Identification of potential genomic regions and candidate genes for egg albumen quality by a genome-wide association study

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

Lonicera flos and Cnicus japonicus extracts improved egg quality partly by modulating antioxidant status, inflammatory-related cytokines and shell matrix protein expression of oviduct in laying hens

This study was conducted to investigate the effects of Lonicera flos and Cnicus japonicus extracts (LCE) on the laying performance, egg quality, morphology, antioxidant status, inflammatory-related cytokines, and shell matrix protein expression of oviduct in laying hens. A total of 1,728 Roman Pink laying hens aged 73-wk-old were randomly assigned into 4 groups (18 replicates/group, 24 layers/replicate) fed basal diets supplemented with 0, 300, 500, and 1,000 mg of LCE per kg of diet, respectively. The trial lasted for 11 wk, including 2-wk adjustment period and 9-wk testing period. The results indicated that laying hens fed diets supplemented with LCE linearly increased egg weight, yolk color and shell thickness at wk 78 and albumen height, Haugh unit and shell thickness at wk 83 (P < 0.05). At wk 78, LCE groups linearly affected the hydrogen peroxide content in magnum (P < 0.05) and 300 mg/kg LCE groups had the highest catalase activity in isthmus (P < 0.05). At wk 83, LCE groups linearly reduced (P < 0.05) hydrogen peroxide content in the magnum and isthmus and malondialdehyde content in the uterus whereas increased catalase activity in isthmus (P < 0.05). Furthermore, LCE levels quadratically affected glutathione peroxidase activity in isthmus at wk 83 (P < 0.05). At wk 78, the mRNA expressions of inducible nitric oxide synthase and interferon-γ in isthmus and ovalbumin and ovocleidin-116 in uterus had linear effects in response to LCE levels (P < 0.05) and 1,000 mg/kg LCE group had the lowest mRNA expression of interleukin-6 in magnum (P < 0.05). At wk 83, LCE supplementation linearly decreased the mRNA expression of interleukin-1β, interferon-γ and tumor necrosis factor-α in magnum and tumor necrosis factor-α and inducible nitric oxide synthase in uterus (P < 0.05). It is concluded that LCE improved egg quality partly by modulating antioxidant status, inflammatory-related cytokines and shell matrix protein expression of oviduct in laying hens.

The impacts of fermented feed on laying performance, egg quality, immune function, intestinal morphology and microbiota of laying hens in the late laying cycle

Fermented feed has the potential to improve poultry gastrointestinal microecological environment, health condition and production performance. Thus, the present study was undertaken to explore the effects of fermented feed on the laying performance, egg quality, immune function, intestinal morphology and microbiota of laying hens in the late laying cycle. A total of 360 healthy Hy-Line Brown laying hens aged 80 weeks were used to conduct a 56-day study. All hens were randomly separated into two treatment groups, with five replicates of 36 hens each as follows: basal diet containing 0.0% fermented feed (CON) and 20% fermented feed (FF). Subsequent analyses revealed that fermented feed supplementation was associated with significant increases in laying rates together with reduced broken egg rates and feed conversion ratio for hens in FF group (P < 0.05). There were additionally significant increases in both albumen height and Haugh unit values in hens following fermented feed supplementation (P < 0.05). Fermented feed was also associated with increases in duodenal, jejunal and ileac villus height (P < 0.05). Laying hens fed fermented feed had higher immune globulin (Ig)A, IgG, IgM levels (P < 0.01,) and higher interleukin 2, interleukin 6, tumour necrosis factor α and interferon γ (P < 0.05) concentrations than CON. Analysis of the microbiota in these laying hens revealed the alpha diversity was not significantly affected by fermented feed supplementation. Firmicutes abundance was reduced in caecal samples from FF hens relative to those from CON hens (30.61 vs 35.12%, P < 0.05). At the genus level, fermented feed was associated with improvements in relative Lactobacillus, Megasphaera and Peptococcus abundance and decreased Campylobacter abundance in laying hens. These results suggest that fermented feed supplementation may be beneficial to the laying performance, egg quality, immunological function, intestinal villus growth and caecal microecological environment of laying hens at the end of the laying cycle.

Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken

In evolutionary ecology, an “ecotype” is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining ecological niche modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within-ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. While most SRs are ecotype-specific, the biological pathways perturbed by overlapping genes are largely shared among ecotypes. A few biological pathways were shared amongst most ecotypes and the genes involved showed functions important for scavenging chickens, e.g., neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using redundancy analysis (RDA) allowed for correlating ∼33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype × environment (G × E) interactions.

