Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS)
To explore the impact of epigenetic modifications on egg-laying traits in geese, we employed genome-wide bisulfite sequencing (WGBS) to analyze DNA methylation patterns in pituitary tissues of high-(HYP) and low-yield (LYP) Sichuan White geese. We achieved high-quality sequencing data (mean 19.09 Gb...
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MDPI AG
2025-02-01
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| author | Lin Ma Xianzhi Zhao Guoda A Tongtong Song Meng Wu Zhihao Yan Min Xiao Wenbo Jiang Yixiao Gao Haiwei Wang Zhuping Chen Keshan Zhang Jiajia Xue Yi Luo Chao Wang Youhui Xie Ying Chen Guangliang Gao Qigui Wang |
| author_facet | Lin Ma Xianzhi Zhao Guoda A Tongtong Song Meng Wu Zhihao Yan Min Xiao Wenbo Jiang Yixiao Gao Haiwei Wang Zhuping Chen Keshan Zhang Jiajia Xue Yi Luo Chao Wang Youhui Xie Ying Chen Guangliang Gao Qigui Wang |
| author_sort | Lin Ma |
| collection | DOAJ |
| description | To explore the impact of epigenetic modifications on egg-laying traits in geese, we employed genome-wide bisulfite sequencing (WGBS) to analyze DNA methylation patterns in pituitary tissues of high-(HYP) and low-yield (LYP) Sichuan White geese. We achieved high-quality sequencing data (mean 19.09 Gb raw reads, 15.49 Gb clean reads, 79.1% unique mapping rate) with a bisulfite conversion efficiency of 99.88%. Comparative analysis revealed 2394 differentially methylated regions (DMRs) and 422 differentially methylated genes (DMGs) between HYP and LYP groups. We identified five key differentially methylated candidate genes (<i>BMPER</i>, <i>INHA</i>, <i>NMBR</i>, <i>NK3R</i>, and <i>DSG2</i>) linked to egg-laying traits in Sichuan White geese. Integrated GO and KEGG enrichment analysis conducted to explore the role of regulatory networks of epigenetic modification on egg-laying traits in Sichuan White geese identified multiple metabolic pathways associated with egg-laying traits (promoting egg transport, ovulation, and yolk protein synthesis and secretion), thus providing a basis for subsequent functional verification. |
| format | Article |
| id | doaj-art-a0a417200ac34f528cc00406cb15eb0d |
| institution | DOAJ |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj-art-a0a417200ac34f528cc00406cb15eb0d2025-08-20T02:44:52ZengMDPI AGBiology2079-77372025-02-0114215410.3390/biology14020154Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS)Lin Ma0Xianzhi Zhao1Guoda A2Tongtong Song3Meng Wu4Zhihao Yan5Min Xiao6Wenbo Jiang7Yixiao Gao8Haiwei Wang9Zhuping Chen10Keshan Zhang11Jiajia Xue12Yi Luo13Chao Wang14Youhui Xie15Ying Chen16Guangliang Gao17Qigui Wang18Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaCollege of Animal Sciences and Technology, Northeast Agricultural University, Harbin 150030, ChinaCollege of Animal Sciences and Technology, Northeast Agricultural University, Harbin 150030, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 402460, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 402460, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 402460, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 402460, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, ChinaTo explore the impact of epigenetic modifications on egg-laying traits in geese, we employed genome-wide bisulfite sequencing (WGBS) to analyze DNA methylation patterns in pituitary tissues of high-(HYP) and low-yield (LYP) Sichuan White geese. We achieved high-quality sequencing data (mean 19.09 Gb raw reads, 15.49 Gb clean reads, 79.1% unique mapping rate) with a bisulfite conversion efficiency of 99.88%. Comparative analysis revealed 2394 differentially methylated regions (DMRs) and 422 differentially methylated genes (DMGs) between HYP and LYP groups. We identified five key differentially methylated candidate genes (<i>BMPER</i>, <i>INHA</i>, <i>NMBR</i>, <i>NK3R</i>, and <i>DSG2</i>) linked to egg-laying traits in Sichuan White geese. Integrated GO and KEGG enrichment analysis conducted to explore the role of regulatory networks of epigenetic modification on egg-laying traits in Sichuan White geese identified multiple metabolic pathways associated with egg-laying traits (promoting egg transport, ovulation, and yolk protein synthesis and secretion), thus providing a basis for subsequent functional verification.https://www.mdpi.com/2079-7737/14/2/154Sichuan white geeseegg-laying traitspituitarywhole-genome bisulfite sequencing (WGBS) |
| spellingShingle | Lin Ma Xianzhi Zhao Guoda A Tongtong Song Meng Wu Zhihao Yan Min Xiao Wenbo Jiang Yixiao Gao Haiwei Wang Zhuping Chen Keshan Zhang Jiajia Xue Yi Luo Chao Wang Youhui Xie Ying Chen Guangliang Gao Qigui Wang Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS) Biology Sichuan white geese egg-laying traits pituitary whole-genome bisulfite sequencing (WGBS) |
| title | Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS) |
| title_full | Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS) |
| title_fullStr | Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS) |
| title_full_unstemmed | Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS) |
| title_short | Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS) |
| title_sort | identification of dna methylation differences in pituitary tissues of sichuan white geese using whole genome bisulfite sequencing wgbs |
| topic | Sichuan white geese egg-laying traits pituitary whole-genome bisulfite sequencing (WGBS) |
| url | https://www.mdpi.com/2079-7737/14/2/154 |
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