• 中文核心期刊
  • CSCD来源期刊
  • 中国科技核心期刊
  • CA、CABI、ZR收录期刊

金定鸭与龙岩山麻鸭的选择信号差异分析

Differences on Genetic Selection Signals of Jinding Ducks and Longyan Shanma Ducks

    摘要
  • 摘要:
    目的 对金定鸭与龙岩山麻鸭进行选择信号分析，筛选与重要经济性状差异相关的基因和通路，为筛选蛋鸭重要性状分子标记奠定基础。
    方法 选取金定鸭和龙岩山麻鸭各30只进行全基因组重测序，基于重测序数据，利用GATK获得单核苷酸多态性位点（single nucleotide polymorphisms, SNPs）后，对其进行主成分分析（principal component analysis, PCA），再利用群体遗传分化指数（population genetic differentiation index, Fst）和群体核酸多样性比值（π ratio）两种分析方法综合筛选金定鸭和龙岩山麻鸭的受选择信号区域，对候选基因进行GO和KEGG富集分析。
    结果 金定鸭和龙岩山麻鸭重测序共获得307 247 849个SNPs。PCA结果显示，金定鸭和龙岩山麻鸭显著分化；以100 kb为滑动窗口、10 kb为步长分别计算Fst与π ratio值，将Fst top 5%（Fst＞0.353）与π ratio top 5% & bottom 5%（0＜π ratio≤0.41 & π ratio≥1.49）作为受选择区域，共注释到200个候选基因。GO和KEGG分析结果表明，79个候选基因显著富集于204个GO条目（P＜0.05），5条KEGG通路显著富集（P＜0.05），从中筛选到重要经济性状的相关功能基因ELOVL7、HACD4、JAK2、ETV1、HOMER1、HTR1D、ACVR2A、PCSK5、SLC1A3、ANXA1、PTAFR、INHBB、IL31RA。
    结论 金定鸭和龙岩山麻鸭显著分化，对其进行选择信号分析，鉴定到13个与脂类代谢、生长发育、免疫和繁殖相关的候选基因，为蛋鸭重要经济性状的功能基因筛选和分子调控网络解析提供参考。

     

    Abstract:
    Objective Selection signals of egg-laying Jinding duck and Longyan Shanma duck for effective identification of target genes and pathways for breeding were investigated.
    Method Thirty Jinding ducks and Longyan Shanma ducks each were randomly selected for whole-genome resequencing. Based on the sequences, GATK was used to obtain single nucleotide polymorphisms(SNPs) and conduct principal component analysis (PCA). Subsequently, the population genetic differentiation index, Fst, and the population nucleotide diversity ratio, π ratio, were used to comprehensively screen for selection signals. Candidate genes were subjected to GO and KEGG enrichment analysis for functional confirmations.
    Result A vast number of 307 247 849 SNPs were obtained by the resequencing. Significant genetic differentiations between Jinding duck and Longyan Shanma duck were indicated by PCA. The Fst and π ratio calculated by using a sliding window of 100 kb and a step size of 10 kb, respectively, were separated by the following thresholds into groups of top 5% Fst at Fst＞0.353, top 5% π ratio at π ratio≥1.49, and bottom 5% π ratio at 0＜π ratio≤0.41. As a result, 200 annotated genes in the overlapping signal regions were identified to be the candidates for the selection. Subsequently, analyses revealed that 79 of these genes were significantly enriched in 204 GO functions and 5 KEGG pathways. And the functional genes related to the economic traits of interest were identified to include ELOVL7, HACD4, JAK2, ETV1, HOMER1, HTR1D, ACVR2A, PCSK5, SLC1A3, ANXA1, PTAFR, INHBB, and IL31RA.
    Conclusion Genetically, Jinding duck and Longyan Shanma duck were significantly different. This study identified selection signals of 13 genes related to lipid metabolism, growth and development, immunity, and reproduction that could significantly facilitate breeding fowls with desired traits.

     

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