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Genetic Breeding of Poultry
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Genetic Breeding of Poultry

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 25 May 2025 | Viewed by 7862

Special Issue Editor

Dr. Qisheng Zuo

E-Mail Website
Guest Editor
1. Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
2. Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
Interests: embryonic stem cell; primordial germ cell; gene editing; multi-omics analysis; expression regulation; signal path

Special Issue Information

Dear Colleagues,

In order to meet people's living needs, millions of poultry are raised worldwide for meat and egg production annually, making it crucial to develop the genetic improvement and breeding processes in the poultry industry. In the process of breeding, the selection of genes and variants associated with the traits of interest is particularly important. These can include disease resistance, growth traits, and reproductive performance. Multi-omics analysis can be used to explore the biological functions and molecular mechanisms of key genes and their regulation. Appropriate breeding methods can significantly improve production potential. Stem cell technology and molecular breeding have an increasing role to play in the modern poultry industry. This Special Issue will present the latest research related to poultry breeding and will cover various aspects, providing a variety of solution strategies for the improvement of the poultry breeding process.

Dr. Qisheng Zuo
Guest Editor

Manuscript Submission Information

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Keywords

  • poultry
  • genetics
  • breeding
  • multi-omics
  • gene-editing
  • stem cells
  • production
  • trait
  • gene expression
  • gene regulation

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Published Papers (7 papers)

