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Ma Y, Cai C, Li J, Zhang L, Ma J, Jiang R, Zhang Y, Tian Y, Kang X, Han R. Genome-wide DNA methylation and transcriptome analyses reveal important epigenetic genes associated with Valgus-varus deformity in broilers. Br Poult Sci 2023. [PMID: 37132532 DOI: 10.1080/00071668.2023.2208264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
1. Valgus-varus deformity (VVD) is a common leg bone problem in broilers that causes serious economic losses to the breeding industry. The genetic etiology of VVD is not clear, which restricts the genetic control of VVD.2. In this study, knee cartilage of 35-day-old VVD and normal broilers was sequenced by whole-genome bisulphite sequencing (WGBS). The unique whole-genome DNA methylation profile of VVD broilers was described, and the methylation data and transcription data were used for joint analysis.3. The mean methylation level of the VVD group was greater than that in the normal group. A total of 4315 differentially methylated regions (DMRs) were detected from methylation data, with the highest DMR density on chromosomes 25, 27, 31 and 33. DMRs were mainly located in introns, which accounted for more than 60%, followed by promoter and exon regions.4. A total of 2326 differentially methylated genes (DMGs) were identified from DMRs, including 1159 genes with upregulated DMRs, 936 genes with downregulated DMRs, and 231 genes with two types of DMRs.5. The ESPL1 gene may be an important epigenetic gene of VVD. The methylation of particular CpG17, CpG18 and CpG19 sites in the promoter region of the ESPL1 gene may hinder the binding of transcription factors and promoters and increase the expression of ESPL1.
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Affiliation(s)
- Yanchao Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
| | - Chunxia Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
| | - Jianzeng Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
| | - Lujie Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
| | - Jiali Ma
- College of software, Henan Agricultural University, Xuchang 461101, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China
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