3种烟草基因组SSR位点信息分析和标记开发

Survey of SSR Loci Information in Three Tobacco Genomes and Development of SSR Markers

利用生物信息学方法对绒毛状烟草、林烟草和本塞姆氏烟草3份烟草野生种基因组数据中的SSR位点信息进行了分析。结果表明,在全长分别为2.14Gb、2.44Gb和2.59Gb的绒毛状烟草、林烟草和本塞姆氏烟草基因组中分别获得153 357个、196 493个和278 784个SSR位点,平均相隔13.94kb、12.42kb和9.31kb出现一个SSR。在SSR位点分布区域上,绝大部分的SSR位点分布在内含子和UTR（尤其是5′-UTR）区域;在SSR基序类型上,主要集中在二、三碱基基序且二者占总SSR位点数目的80%以上,并以二碱基基序类型丰度最高;在SSR基序结构上,基因组中出现频率及数量最高的是含有A（T）n的基序结构;在SSR基序的重复次数上,除单碱基基序类型外,重复次数多在3~10次之间。利用分别属于5个不同烟草组的8份烟草材料验证所合成的300对引物,所有合成的引物均能扩增获得目标片段,其中有80对引物存在扩增多态性。表明来源于绒毛状烟草、林烟草和本塞姆氏烟草基因组的SSR标记在亲缘关系相对较近的烟草种间具有高度保守性和通用性,基于此3份烟草野生种基因组数据开发SSR引物用于后续的相关遗传研究具有可行性。

Simple sequence repeats（SSRs）in the whole genomes of three wild tobaccos-Nicotiana tomentosiformis,Nicotiana sylvestris and Nicotiana benthamiana downloaded from the China Tobacco Genome Database（CTGDB）was analyzed by the bioinformatics method.A total of 153 357,196 493 and 278 784 SSR loci were mined out in the 2.14 Gb,2.44 Gb and 2.59 Gb of the three wild tobaccos＇ genomic sequences,and the average distance between SSR loci was approximately 13.94 kb,12.42 kb and 9.31 kb,respectively.Almost all the SSR loci were distributed in intron domains and UTR domains（especially the 5′-UTR）.Di-nucleotide and tri-nucleotide repeats,totally accounting for more than 80%,were the main motif types and the di-nucleotide was the most abundance in all SSRs.The highest frequency and the most abundance of SSR motifs configuration were A（T）n.Except the mono-nucleotide motif type,the repeat number of the motif types was between 3and 10.Three hundred SSR primer pairs randomly synthesized from three wild tobacco genomes were subjected to PCR using 8tobacco accessions as materials which belong to 5different species of the genus Nicotianaand the results showed that all the primer pairs could produce clear,stableand target bands,of which 80 SSR primers were polymorphic.The results indicated that SSR loci in the closer genetic relationship among tobacco species were highly conserved and could be used in the following research.It is meaningful to develop SSR primer pairs from wild tobacco genomic data for the application of relative genetic analysis.