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Research

22 pages, 2546 KiB  
Article
Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F2 Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White
by Natalia A. Volkova, Michael N. Romanov, Alan Yu. Dzhagaev, Polina V. Larionova, Ludmila A. Volkova, Alexandra S. Abdelmanova, Anastasia N. Vetokh, Darren K. Griffin and Natalia A. Zinovieva
Genes 2025, 16(5), 583; https://doi.org/10.3390/genes16050583 - 15 May 2025
Viewed by 73
Abstract
Background/Objectives: Finding single nucleotide polymorphisms (SNPs) and candidate genes that influence the expression of key traits is essential for genomic selection and helps improve the efficiency of poultry production. Here, we aimed to conduct a genome-wide association study (GWAS) for egg production [...] Read more.
Background/Objectives: Finding single nucleotide polymorphisms (SNPs) and candidate genes that influence the expression of key traits is essential for genomic selection and helps improve the efficiency of poultry production. Here, we aimed to conduct a genome-wide association study (GWAS) for egg production traits in an F2 resource population of chickens (Gallus gallus). Methods: The examined F2 population was produced by crossing two divergently selected breeds with contrasting phenotypes for egg performance traits, namely Russian White (of higher egg production) and Cornish White (of lower egg production). Sampled birds (n = 142) were genotyped using the Illumina Chicken 60K SNP iSelect BeadChip. Results: In the course of the GWAS analysis, we were able to clarify significant associations with phenotypic traits of interest and economic value by using 47,432 SNPs after the genotype dataset was filtered. At the threshold p < 1.06 × 10−6, we found 23 prioritized candidate genes (PCGs) associated with egg weight at the age of 42–52 weeks (FGF14, GCK), duration of egg laying (CNTN4), egg laying cycle (SAMD12) and egg laying interval (PHF5A, AKR1B1, CALD1, ATP7B, PIK3R4, PTK2, PRKCE, FAT1, PCM1, CC2D2A, BMS1, SEMA6D, CDH13, SLIT3, ATP10B, ISCU, LRRC75A, LETM2, ANKRD24). Moreover, two SNPs were co-localized within the FGF14 gene. Conclusions: Based on our GWAS findings, the revealed SNPs and candidate genes can be used as genetic markers for egg weight and other performance characteristics in chickens to attain genetic enhancement in production and for further genomic selection. Full article
(This article belongs to the Special Issue Genetic Breeding of Poultry)
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15 pages, 2359 KiB  
Article
The Effects of Ferulic Acid on the Growth Performance, Immune Function, Antioxidant Capacity, and Intestinal Microbiota of Broiler Chickens
by Xianguo Yi, Quanchao Ma, Zhili Li, Yuli Hu, Haigang Wu, Rui Wang, Xuyang Sun, Enen Wang, Chaofeng Ma and Qingmin Qin
Genes 2025, 16(5), 572; https://doi.org/10.3390/genes16050572 - 13 May 2025
Viewed by 134
Abstract
Objectives: Ferulic acid is a natural and safe herbal feed additive. This study aims to evaluate the effects of ferulic acid on the growth performance, anti-inflammatory and antioxidant capacities, immune function, and intestinal microbiota of broiler chickens. Methods: A total of 320 broiler [...] Read more.
Objectives: Ferulic acid is a natural and safe herbal feed additive. This study aims to evaluate the effects of ferulic acid on the growth performance, anti-inflammatory and antioxidant capacities, immune function, and intestinal microbiota of broiler chickens. Methods: A total of 320 broiler chickens, aged 14 days, were randomly divided into four groups: a blank control group (MA group), a low-concentration ferulic acid group (BM group, 10 mg/kg), a medium-concentration ferulic acid group (CM group, 30 mg/kg), and a high-concentration ferulic acid group (DM group, 90 mg/kg) after a 14-day acclimatization period. The experiment lasted for 28 days, and the chickens were dissected on day 29. Results: The results showed that compared to the MA group, the feed-to-meat ratio in the CM and DM groups was significantly reduced. The activity of duodenal trypsin in the CM and DM groups was significantly enhanced, and the activity of pancreatic protease in the DM group was significantly increased. The serum levels of urea nitrogen, creatinine, and triglycerides were significantly elevated in the CM and DM groups. The serum malondialdehyde (MDA) levels in the BM, CM, and DM groups were significantly reduced, while the activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) were significantly increased in the CM and DM groups. The serum interleukin-2 (IL-2) levels in the BM group were significantly decreased, while interferon-gamma (IFN-γ) levels in the CM group and complement component 3 (C-3) levels in the DM group were significantly increased. The mRNA expression levels of TLR4, MyD88, NF-κB, TNF-α, NLRP3, IL-1β, and IL-18 in the jejunum of the DM group were significantly reduced. The diversity of cecal microbiota in the ferulic acid groups changed, with a certain degree of increase in the relative abundance of Spirulina and Ruminococcus. The relative abundance of Escherichia coli in the DM group significantly increased, altering the metabolic function of the cecal microbiota in broiler chickens. Conclusions: The above results indicate that ferulic acid, as a novel feed additive for broiler chickens, has an impact on the growth performance, anti-inflammatory and antioxidant capacity, immune function, and intestinal microbiota of broiler chickens. Full article
(This article belongs to the Special Issue Genetic Breeding of Poultry)
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13 pages, 2906 KiB  
Article
The Chicken HDAC4 Promoter and Its Regulation by MYC and HIF1A
by Yingjie Wang, Ruihong Kong, Ke Xie, Xu Wang, Han Wu and Yani Zhang
