基于SLAF-seq技术的苗药八爪金龙遗传分析

Genetic analysis in Radix Ardisia based on SLAF-seq technology

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1769265个SLAF标签,其中379829个多态性SLAF标签,共开发2299640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。

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,1769265 high quality SLAF tags were obtained,including 379829 polymorphic SLAF tags,and a total of 2299640 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 and ZSJ1-6.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.