| 摘要: |
| 为探究苗药八爪金龙群体遗传进化和亲缘关系的远近,该研究利用简化基因组测序技术(SLAF-seq)对42份八爪金龙样品进行测序,获得多态性SLAF 标签。同时采用GATK 和SAMtools软件在多态性SLAF中检测单核苷酸多态性(SNP)分子标记,并利用SNP分子标记分析八爪金龙样品间的遗传分化关系。结果表明:(1)42份八爪金龙共获得246.35 Mb reads,测序质量值Q30 的平均值为95.66%,GC 含量的平均值为41.14%。(2)通过生物信息学的分析,获得1 769 265个SLAF 标签,其中379 829个多态性SLAF 标签,共开发2 299 640个SNPs分子标记。(3)利用开发的SNPs数据构建八爪金龙的系统发育树, 42份八爪金龙分成两个大的类群。第一类群为细柄百两和原变种百两金; 第二类群由贵州朱砂根、红凉伞、湖北朱砂根和江西朱砂根组成。江西朱砂根与其余群体关系较远,有明显的分群现象。该研究从基因组水平揭示不同地区八爪金龙资源之间的遗传关系,为八爪金龙种质资源的鉴定和遗传多样性分析提供了理论基础,所开发的SNP 位点可进一步用于挖掘与品质、抗逆性等相关的基因。 |
| 关键词: 八爪金龙, SLAF-seq, SNP, 遗传进化, 亲缘关系 |
| DOI：10.11931/guihaia.gxzw202006045 |
| 分类号:Q943 |
| 文章编号:1000-3142(2021)07-1145-10 |
| Fund project:国家重点研发计划项目(2018YFC1708100); 贵州省高层次创新型人才培养项目(黔科合人才 [2015]4032号); 贵州省科技厅学术新苗项目(黔科合平台人才 [2018]5766号-9); 贵州中医药大学博士启动基金([2019]04号)[Supported by the National Key Research and Development Programs(2018YFC1708100); Guizhou Province “Hundred” Innovative Talents Project(QKHRC [2015]4032); Guizhou Provincial Department of Science and Technology Academic Seedling Project(QKHPTRC [2018]5766-9); Doctor foundation of Guizhou University of Chinese Medicine([2019]04)]。 |
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| Genetic analysis in Radix Ardisia based on SLAF-seq technology |
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LIU Chang, PAN Jie, LIU Xiongwei, DING Jingxin, ZHOU Ying*
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College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guizhou 550025, China
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| Abstract: |
| In order to explore the genetic evolution and relationship in Radix Ardisia, the 42 materials were used to sequencing base on specific loci amplified fragment sequencing(SLAF-seq). Based on polymorphic SLAF tags, single nucleotide polymorphisms(SNPs)were identified by the GATK and SAMtools softwares, and to analysis the genetic differentiation. The results were as follows:(1)A total of 246.35 Mb reads data were obtained by SLAF-seq, the average of Q30 and GC content was 95.66% and 41.14%, respectively.(2)In total, 1 769 265 high quality SLAF tags were obtained, including 379 829 polymorphic SLAF tags, and a total of 2 299 640 SNPs were obtained.(3)Through the SNPs data, Radix Ardisia were divided into two groups. The first group contained BLX1-8 and BLY1-8, the second group contained ZSG1-8, HL, ZSH1-6 andZSJ1-6. The results revealed the genetic relationships in the genomic level and provided theoretical basis for germplasm identification and genetic diversity analysis of Radix Ardisia and developed SNPs could be further used for excavating the gene related resistant, quality and so on. |
| Key words: Radix Ardisia, SLAF-seq, SNP, genetic evolution, genetic relationship |