Genes 2024, 15(12), 1518; https://doi.org/10.3390/genes15121518 - 26 Nov 2024
Viewed by 801
Abstract
Background: Histone deacetylase 4 (HDAC4) is a member of the class II histone deacetylase family, whose members play a crucial role in various biological processes. An in-depth investigation of the transcriptional characteristics of chicken HDAC4 can provide fundamental insights into its [...] Read more.
Background: Histone deacetylase 4 (HDAC4) is a member of the class II histone deacetylase family, whose members play a crucial role in various biological processes. An in-depth investigation of the transcriptional characteristics of chicken HDAC4 can provide fundamental insights into its function. Methods: We examined HDAC4 expression in chicken embryonic stem cells (ESC) and spermatogonial stem cells (SSC) and cloned a 444 bp fragment from upstream of the chicken HDAC4 transcription start site. Subsequently, we constructed pEGFP-HDAC4 and a series of 5′-deletion luciferase reporter constructs, which we transfected into DF-1 cells to measure their transcriptional activity. The regulatory mechanisms of chicken HDAC4 expression were investigated by performing trichostatin A (TSA) treatment, deleting putative transcription factor binding sites, and altering transcription factor expression levels. Results: HDAC4 exhibited higher expression in SSC than in ESC. We confirmed that the upstream region from −295 bp to 0 bp is the core transcriptional region of HDAC4. TSA effectively inhibited HDAC4 transcription, and bioinformatics analysis indicated that the chicken core HDAC4 promoter sequence exhibits high homology with those of other avian species. The myelocytomatosis viral oncogene homolog (MYC) and hypoxia-inducible factor 1 α (HIF1A) transcription factors were predicted to bind to this core region. Treatment with TSA for 24 h resulted in the upregulation of MYC and HIF1A, which repressed HDAC4 transcription. Conclusions: Our results provide a basis for subsequent investigations into the regulation of HDAC4 expression and biological function. Full article
(This article belongs to the Special Issue Genetic Breeding of Poultry)
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13 pages, 3307 KiB  
Article
Influence and Optimization of Diverse Culture Systems on Chicken Embryonic Stem Cell Culture
by Wenjie Ren, Jun Wu, Xiaohang Lu, Dan Zheng, Guangzheng Liu, Gaoyuan Wu, Yixiu Peng, Kai Jin, Guohui Li, Wei Han, Xiang-Shun Cui, Guohong Chen, Bichun Li and Ying-Jie Niu
Genes 2024, 15(11), 1400; https://doi.org/10.3390/genes15111400 - 30 Oct 2024
Viewed by 1513
Abstract
Background: The importance of embryonic stem cells (ESCs) in chickens is undeniable, as they can be applied across various fields, including animal modeling, developmental biology, cell fate research, drug screening, toxicity testing, and gene function studies. However, a widely applicable culture system for [...] Read more.
Background: The importance of embryonic stem cells (ESCs) in chickens is undeniable, as they can be applied across various fields, including animal modeling, developmental biology, cell fate research, drug screening, toxicity testing, and gene function studies. However, a widely applicable culture system for chicken ESCs has yet to be developed. Objectives: This study aimed to investigate the effects of different culture systems on the derivation and maintenance of chicken ESCs, with a focus on optimizing the selected culture conditions. Methods: To achieve this, we tested the effectiveness of various species-specific ESC media in the derivation and culture of chicken PGCs, while incorporating different small molecule compounds to optimize the process. The pluripotency and differentiation potential of the resulting ESC-like cells were also evaluated. Results: The combination of PD0325901, SB431542, and LIF (R2i+LIF system) was found to be effective in generating chicken ESC-like clones. Further experiments showed that enhancing the R2i+LIF system with cytokines such as SCF and FGF2 significantly extended the culture period and increased the passage number of chicken ESC-like cells. These ESC-like cells were characterized through positive alkaline phosphatase staining and the expression of pluripotency markers POUV, NANOG, and SOX2. Additionally, differentiation assays confirmed their ability to form the three germ layers. Conclusions: The newly developed culture system provides suitable conditions for the short-term culture of chicken ESCs. However, further optimization is required to establish a system that can sustain long-term maintenance. Full article
(This article belongs to the Special Issue Genetic Breeding of Poultry)
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13 pages, 4687 KiB  
Article
A Study of JUN’s Promoter Region and Its Regulators in Chickens
by Ruihong Kong, Jieyao Shi, Ke Xie, Han Wu, Xu Wang, Yani Zhang and Yingjie Wang
Genes 2024, 15(10), 1351; https://doi.org/10.3390/genes15101351 - 21 Oct 2024
Viewed by 1194
Abstract
Background: The Jun proto-oncogene (JUN), also referred to as C-JUN, is an integral component of the JNK signaling pathway, which is crucial for the formation and differentiation of spermatogonial stem cells (SSCs). Investigations into the transcriptional regulation of chicken JUN [...] Read more.