Genome-wide association studies for egg quality traits in White Leghorn layers using low-pass sequencing and SNP chip data

Low-pass sequencing data have been proposed as an alternative to single nucleotide polymorphism (SNP) chips in genome-wide association studies (GWAS) of several species. However, it has not been used in layer chickens yet. This study aims at comparing the GWAS results of White Leghorn chickens using low-pass sequencing data (1×) and 54 k SNP chip data. Ten commercially relevant egg quality traits including albumen height, shell strength, shell colour, egg weight and yolk weight collected from up to 1,420 White Leghorn chickens were analysed. The results showed that the genomic heritability estimates based on low-pass sequencing data were higher than those based on SNP chip data. Although two GWAS analyses showed similar overall landscape for most traits, low-pass sequencing captured some significant SNPs that were not on the SNP chip. In GWAS analysis using 54 k SNP chip data, after including more individuals (up to 5,700), additional significant SNPs not detected by low-pass sequencing data were found. In conclusion, GWAS using low-pass sequencing data showed similar results to those with SNP chip data and may require much larger sample sizes to show measurable advantages.

Genotype affects free amino acids of egg yolk and albumen in Japanese indigenous breeds and commercial Brown layer chickens

Using a variety of genetic resources, the aim of this study is to see how genetic background affects egg traits in chickens. Three different chicken genotypes (a commercial Brown layer, BOR; 2 Japanese indigenous breeds, NGY and YKD) were investigated effects on genotype in 10 external and internal egg quality traits along with 20 yolk and albumen free amino acid traits. Significant effects on genotype in 10 external and internal egg quality traits and 18 yolk and 17 albumen amino acid traits were found (P < 0.05). In sizes and weights of egg and eggshell redness, there were significant differences among all combinations of genotype (BOR > NGY > YKD). In 14 yolk (Asn, Ser, Gln, Gly, His, Arg, Ala, Pro, Tyr, Val, Met, Leu, Phe, and Lys) and 8 albumen amino acid traits (Gln, Gly, His, Arg, Val, Ile, Leu, and Lys), BOR was significantly higher than NGY and YKD, while the opposite relations were seen in 2 amino acid traits (Cys and GABA). Moreover, phenotypic correlation analyses revealed that positive correlations among amino acid traits within each yolk and albumen were broadly seen (0.30 < r < 0.98, P < 0.05). However, there are almost no phenotypic correlations in amino acids between yolk and albumen in BOR and NGY, but negative correlations in YKD, which implying a potential use of untapped genetic resources for modifying amino acid balance. These results indicate genetic background affects not only sizes and weights of egg but also amino acid contents and their balance of yolk and albumen.

Effects of magnolol on egg production, egg quality, antioxidant capacity, and intestinal health of laying hens in the late phase of the laying cycle

Magnolol is a multifunctional plant polyphenol. To evaluate the effects of magnolol on laying hens in the late laying period, 360 (50-week-old) laying hens were randomly assigned to 4 dietary treatments: a non-supplemented control diet (C), and control diets supplemented with 100, 200, and 300 mg/kg of magnolol (M100, M200, and M300), respectively. Each treatment had 6 replicates with 15 hens per replicate. Results showed that dietary supplementation of 200 and 300 mg/kg of magnolol increased the laying rate and the M200 group had a lower feed conversion ratio (P < 0.05). Magnolol supplementation (200 and 300 mg/kg) could linearly increase albumen height and Haugh unit of fresh eggs in the late phase of the laying cycle (P < 0.01). And magnolol linearly alleviated the decline of the albumen height and Haugh unit of eggs stored for 14 d (P < 0.01). The total superoxide dismutase activity in the ovaries of M100 group was greater than that in the other treatments (P < 0.05). As dietary magnolol levels increased, villus height of jejunum and ileum linearly increased (P < 0.01). M200 and M300 groups had higher expression level of occludin in the ileum compared with group C (P < 0.01). The level of nitric oxide production and inducible nitric oxide synthase expression in the ileum of M200 group were lower than that in the C group (P < 0.05). In conclusion, dietary supplementation of 200 and 300 mg/kg magnolol can improve hen performance, albumen quality of fresh and storage eggs, and hepatic lipid metabolism in the late laying cycle. Also, magnolol has a good effect on increasing villi and improving the intestinal mucosal mechanical barrier function.