 35 and 45 WPP compared with other flocks. No differences in body weight and physical egg quality were observed between groups except for egg shell strength which was higher (P < 0.05) in the CT flocks. These data suggest that better production performance and plumage, which suggests improved health, can be achieved through the application of a TT strategy. The insights gained from this research should help to justify the extra cost and labor associated with the TT strategy.

Accuracy of genomic prediction of shell quality in a White Leghorn line

Several genomic methods were applied for predicting shell quality traits recorded at 4 different hen ages in a White Leghorn line. The accuracies of genomic prediction of single-step GBLUP and single-trait Bayes B were compared with predictions of breeding values based on pedigree-BLUP under single-trait or multitrait models. Breaking strength (BS) and dynamic stiffness (Kdyn) measurements were collected on 18,524 birds from 3 consecutive generations, of which 4,164 animals also had genotypes from an Affymetrix 50K panel containing 49,591 SNPs after quality control edits. All traits had low to moderate heritability, ranging from 0.17 for BS to 0.34 for Kdyn. The highest accuracies of prediction were obtained for the multitrait single-step model. The use of marker information resulted in higher prediction accuracies than pedigree-based models for almost all traits. A genome-wide association study based on a Bayes B model was conducted to detect regions explaining the largest proportion of genetic variance. Across all 8 shell quality traits analyzed, 7 regions each explaining over 2% of genetic variance and 54 regions each explaining over 1% of genetic variance were identified. The windows explaining a large proportion of genetic variance overlapped with several potential candidate genes with biological functions linked to shell formation. A multitrait repeatability model using a single-step method is recommended for genomic evaluation of shell quality in layer chickens.

Genetic parameters of the thick-to-thin albumen ratio and egg compositional traits in layer-type chickens

1. Generating a robust egg albumen is one of the major factors contributing to interior egg quality owing to its nutritive value and superior appearance. However, the genetic factors regulating the proportion of thick albumen are poorly understood. 2. In this study, 1330 eggs were collected from 450 Rhode Island White layers, aged 40 weeks, to measure egg compositional traits for three successive days. The restricted maximum likelihood method was applied to estimate genetic parameters for the thick-to-thin albumen ratio and other egg compositional traits. A univariate animal model was fitted to calculate heritability for each trait. 3. The heritabilities of egg weight, yolk weight, albumen height, Haugh units, percentages of yolk, thick albumen, thin albumen and the thick-to-thin albumen ratio were 0.32, 0.34, 0.28, 0.47, 0.61, 0.39, 0.31, and 0.45, respectively. The percentage of thick albumen was negatively correlated genetically with all traits, and percentage of thin albumen was negatively correlated genetically with all traits except for Haugh units. The thick-to-thin albumen ratio was positively correlated genetically with egg weight, albumen height and Haugh units, with correlations ranging from 0.21 to 0.54. 4. The results indicated that the percentage of thick albumen and the thick-to-thin albumen ratio were found to be moderately to highly heritable, and selection for the thick-to-thin albumen ratio could be conducive to the improvement of egg albumen quality.

Repeatability vs. multiple-trait models to evaluate shell dynamic stiffness for layer chickens

Shell quality is one of the most important traits for improvement in layer chickens. Proper consideration of repeated records can increase the accuracy of estimated breeding values and thus genetic improvement of shell quality. The objective of this study was to compare different models for genetic evaluation of the collected data. For this study, 81,646 dynamic stiffness records on 21,321 brown egg layers and 93,748 records on 24,678 white egg layers from 4 generations were analyzed. Across generations, data were collected at 2 to 4 ages (at approximately 26, 42, 65, and 86 wk), with repeated records at each age. Seven models were compared, including 5 repeatability models with increasing complexity, a random regression model, and a multitrait model. The models were compared using Akaike Information Criteria with significance testing of nested models with a Log Likelihood Ratio test. Estimates of heritability were 0.31-0.36 for the brown line and 0.23-0.26 for the white line, but repeatability was higher for the model with age-specific permanent environment effects (0.59 for both lines) than for the model with an overall permanent environmental effects (0.47 for the brown and 0.41 for the white line). The model that allowed for permanent environmental effect within age and heterogeneous residual variance between ages resulted in improved fit compared to the traditional model that fits single permanent environment and residual effects, but was inferior in fit and predictive ability to the full multiple-trait model. The random regression model had better fit to the data than repeatability models but slightly worse than the multiple-trait model. For traits with repeated records at different ages, repeatability within and across ages as well as genetic correlations should be considered while choosing the number of records collected per individual as well as the model for genetic evaluation.