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    基于选择清除分析鉴定影响枣果实大小的基因

    Identification of genes related with jujube fruit size based on selective sweep analysis

    • 摘要:
      目的通过全基因组水平上比较大果型和小果型两种类型枣品种间遗传多样性水平,检测基因组的选择清除区域,以期鉴定影响枣果实大小的潜在相关基因,为解析枣果实大小差异形成的分子机制奠定基础。
      方法本研究通过利用12个大果类型枣品种和25个小果类型枣品种群体的简化基因组测序,获得SNP标记后进行主成分和遗传多样性分析,解析枣品种的群体遗传关系;同时,基于遗传分化系数(Fst)和核苷酸多态性(π)进行选择信号检测,进一步对受选择区域所包含的基因进行基因功能及通路的生物信息学分析,并对其中与细胞周期调节以及激素相关的基因在‘桐柏大枣’和酸枣果实中的相对表达量进行了比较分析。
      结果共获得130 077个高质量的SNPs,大果群体的遗传多样性(π:0.32)低于小果群体(π:0.33),大果和小果群体分别检测到83和149个受选择基因。通过基因的功能注释和富集分析,我们确定了6个参与细胞周期或激素合成调控途径的候选基因(LOC107404981、LOC107406728、LOC107424132、LOC107426306、LOC107418232、LOC107432595)。qRT-PCR检测发现,LOC107424132、LOC107426306、LOC107418232、LOC107432595表达量在花后75天增加,候选基因LOC107404981、LOC107406728的表达量在花后45天和75天显著增加。进一步分析发现这些候选基因在枣品种和酸枣之间存在差异表达。
      结论结果表明LOC107404981、LOC107406728基因可能与枣果实大小的分子调控有关,为进一步揭示该基因的调控机制奠定了基础。

       

      Abstract:
      ObjectiveThe purpose of this study was to compare the differences in genetic diversity of jujube (Ziziphus jujuba), and to detect the selection sweep regions between the large fruit and small fruit groups. We hope to detect the genomic selection regions related with fruit size, laying a foundation for the analysis of the molecular mechanism of fruit size regulation.
      MethodThe single nucleotide polymorphisms (SNPs) were called based on the genotyping-by-sequencing data of 37 jujube accessions, including 12 large fruit accessions and 25 small fruit accessions, and then the principal component analysis and genetic diversity analysis were carried out to analyze the genetic relationship of the jujube accessions. The genetic differentiation coefficient (Fst) and the nucleotide diversity (π) were calculated to detect the selection signals. The important genes in these selected regions were analyzed by GO and KEGG analysis. The relative expression levels of the potential genes related with fruit size were further analyzed in Z. jujuba ‘Tongbaidazao’ and Z. jujuba var. spinosa at six stages of fruit development.
      ResultA total of 130 077 high-quality SNPs were obtained. The genetic diversity of the large fruit group (π: 0.32) was lower than that of the small fruit group (π: 0.33). We detected 83 and 149 sweep regions for large fruit and small fruit groups, respectively. Furthermore, we identified six candidate genes (LOC107404981, LOC107406728, LOC107424132, LOC107426306, LOC107418232, LOC107432595) involved in the regulation of cell cycle or hormone synthesis pathways. qRT-PCR showed that the expression of LOC107424132, LOC107426306, LOC107418232 and LOC107432595 increased at 75 days after flowering, while the expression of candidate genes LOC107404981 and LOC107406728 increased significantly at 45 days and 75 days after flowering, in agreement with the development curve of fruit size. We further found their differential expression between a large jujube cultivar and a sour jujube accession.
      CouclusionLOC107404981 and LOC107406728 were possibly involved in the molecular regulation of jujube fruit size, and further researches are expected to reveal specific molecular functions.

       

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