洋葱转录组SSR信息分析及其多态性研究

Analysis on SSR Information in Transcriptome of Onion and the Polymorphism

采用生物信息学方法分析洋葱(Allium cepa L.)转录组中的SSR位点信息,并设计简单重复序列(SSR)引物,以期为洋葱分子标记辅助育种提供有力工具。利用MISA工具筛选了洋葱转录组测序获得的106 932条unigenes(84.04 Mb),并对其SSR位点信息进行了分析,共筛选得到5 959个SSR位点(占总unigenes的5.10%),其发生频率为1/14.1 kb。SSRs位点中主导类型是以AAG/CTT(占总SSRs的10.20%)为主的三核苷酸重复,占总SSRs的37.27%;其次是单、二核苷酸重复,其出现频率分别为30.91%和24.75%。利用Primer5共设计出5 258对SSR引物。随机选择20对引物进行PCR扩增,其中12对扩增出清晰可重复的条带,9对在24个不同类型洋葱材料中表现出多态性。利用UPGMA作图,将24个洋葱材料分为4类。

Bioinformatics methods were used to analyze the onion(Allium cepa L.)transcriptome SSR loci information and designed simple sequence repeat(SSR)primers,so as to provide a powerful tool for screening onion molecular marker assisted breeding. Five thousand nine hundred and fifty-nine SSR loci(5.10%)were obtained from 106 932 unigenes(84.04 Mb)by using MISA software to screen the onion transcriptome sequencing,and its frequency was 1/14.1 kb. Trinucleotide repeat was the main type,accounted for as much as 37.27% of all SSRs. The AAG/CTT were the predominant repeat types(10.20%),followed by mononucleotide repeat motif(30.91%)and dinucleotide repeat motif(24.75%). Five thousand two hundred and fifty-eight pairs of SSR primers were designed using Primer 5. Randomly 20 pairs of primers were selected for PCR amplification,12 amplified on clear and reproducible bands,9 in 24 different types showed polymorphism in onion material. Twenty-four onions plants were divided into 4 groups by UPGMA.