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| 产蛋高峰期和后期莆田黑鸭肝脏差异表达基因及全基因组差异甲基化分析 |
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潘成福,林蔚龙,刘长涛,李丽,章琳俐,刘晓盼,黄靓,缪中纬,辛清武,黄种彬,郑嫩珠,林瑞意,朱志明
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1.福建省农业科学院 畜牧兽医研究所 福建省畜禽遗传育种重点实验室，福建 福州 350013;2.福建农林大学 动物科学学院，福建 福州 350002;3.石狮市种业发展中心，福建 石狮 362700
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| 摘要: |
| 【 目的】对产蛋高峰期和产蛋后期的莆田黑鸭肝脏组织差异表达基因和全基因组差异甲基化基因进 行分析，筛选不同产蛋阶段肝脏组织的差异甲基化和差异表达基因，为莆田黑鸭产蛋后期产蛋率下降的分子机制研究 提供新的见解。【 方法】选取产蛋高峰期（300日龄）和产蛋后期（500日龄）的莆田黑鸭各3只，屠宰采集肝脏组织，提取DNA和RNA，构建DNA文库和cDNA文库，然后分别进行转录组测序（RNA-seq）和全基因组甲基化测序，筛选差异表达基因和差异甲基化基因。对差异表达和差异甲基化基因进行GO和KEGG富集分析，筛选既差异表达又差异甲基化的基因。选取5个差异表达基因，进行转录组测序结果的实时荧光定量PCR验证。【 结果从产蛋高峰期到产 蛋后期，发现105个基因表达量显著上调，50个基因表达量显著下调。GO和KEGG富集分析显示，差异表达基因主 要参与异种代谢、细胞对外来刺激的反应、长链脂肪酸代谢、不饱和脂肪酸代谢等过程，在代谢途径、细胞色素P450对外源性药物的代谢作用等通路起着重要作用。通过CpG位点分析鉴定差异甲基化区域（differentially methylated region，DMR），得到不同产蛋阶段肝脏组织的DMR共16 700个，其中高甲基化区域有12 014 个，低甲基化区域有4 686个。对差异甲基化与差异表达基因进行关联分析，发现了2个甲基化水平下降而表达量上升的基因：LOC113840537和LOC119715140（基因ID）。对选取的上调基因ETNPPL、CETP、ENPP1和下调基因NPC2、PTGR1进行实时荧光定量PCR验证，结果与转录组测序结果一致，说明转录组测序结果是可靠的。【 结论】从差异表达基因中筛选出CETP、ENPP1、ETNPPL、NPC2、PTGR1等5个脂质代谢相关基因，关联分析得到2个既差异甲基化又差异表达的基因LOC113840537和LOC119715140。 |
| 关键词: 莆田黑鸭 产蛋性状 转录组 全基因组甲基化 分子调控 |
| DOI：10. 13207/j. jnwafu. 2026. 09. 011 |
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| 基金项目:国家重点研发计划项目（2024YFD1300902）；福建省科技重大专项（2024NZ029028）；福建省种业创新项目（Zycxny2021014）；福建省 5511 协同创新工程项目（XTCXGC2021008） |
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| Analysis of differentially expressed genes and whole genome differential methylation in the liver of Putian black ducks during the peak and late laying periods |
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PAN Chengfu1,2, LIN Weilong2, LIU Changtao1,3, LI Li1, ZHANG Linli1, LIU Xiaopan1, HUANG Liang1, MIAO Zhongwei1, XIN Qingwu1, HUANG Zhongbin4, ZHENG Nenzhu1, LIN Ruiyi2, ZHU Zhiming1
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1.Fujian Key Laboratory of Animal Genetics and Breeding，Institute of Animal Husbandry and Veterinary Medicine，Fujian Academy of Agricultural Sciences，Fuzhou，Fujian 350013，China;2.College of Animal Science，Fujian Agriculture and Forestry University，Fuzhou，Fujian 350002，China;3.College of Animal Science，Fujian Agriculture and Forestry University，Fuzhou，Fuj;4.Seed Industry Development Center of Shishi，Shishi，Fujian 362700，China
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| Abstract: |
| 【 Objecitve】To explore the molecular mechanism underlying the decline in egg production rate of Putian black ducks during the late laying period，analysis of the differentially expressed genes and whole genome methylation differences in their liver tissues at the peak and late laying stages was conducted，and the key differentially methylated and differentially expressed genes associated with egg production were screened.【Method】In the experiment，three Putian black ducks at the peak laying period（300 days of age） and three at the late laying period（500 days of age） were selected respectively. After slaughter，liver tissue samples were collected，and DNA and RNA were extracted to construct DNA libraries and cDNA libraries. Then transcriptome sequencing（RNA-seq） and whole genome bisulfite sequencing（WGBS） were performed respectively for analysis.GO and KEGG enrichment analysis was performed on the differentially expressed genes（DEGs） and differ-entially methylated genes（DMGs），and genes both differentially expressed and differentially methylated were screened out. Five DEGs were selected for reverse transcription quantitative realtime PCR（RT-qPCR） to validate the transcriptome sequencing results.【Result】From the peak to late laying period，105 genes with sig-nificantly upregulated expression and 50 genes with significantly downregulated expression were identified. GO and KEGG enrichment analysis showed that the DEGs were mainly involved in biological processes including xenobiotic metabolism，cellular response to external stimuli，long-chain fatty acid metabolism，and unsaturated fatty acid metabolism，and played important roles in pathways including metabolic pathways，and xenobiotic drug metabolism mediated by cytochrome P450. CpG site analysis revealed 16 700 differentially methylated regions （DMRs），including 12 014 hypermethylated regions and 4 686 hypomethylated regions. Correlation analysis found two genes（LOC113840537 and LOC119715140） with decreased methylation level and increased expres? sion level. RT-qPCR result of selected upregulated genes（ETNPPL，CETP，ENPP1） and downregulated genes（NPC2，PTGR1） was consistent with the results of RNA-seq，indicating that the transcriptome sequencing results were reliable.【Conclusion】Five DEGs related to lipid metabolism were screened out，namely CETP，ENPP1，ETNPPL，NPC2，and PTGR1.Through correlation analysis，two genes（LOC113840537 and LOC119715140） that were both differentially methylated and differentially expressed were identified. |
| Key words: Putian black duck egg-laying traits transcriptome whole genome methylation molecular regu⁃lation |
