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Yang K, Zhang J, Zhao Y, Shao Y, Zhai M, Liu H, Zhang L. Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers. BIOLOGY 2023; 12:1397. [PMID: 37997996 PMCID: PMC10669838 DOI: 10.3390/biology12111397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.
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Affiliation(s)
- Kai Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Jian Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Yuelei Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Yonggang Shao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Manjun Zhai
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
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El-Magd MA, Abdelfattah-Hassan A, Elsisy RA, Hawsawi YM, Oyouni AA, Al-Amer OM, El-Shetry ES. Expression and function of Ebf1 gene during chondrogenesis in chick embryo limb buds. Gene 2021; 803:145895. [PMID: 34384862 DOI: 10.1016/j.gene.2021.145895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/17/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022]
Abstract
The expression profile of early B-cell factor (Ebf) genes and loss of function experiments denote a crucial role for these genes during the late stage of skeletogenesis. However, little is known regarding the expression and function of these genes during the early stage of skeletogenesis. Therefore, this study aimed to detail the spatiotemporal expression pattern of cEbf1, in comparison to cEbf2 and cEbf3, in chick limb buds and investigate its function during chondrogenesis. cEbf1-3 were co-expressed in the distal mesenchyme from a very early stage and later in the outer perichondrium and the surrounding noncartilaginous mesenchymal cells. Ebf1 loss of function through injection of RCASBP virus-carrying Ebf1 dominant-negative form (ΔEbf1) into the wing buds resulted in shortened skeletal elements with a clear defect in the chondrocyte differentiation program. In RCASBP-ΔEbf1 injected wing, the chondrogenesis was initiated normally but hindered at the maturation stage. Subsequently, the chondrocytes failed to become mature or hypertrophic and the long bone diaphysis was not properly developed. The final phenotype included shorter, thicker, and fused long bones. These phenotypic changes were associated with downregulation of the early [Sox9 and collagen type II (Col2a1)] and the late [alkaline phosphatase (AP)] chondrocytes differentiation markers in the limb buds. These results conclude that cEbf1 could be involved in a molecular cascade that promotes the terminal stages of chondrogenesis in the long bone anlagen.
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Affiliation(s)
- Mohammed A El-Magd
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, Post Box 33516, Kafrelsheikh, Egypt.
| | - Ahmed Abdelfattah-Hassan
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Rasha A Elsisy
- Department of Anatomy, Faculty of Medicine, Kafrelsheikh University, Post Box 33516, Kafrelsheikh, Egypt
| | - Yousef M Hawsawi
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah 21499, P.O. Box 40047, Saudi Arabia; College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Atif A Oyouni
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia; Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
| | - Osama M Al-Amer
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Eman S El-Shetry
- Department of Human Anatomy and Embryology, Faculty of Medicine, Zagazig University, Egypt
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Chen MJ, Xie WY, Jiang SG, Wang XQ, Yan HC, Gao CQ. Molecular Signaling and Nutritional Regulation in the Context of Poultry Feather Growth and Regeneration. Front Physiol 2020; 10:1609. [PMID: 32038289 PMCID: PMC6985464 DOI: 10.3389/fphys.2019.01609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 12/23/2019] [Indexed: 12/03/2022] Open
Abstract
The normal growth and regeneration of feathers is important for improving the welfare and economic value of poultry. Feather follicle stem cells are the basis for driving feather development and are regulated by various molecular signaling pathways in the feather follicle microenvironment. To date, the roles of the Wnt, Bone Morphogenetic Protein (BMP), Notch, and Sonic Hedgehog (SHH) signaling pathways in the regulation of feather growth and regeneration are among the best understood. While these pathways regulate feather morphogenesis in different stages, their dysregulation results in a low feather growth rate, poor quality of plumage, and depilation. Additionally, exogenous nutrient intervention can affect the feather follicle cycle, promote the formation of the feather shaft and feather branches, preventing plumage abnormalities. This review focuses on our understanding of the signaling pathways involved in the transcriptional control of feather morphogenesis and explores the impact of nutritional factors on feather growth and regeneration in poultry. This work may help to develop novel mechanisms by which follicle stem cells can be manipulated to produce superior plumage that enhances poultry carcass quality.
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Affiliation(s)
- Meng-Jie Chen
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Wen-Yan Xie
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Shi-Guang Jiang
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiu-Qi Wang
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Hui-Chao Yan
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Chun-Qi Gao
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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El-Magd MA, Elsayed SA, El-Shetry ES, Abdelfattah-Hassan A, Saleh AA, Allen S, McGonnell I, Patel K. The role of chick Ebf genes in the mediolateral patterning of the somites. Genesis 2019; 57:e23339. [PMID: 31724301 DOI: 10.1002/dvg.23339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 11/06/2022]
Abstract
This study was conducted to check whether the three chick Early B-cell Factor (Ebf) genes, particularly cEbf1, would be targets for Shh and Bmp signals during somites mediolateral (ML) patterning. Tissue manipulations and gain and loss of function experiments for Shh and Bmp4 were performed and the results revealed that cEbf1 expression was initiated in the cranial presomitic mesoderm by low dose of Bmp4 from the lateral mesoderm and maintained in the ventromedial part of the epithelial somite and the medial sclerotome by Shh from the notochord; while cEbf2/3 expression was induced and maintained by Bmp4 and inhibited by high dose of Shh. To determine whether Ebf1 plays a role in somite patterning, transfection of a dominant-negative construct was carried out; this showed suppression of cPax1 expression in the medial sclerotome and upregulation and medial expansion of cEbf3 and cPax3 expression in sclerotome and dermomyotome, respectively, suggesting that Ebf1 is important for ML patterning. Thus, it is possible that low doses of Bmp4 set up Ebf1 expression which, together with Shh from the notochord, leads to establishment of the medial sclerotome and suppression of lateral identities. These data also conclude that Bmp4 is required in both the medial and lateral domain of the somitic mesoderm to keep the ML identity of the sclerotome through maintenance of cEbf gene expression. These striking findings are novel and give a new insight on the role of Bmp4 on mediolateral patterning of somites.
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Affiliation(s)
- Mohammed A El-Magd
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kfrelsheikh, Egypt
| | - Shafika A Elsayed
- Department of Histology and Cytology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Eman S El-Shetry
- Department of Human Anatomy and Embryology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmed Abdelfattah-Hassan
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Ayman A Saleh
- Department of Animal Wealth Development, Genetics and Genetic Engineering, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Steve Allen
- Department of Veterinary Basic Sciences, Royal Veterinary College, London, United Kingdom
| | - Imelda McGonnell
- Department of Veterinary Basic Sciences, Royal Veterinary College, London, United Kingdom
| | - Ketan Patel
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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El-Magd MA, Saleh AA, Farrag F, Abd El-Aziz RM, Ali HA, Salama MF. Regulation of Chick Ebf1-3 Gene Expression in the Pharyngeal Arches, Cranial Sensory Ganglia and Placodes. Cells Tissues Organs 2015; 199:278-93. [DOI: 10.1159/000369880] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2014] [Indexed: 11/19/2022] Open
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El-Magd MA, Allen S, McGonnell I, Mansour AA, Otto A, Patel K. Shh regulates chick Ebf1 gene expression in somite development. Gene 2015; 554:87-95. [DOI: 10.1016/j.gene.2014.10.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 11/16/2022]
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