丝瓜转录组SSR位点分析及其分子标记开发

Analysis on SSR Loci in Transcriptome and Development of Molecular Markers in Luffa cylindrica

对丝瓜(Luffa cylindrica)开展转录组测序分析,共获得58 073条unigene(序列总长约52 087 451 bp),共检测到8 693个SSR(simple sequence repeat)位点,平均分布距离为5.99 Kb;其中,SSR位点中主导类型为二核苷酸重复类型,占总SSR的45.89%;其次,三核苷酸重复类型,占38.89%。二核苷酸重复基序中以AG/CT为主,三核苷酸重复基序以AAG/CTT为主。通过Primer 3.0设计得到7 563对SSR引物,随机选择30对SSR引物,对32种不同来源的丝瓜进行多态性验证分析,其中,22对(占73.33%)引物表现稳定可重复的多态性。利用UPGMA作图,将32份供试材料分为普通丝瓜和有棱丝瓜2类,这2类丝瓜可以进一步分别被分为2个亚群,丝瓜类群的划分与有无棱沟密切相关,与形状、颜色有较高的相关性。通过对丝瓜转录组分析可获得较高频率的SSR位点且类型丰富,为丝瓜遗传多样性分析和遗传图谱构建提供更加丰富可靠的标记选择。

A total of 58 073 unigenes（52 087 451 bp） were obtained and then 8 693 simple sequence repeats（SSR） loci were identified by transcriptome sequenceing analysis in Luffa cylindrica. The mean distribution distance of loci was 5.99 Kb in the unigenes. Among all SSR loci, dinucleotide repeat was the main type（45.89%）, followed by trinucleotide repeat motif（38.89%）. AG/CT and AAG/CTT were the most frequent motifs in dinucleotide and trinucleotide repeats, respectively. A total of 7 563 SSR primers were designed and 30 primers were randomly selected for PCR amplification using 32 loofah materials, of which 22 primers could amplify clearly and reproducibly and showed polymorphism among the materials. According to the UPGMA analysis, 32 plants were divided into 2 groups： Luffa cylindrica Roem and Luffa acutangula Roxb, the 2 groups were divided into 2 sub-groupsis according to fruit shape, respectively. Classification was closely related to the presence or absence of ridges and had a highly correlated with fruit shape and color. These results indicated that high frequency and various types of SSR markers could be acquired in loofah by transcriptome sequencing analysis. And the large quantities of SSR markers would provide more reliable markers for genetic diversity analysis and genetic mapping construction in Luffa cylindrica.