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| 金定鸭与台湾褐色菜鸭遗传差异全基因组选择信号分析 |
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朱志明,李辉煌,王均辉,赵邦哲,施文莉,蔡倩楠,刘长涛,李丽,辛清武,缪中纬,章琳俐,刘晓盼,黄种彬,郑嫩珠
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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.福建省畜牧总站，福建 福州 350003;4.石狮市种业发展中心，福建 石狮 362700
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| 摘要: |
| 【目的】对金定鸭与台湾褐色菜鸭进行选择信号分析，挖掘这2个蛋鸭品种在长期进化过程中受到强烈选择的重要经济性状相关候选基因，为揭示优异性状形成的遗传差异奠定基础。【方法】选取金定鸭和台湾褐色菜鸭各30只进行全基因组重测序，经过滤获取高质量单核苷酸多态性位点（SNPs）后，对其进行主成分分析（PCA），确定其遗传分化情况；然后采用群体遗传分化指数（Fst）和群体核酸多样性比值（π ratio）2种方法综合筛选金定鸭和台湾褐色菜鸭的受选择信号，分析其遗传差异。【结果】金定鸭和台湾褐色菜鸭重测序分别获得5.68和5.59 Gb高质量数据，分别检测到152 238 286和155 009 562个SNPs，其SNP位点分布相似。主成分分析结果显示，金定鸭和台湾褐色菜鸭显著分化；以100 kb为窗口、10 kb为步长分别计算Fst与π ratio值，将Fst top 5%（Fst＞0.482）与π ratio top 5% & bottom 5%（0＜π ratio≤0.47 & π ratio≥3.00）作为信号重叠区域，共注释到208个候选基因。对这208个候选基因进行GO与KEGG富集分析，发现金定鸭在免疫、脂质代谢、肌肉生长发育等方面受到更强烈的选择，筛选到IL15、CCL3、CD180、AKT1、PPARGC1A、PRKAA1、FASN、PIK3R1等功能基因。【结论】金定鸭和台湾褐色菜鸭显著分化，金定鸭在免疫、脂质代谢、肌肉生长发育等方面受到强烈选择。 |
| 关键词: 金定鸭 台湾褐色菜鸭 全基因组重测序 选择信号 候选基因 |
| DOI：10.13207/j.cnki.jnwafu.2025.09.001 |
| 分类号: |
| 基金项目:国家重点研发计划项目（2024YFD1300902）；福建省农业科技重大专项（2024NZ029028）；福建省5511协同创新工程项目(XTCXGC2021008)；福建省省属公益类项目(2021R1026005) |
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| Analysis of genetic differences between Jinding duck and Taiwan brown tsaiya duck by genome-wide selection signals |
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ZHU Zhiming1, LI Huihuang2, WANG Junhui3, ZHAO Bangzhe1,2, SHI Wenli1,4, CAI Qingnan1,4, LIU Changtao1,4, LI Li1, XIN Qingwu1, MIAO Zhongwei1, ZHANG Linli1, LIU Xiaopan1, HUANG Zhongbin5, ZHENG Nenzhu1
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1.Institute of Animal Husbandry and Veterinary Medicine,Fujian Academy of Agricultural Sciences/Fujian Key Laboratory of Animal Genetics and Breeding,Fuzhou，Fujian 350013，China;2.College of Animal Science,Fujian Agriculture and Forestry University,Fuzhou,Fujian 350002，China;3.Fujian Provincial Animal Husbandry Station,Fuzhou，Fujian 350003，China;4.College of Animal Science,Fujian Agriculture and Forestry University,Fuzhou,Fuji;5.Seed Industry Development Center of Shishi,Shishi，Fujian 362700，China
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| Abstract: |
| 【Objecitve】This study aimed to analyze the selection signals of Jinding duck and Taiwan brown tsaiya duck,and identify candidate genes associated with important economic traits that have undergone strong selection during the long-term breeding process of these two laying duck breeds,laying a foundation for elucidating the genetic differences underlying the development of desirable traits.【Method】30 Jinding ducks and 30 Taiwan brown tsaiya ducks were selected for whole-genome resequencing.After filtering out high-quality SNPs,principal component analysis (PCA) was conducted to assess the genetic differentiation between Jinding ducks and Taiwan brown tsaiya ducks.Subsequently,population genetic differentiation index (Fst) and population nucleotide diversity ratio (π ratio) were used to comprehensively screen selection signals of Jinding duck and Taiwan brown tsaiya duck and analyze their genetic differences.【Result】 5.68 and 5.59 Gb clean data were obtained from resequencing of Jinding duck and Taiwan brown duck,respectively.152 238 286 SNPs were detected in Jinding duck genome,and 155 009 562 SNPs were detected in Taiwan brown tsaiya duck genome,with similar distribution.The PCA results indicated significant differentiation between Jinding duck and Taiwan brown tsaiya duck.Fst and π ratio values were calculated with a sliding window approach with a size of 100 kb and a step size of 10 kb respectively,and then the Fst top 5%（Fst＞0.482）and π ratio top 5% & bottom 5%（0＜π ratio≤0.47 & π ratio ≥3.00）were used as selective signal overlap area.A total of 208 candidate genes were annotated within signal overlap area by the two analysis methods.Furthermore,GO and KEGG enrichment analysis was performed on these 208 candidate genes,indicating that Jinding duck was more strongly selected in immune,lipid metabolism,muscle growth and development.Functional genes IL15,CCL3,CD180,AKT1,PPARGC1A,PRKAA1,FASN,PIK3R1 were screened.【Conclusion】Jinding duck and Taiwan brown tsaiya duck show significant differentiation,and Jinding duck is strongly selected in immune,lipid metabolism,muscle growth and development. |
| Key words: Jinding duck Taiwan brown tsaiya duck whole genome resequencing selection signal candidate genes |