Background: The Jun proto-oncogene (JUN), also referred to as C-JUN, is an integral component of the JNK signaling pathway, which is crucial for the formation and differentiation of spermatogonial stem cells (SSCs). Investigations into the transcriptional regulation of chicken JUN can offer a molecular foundation for elucidating its mechanistic role in SSCs. Methods: In this study, we successfully cloned a 2000 bp upstream sequence of the JUN transcription start site and constructed a series of pGL3 recombinant vectors containing JUN promoters of varying lengths. Results: We verified the promoter activity of the 2000 bp upstream sequence by assessing the fluorescence intensity of DF-1 and identified the promoter activities of different regions via dual-luciferase assays. The transcription of JUN and its promoter region spanning −700 to 0 bp was modulated by an activator of the JNK signaling pathway. Bioinformatics analysis revealed that this −700 to 0 bp region was highly conserved among avian species and predicted the presence of binding sites for Wilms tumor 1 (WT1) and CCAAT/enhancer binding protein alpha (CEBPA). The JNK signaling pathway activator was found to upregulate the expression of these transcription factors in DF-1 cells. Through the deletion of binding sites and the overexpression of WT1 and CEBPA, we demonstrated that WT1 inhibited the transcription of JUN, while CEBPA promoted it. Conclusions: In conclusion, the −700 to 0 bp region is the key region of the JUN promoter, with WT1 inhibiting JUN transcription. The results of the study not only provide ideas for exploring the regulatory mechanism of JUN in chicken SSCs, but also lay an important foundation for the study of avian SSCs. Full article
(This article belongs to the Special Issue Genetic Breeding of Poultry)
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14 pages, 4077 KiB  
Article
Identification of Two Potential Gene Insertion Sites for Gene Editing on the Chicken Z/W Chromosomes
by Gaoyuan Wu, Youchen Liang, Chen Chen, Guohong Chen, Qisheng Zuo, Yingjie Niu, Jiuzhou Song, Wei Han, Kai Jin and Bichun Li
Genes 2024, 15(7), 962; https://doi.org/10.3390/genes15070962 - 22 Jul 2024
Viewed by 1660
Abstract
The identification of accurate gene insertion sites on chicken sex chromosomes is crucial for advancing sex control breeding materials. In this study, the intergenic region NC_006127.4 on the chicken Z chromosome and the non-repetitive sequence EE0.6 on the W chromosome were selected as [...] Read more.
The identification of accurate gene insertion sites on chicken sex chromosomes is crucial for advancing sex control breeding materials. In this study, the intergenic region NC_006127.4 on the chicken Z chromosome and the non-repetitive sequence EE0.6 on the W chromosome were selected as potential gene insertion sites. Gene knockout vectors targeting these sites were constructed and transfected into DF-1 cells. T7E1 enzyme cleavage and luciferase reporter enzyme analyses revealed knockout efficiencies of 80.00% (16/20), 75.00% (15/20), and 75.00% (15/20) for the three sgRNAs targeting the EE0.6 site. For the three sgRNAs targeting the NC_006127.4 site, knockout efficiencies were 70.00% (14/20), 60.00% (12/20), and 45.00% (9/20). Gel electrophoresis and high-throughput sequencing were performed to detect potential off-target effects, showing no significant off-target effects for the knockout vectors at the two sites. EdU and CCK-8 proliferation assays revealed no significant difference in cell proliferation activity between the knockout and control groups. These results demonstrate that the EE0.6 and NC_006127.4 sites can serve as gene insertion sites on chicken sex chromosomes for gene editing without affecting normal cell proliferation. Full article
(This article belongs to the Special Issue Genetic Breeding of Poultry)
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13 pages, 2821 KiB  
Article
DDX5 Can Act as a Transcription Factor Participating in the Formation of Chicken PGCs by Targeting BMP4
by Qisheng Zuo, Wei Gong, Zeling Yao, Kai Jin, Yingjie Niu, Yani Zhang and Bichun Li
Genes 2024, 15(7), 841; https://doi.org/10.3390/genes15070841 - 26 Jun 2024
Cited by 1 | Viewed by 1814
Abstract
As an RNA binding protein (RBP), DDX5 is widely involved in the regulation of various biological activities. While recent studies have confirmed that DDX5 can act as a transcriptional cofactor that is involved in the formation of gametes, few studies have investigated whether [...] Read more.
As an RNA binding protein (RBP), DDX5 is widely involved in the regulation of various biological activities. While recent studies have confirmed that DDX5 can act as a transcriptional cofactor that is involved in the formation of gametes, few studies have investigated whether DDX5 can be used as a transcription factor to regulate the formation of primordial germ cells (PGCs). In this study, we found that DDX5 was significantly up-regulated during chicken PGC formation. Under different PGC induction models, the overexpression of DDX5 not only up-regulates PGC markers but also significantly improves the formation efficiency of primordial germ cell-like cells (PGCLC). Conversely, the inhibition of DDX5 expression can significantly inhibit both the expression of PGC markers and PGCLC formation efficiency. The effect of DDX5 on PGC formation in vivo was consistent with that seen in vitro. Interestingly, DDX5 not only participates in the formation of PGCs but also positively regulates their migration and proliferation. In the process of studying the mechanism by which DDX5 regulates PGC formation, we found that DDX5 acts as a transcription factor to bind to the promoter region of BMP4—a key gene for PGC formation—and activates the expression of BMP4. In summary, we confirm that DDX5 can act as a positive transcription factor to regulate the formation of PGCs in chickens. The obtained results not only enhance our understanding of the way in which DDX5 regulates the development of germ cells but also provide a new target for systematically optimizing the culture and induction system of PGCs in chickens in vitro. Full article
(This article belongs to the Special Issue Genetic Breeding of Poultry)
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