Exploration of Key Gene Mining and Formation Mechanisms for the White-Shelled Egg Trait in Chickens
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE278256 | GEO | 2025/10/10
REPOSITORIES: GEO
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Project description:Exploration of Key Gene Mining and Formation Mechanisms for the White-Shelled Egg Trait in Chickens
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Project description:Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.
| S-EPMC8469556 | biostudies-literature
Project description:Dongxiang blue-shelled chicken, an indigenous chicken breed in China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The recent selection has also resulted in a significant difference in egg production. The red comb line (RCL) chicken produces significantly higher number of eggs than that by the dark comb line (DCL) chicken. The objective of this study was to explore potential mechanisms involved in the relationship between comb color and egg production among chickens. We performed genome-wide association study to identify candidate genes associated with chicken comb color using SNP array data, and we conducted selective sweep analysis to identify putative regions of selection harboring pleiotropic genes affecting both comb color and egg production.
2019-06-04 | GSE124906 | GEO
Project description:For healthy development, an avian embryo needs the nutritional and functional molecules maternally deposited in avian eggs. Egg white not only provides nutritional components but also exhibits functional properties, such as defenses against microbial invasion. However, the roles of the more detailed messages in embryo development remain unclear. In this study, a tandem mass tag labeling quantitation approach was used to innovatively identify the differential proteins in the egg whites of fresh eggs produced by hens with divergent high/low hatchability and in the egg whites of embryonated eggs with healthy and dead embryos. A total of 378 proteins were quantified in egg white, which is the most complete proteome identified for egg white to date, and up to 102 differential proteins were identified. GO enrichment, pathway, and hierarchical clustering analysis revealed some of the differential proteins that are the main participants in several biological processes, including blood coagulation, intermediate filament, antibacterial activity, and neurodevelopment. A list of 11 putative protein biomarkers, such as keratin (KRT19, KRT12, KRT15, and KRT6A), which is involved in cell architecture, and fibrinogen (fibrinogen alpha chain, fibrinogen beta chain, and fibrinogen gamma chain), which is related to blood coagulation, were ultimately screened. The current study screened egg white proteins that can predict low hatchability and embryonic death and deciphered the role of these proteins in embryonic development, which is meaningful for the comprehensive understanding of embryonic growth.
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Project description:The prevalence of obesity-related metabolic diseases caused by insulin resistance is rapidly increasing worldwide. Adiponectin (ADPN), a hormone derived from adipose tissue, is a potential therapeutic agent for insulin resistance. Chickens are considered efficient bioreactors for recombinant protein production because they secrete large amounts of high-concentration proteins from the oviduct. Additionally, chickens express high levels of high-molecular-weight (HMW) ADPN, which is considered the active form in the body. Therefore, in this study, a gene-targeted chicken model was produced in which the gene encoding human ADPN was inserted into Ovalbumin (OVA) using the CRISPR/Cas9 system, and the characteristics of the resulting recombinant ADPN protein were evaluated. As a result, human ADPN was expressed in G1 hen oviducts and egg whites of OVA ADPN knock-in (KI) chickens. The concentration of ADPN in egg white ranged from 1.47 to 4.59 mg/mL, of which HMW ADPN accounted for ∼29% (0.24-1.49 mg/mL). Importantly, egg white-derived ADPN promoted expression of genes related to fatty acid oxidation and activated the 5'-AMP-activated protein kinase (AMPK) signaling pathway in muscle cells. In summary, the OVA gene-targeted chicken bioreactor proved to be an advantageous model for production of human ADPN, and the resulting protein was of sufficient quantity and efficacy for industrial use.
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Project description:Binning of metagenomic data collected from Lagria villosa beetle eggs
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Project description:Increased commercial demand for monoclonal antibodies (mAbs) has resulted in the urgent need to establish efficient production systems. We previously developed a transgenic chicken bioreactor system that effectively produced human cytokines in egg whites using genome-edited transgenic chickens. Here, we describe the application of this system to mAb production. The genes encoding the heavy and light chains of humanized anti-HER2 mAb, linked by a 2A peptide sequence, were integrated into the chicken ovalbumin gene locus using a CRISPR/Cas9 protocol. The knock-in hens produced a fully assembled humanized mAb in their eggs. The mAb expression level in the egg white was 1.4-1.9 mg/mL, as determined by ELISA. Furthermore, the antigen binding affinity of the anti-HER2 mAb obtained was estimated to be equal to that of the therapeutic anti-HER2 mAb (trastuzumab). In addition, antigen-specific binding by the egg white mAb was demonstrated by immunofluorescence against HER2-positive and -negative cells. These results indicate that the chicken bioreactor system can efficiently produce mAbs with antigen binding capacity and can serve as an alternative production system for commercial mAbs.
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Project description:The transglutaminase (TGMs) family plays a crucial role in regulating mammalian reproduction, yet its impact on poultry reproductive traits has not been extensively studied. In this study, we identified eight members of the TGMs family in chickens and examined the contributions of genetic variations of coagulation factor XIII A chain (F13A1), transglutaminase 4 (TGM4), and LOC101749664 to selective breeding in commercial layers through genetic variation response pattern analysis. Transcriptome data from various tissues of high- and low-egg-yielding Gushi chickens revealed significant positive correlations between the mRNA expression levels of TGM4 and F13A1 genes and egg production (P < 0.05). Genotype-phenotype correlation analysis showed that 26 single nucleotide polymorphisms (SNPs) within genomic sequences of TGM4 and F13A1 genes exhibited significant associations with egg production traits across different laying periods. Additionally, spatiotemporal expression patterns of TGM4 in ovarian follicles between high- and low-laying chicken breeds determined by RT-qPCR highlighted the pivotal role of TGM4 in follicle development. Functionally, the gain-of-function assay demonstrated that TGM4 promoted granulosa cell proliferation, inhibited apoptosis, and enhanced progesterone synthesis. In conclusion, this is the first study to elucidate the role of the TGMs gene family in regulating egg production in chickens, offering new insights for the selective breeding of layers with improved egg-laying traits.
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Project description:Loss of MOS in female mice disrupts metaphase II arrest, potentially causing infertility and germ cell tumors. Single-egg RNA sequencing revealed widespread gene expression changes in mos -/- eggs, including upregulation of cell cycle regulators like Aurka, Bub3, and Cdk7. Pathways related to RNA metabolism, transcription, and neddylation were also enriched in mos -/- eggs. Notably, the transcriptome of mos -/- eggs differed from that of chemically activated eggs. These results highlight MOS as a key regulator of the meiotic cell cycle and transcriptome integrity essential for oocyte developmental competence.
2025-05-20 | GSE297431 | GEO