基于灯盏花全基因组SSR位点分析及多态性引物开发

SSR Loci Analysis Based on Erigeron breviscapus Genome and Polymorphism Primers Development

本研究利用MISA工具筛选灯盏花基因组测序获得的462 622条scaffolds,对其SSR位点信息进行分析,Primer 3设计SSR引物,随机选取200对引物对60株灯盏花进行多态性扩增分析。研究结果表明:从灯盏花基因组中搜索到的231 852个SSR位点中,二核苷酸基序是主要的重复类型,占总SSR的47.14%;AT/AT是最多的二核苷酸重复基元,占二核苷酸重复基元的74.60%,AAT/ATT是出现最多的三核苷酸重复基元,占三核苷酸重复基元的15%。PCR扩增发现,200对引物中有30对(15%)表现出稳定的多态性差异。灯盏花基因组中SSR位点出现频率高,类型丰富;大量的SSR为灯盏花的遗传多样性分析和遗传图谱构建提供了丰富的候选分子标记,利于开展灯盏花的遗传育种研究。

In this study, 462 622 scaffolds obtained from the sequencing of Erigeron breviscapus genome were screened by MISA, and the SSR loci information of them were analyzed. SSR primers were designed by Primer 3,and 200 pairs of primers were randomly selected for the polymorphism amplification analysis of 60 E. breviscapus plants. The results indicated that a total of 231 852 SSRs were found in the genome of E. breviscapus, in which dinucleotide was the main type, accounting for 47.14% of all SSRs in E. breviscapus. AT/AT were the predominant dinucleotide repeat types, accounting for 74.6% in the dinucleotide. In addition, AAT/ATT were the main repeat types in the tri-nucleotide repeat motifs, which accounted for 15%. PCR amplification found that 30 pairs of primers（15%） showed stable polymorphism difference among 200 pairs of primers. In conclusion, SSR loci in the genome of E. breviscapus were high in frequency and rich in type. A large number of SSR could provide abundant candidate molecular markers for genetic diversity analysis and genetic map construction of E. breviscapus, which would help the genetic breeding research in E. breviscapus.