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Zhang Y, Chen Y, Ji H, Niu Y, He L, Wang W, Yu T, Han R, Tian Y, Liu X, Kang X, Cai H, Li Z. Dynamic m 6A Modification Landscape During the Egg Laying Process of Chickens. Int J Mol Sci 2025; 26:1677. [PMID: 40004144 PMCID: PMC11855680 DOI: 10.3390/ijms26041677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 01/27/2025] [Accepted: 02/05/2025] [Indexed: 02/27/2025] Open
Abstract
RNA N6-methyladenosine (m6A) is one of the most common and widespread reversible epigenetic modifications of mRNAs, and m6A has been shown to play a positive role in regulating follicular development. However, the role of RNA m6A methylation in chicken ovaries and egg production has not been fully studied. In this study, we comprehensively analyzed the m6A transcriptome profiles of high- and low-yield Gushi chickens at 43 weeks of age (43 w). We found that m6A modification differed between the two groups. The m6A peak was positively correlated with the gene expression level, indicating that m6A may play an important role in regulating chicken egg production. In total, 9008 and 15,415 m6A peaks were separately identified in the two groups, including 2241 differential m6A peaks. In addition, seven candidate genes related to egg laying that were significantly enriched in the KEGG pathway related to ovary development and egg laying were identified. In summary, we constructed the first m6A modification map of ovarian tissue of Gushi chickens, and the differences in egg laying in 43 w Gushi chickens may originate from the effect of RNA methylation on the expression of egg-related genes. These findings provide new insights into the regulatory mechanisms of m6A methylation during egg production in Gushi chickens.
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Affiliation(s)
- Yushi Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
| | - Yida Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
| | - Haigang Ji
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
| | - Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
| | - Liyang He
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
| | - Wentao Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
| | - Tong Yu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.Z.); (Y.C.); (H.J.); (Y.N.); (L.H.); (W.W.); (T.Y.); (R.H.); (Y.T.); (X.L.); (X.K.)
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
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Deng C, Li M, Wang T, Duan W, Guo A, Ma G, Yang F, Dai F, Li Q. Integrating genomics and transcriptomics to identify candidate genes for high-altitude adaptation and egg production in Nixi chicken. Br Poult Sci 2024; 65:652-664. [PMID: 38922310 DOI: 10.1080/00071668.2024.2367228] [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: 01/30/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
1. This study combined genome-wide selection signal analysis with RNA-sequencing to identify candidate genes associated with high altitude adaptation and egg production performance in Nixi chickens (NXC).2. Based on the whole-genome data from 20 NXC (♂:10; ♀:10), the population selection signal was analysed by sliding window analysis. The selected genes were screened by combination with the population differentiation statistic (FST). The sequence diversity statistic (θπ). RNA-seq was performed on the ovarian tissues of NXC (n = 6) and Lohmann laying hens (n = 6) to analyse the differentially expressed genes (DEGs) between the two groups. The functional enrichment analysis of the selected genes and differentially expressed genes was performed.3. There were 742 genes under strong positive selection and 509 differentially expressed genes screened in NXC. Integrated analysis of the genome and transcriptome revealing 26 overlapping genes. The candidate genes for adaptation to a high-altitude environment, as well as for egg production, disease resistance, vision and pigmentation in NXC were preliminarily screened.4. The results provided theoretical guidance for further research on the genetic resource protection and utilisation of NXC.
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Affiliation(s)
- C Deng
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - M Li
- School of Mathematics and Computer Science, Yunnan Nationalities University, Kunming, China
| | - T Wang
- School of Pharmacy, Chengdu University, Chengdu, China
| | - W Duan
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - A Guo
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - G Ma
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Yang
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Dai
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Q Li
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
- Kunming Xianghao Technology Co. Ltd., Kunming, China
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Kong S, Cai B, Li X, Zhou Z, Fang X, Yang X, Cai D, Luo X, Guo S, Nie Q. Assessment of selective breeding effects and selection signatures in Qingyuan partridge chicken and its strains. Poult Sci 2024; 103:103626. [PMID: 38513549 PMCID: PMC10966089 DOI: 10.1016/j.psj.2024.103626] [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: 12/22/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 03/23/2024] Open
Abstract
Qingyuan partridge chicken (QYM) is a highly regarded native breed in China, highly esteemed for its exceptional breeding characteristics. However, the investigation into the selection signatures and its strains remains largely unexplored. In this study, blood sampling, DNA extracting, and high-depth resequencing were performed in 27 QYMs. Integrating the genomic data of 14 chicken (70 individuals) breeds from other researches, to analyze the genetic structure, selection signatures, and effects of selective breeding within QYM and its 3 strains (QYMA, QYMB, and QYMC). Population structure analysis revealed an independent QYM cluster, which exhibited distinct from other breeds, with each of its 3 strains displaying distinct clustering patterns. Linkage disequilibrium analysis highlighted QYMB's notably slower decay rate, potentially influenced by selection pressure from various production indicators. Examination of selection signatures uncovered genes and genetic mechanisms associated with genomic changes resulting from extensive selective breeding within the QYM and its strains. Intriguingly, diacylglycerol kinase beta (DGKB) and catenin alpha 2 (CTNNA2) were identified as commonly selected genes across the 3 QYM strains, linked to energy metabolism, muscle development, and fat metabolism. Our research validates the substantial impact of selective breeding on QYM and its strains, concurrently identifying genomic regions and signaling pathways associated with their distinctive characters. This research also establishes a fundamental framework for advancing yellow-feathered broiler breeding strategies.
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Affiliation(s)
- Shaofen Kong
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Bolin Cai
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiaojing Li
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhen Zhou
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiang Fang
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xin Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Danfeng Cai
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xuehui Luo
- Qingyuan Chicken Research Institute, Qingcheng District, Qingyuan City, China
| | - Suyin Guo
- Animal Epidemic Prevention Center, Qingcheng District, Qingyuan City, China
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China.
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