美洲南瓜转录组SSR信息分析及其分子标记开发

Analysis on SSR Information in Transcriptome and Development of Molecular Markers in Summer Squash

该文对美洲南瓜(Cucurbita pepo L.)开展转录组测序分析,共获得83 650条Unigene,利用MISA软件搜索1 Kb以上的15 356条Unigene,共检测出7 478个SSR位点,分布于5 786条Unigene中,出现频率为48.7%,平均分布距离为4.08 Kb。优势重复基序为单核苷酸、二核苷酸和三核苷酸,分别占总SSR的47.90%、20.57%和22.36%。二核苷酸重复基序中以AG/CT为优势重复基序,三核苷酸重复基序以AAG/CTT为主。利用Primer 3.0共设计出5 786对SSR引物。从114对有效扩增引物中随机选择50对引物,对28个美洲南瓜种质进行多态性验证分析,其中35对(占70%)引物表现稳定可重复的多态性。利用UPGMA作图,将28份供试材料分为2类。利用美洲南瓜转录组数据进行SSR标记开发能获得较高频率的SSR位点,且类型丰富,为美洲南瓜遗传多样性分析和遗传图谱构建提供更丰富可靠的标记选择。

83 650 unigenes were obtained by transcriptome sequencing analysis from Cucurbita pepo L. in this study. 15 356 unigenes above 1 kilo base pairs were found by MISA software, and a total of 7 478 SSR locis were identified that were distributed in 5 786 unigenes. The frequency of these SSR locis was 48.7%, and the mean distribution distance of loci was 4.08 Kb. Mean while, the major repeat motifs were mononucleotide, dinucleotide and trinucleotide, which accounted for 47.90%, 20.57% and 22.36%, respectively. Furthermore, the AG/CT were the predominant dinucleotide repeat motifs, and the AAG/CTT were the predominant trinucleotide repeat motifs. 5 786 pairs of SSR primers were designed by Primer 3.0, then 50 pairs of primers were randomly selected from 114 pairs of effective amplification primers for the polymorphism analysis of 28 Cucurbita pepo L. germplasms, and 35 out of 50 SSR primers showed stable and reproducible polymorphism. According to the UPGMA mapping results, 28 Cucurbita pepo L. samples were divided into 2 categories. Using transcriptome data of Cucurbita pepo L. to develop SSR markers could obtain higher frequencies of SSR locis and the types of them were rich. It provides more abundant and reliable marker selection for genetic diversity analysis and genetic map construction of Cucurbita pepo L.