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简单重复序列(simple sequence repeat,SSR)分子标记具有多态性高、重复性好、共显性等特点,已广泛用于蔬菜作物遗传育种研究中。本研究利用MISA软件对菠菜(Spinacia oleracea)转录组SSR位点信息进行分析,开发适用于菠菜的SSR分子标记,并对不同菠菜材料的遗传多样性进行分析。结果显示,在获得的44 796条基因簇(Unigene)中检测出2 045个SSR位点,检测出2 045个SSR位点,分布在1 940条Unigene上,发生频率为4.33%,平均距离为19.81 kb。菠菜SSR中以单、三、四核苷酸重复为主,分别占总SSR的19%、65%和7%,重复长度主要为18~24 bp,占菠菜总SSR的93.55%,以重复次数6次和7次为主,分别占菠菜总SSR的31.42%和31.05%。菠菜转录组中单核苷酸重复类型为A/T,二核苷酸重复主要为GA/TC和AG/CT,三核苷酸重复主要以CAA/TTG、GTT/AAC、GAA/TTC、TGT/ACA和GAT/ATC为主。本研究共设计了2 199对SSR特异位点引物,随机挑选218对引物对9个不同类型的菠菜材料进行扩增检测,其中38对表现出多态性。利用UPGMA做图进行聚类分析,9份菠菜材料聚为3类。本研究通过对菠菜转录组SSR位点信息分析及其分子标记的开发,获得了多态性较为丰富的SSR位点,为菠菜遗传多样性的分析、遗传图谱的构建及分子标记辅助育种提供了基础资料。
Simple sequence repeat (SSR) markers have the characteristics of high polymorphism, good repeatability and codominance. They have been widely used in the research of genetics and breeding of vegetable crops. In this study, we used MISA software to analyze the SSR locus of spinach (Spinacia oleracea) transcriptome, developed SSR markers suitable for spinach, and analyzed the genetic diversity of different spinach materials. The results showed that 2 045 SSR loci were detected in 44 796 gene clusters obtained, 2 045 SSR loci were detected in 1 940 Unigene, the frequency was 4.33%, and the average distance was 19.81 kb. Spinach SSRs were dominated by single, triple and quadruple nucleotide repeats, accounting for 19%, 65% and 7% of the total SSR, respectively. The repeat lengths were mainly 18-24 bp, accounting for 93.55% of total SSR of spinach, 6 times and 7 times respectively, accounting for 31.42% and 31.05% of the total spinach SSR respectively. The single nucleotide repeat types in spinach transcriptome were A / T, the dinucleotide repeats were mainly GA / TC and AG / CT, the trinucleotide repeats were mainly CAA / TTG, GTT / AAC, GAA / TTC, TGT / ACA and GAT / ATC based. In this study, a total of 2,199 SSR loci were designed and 218 pairs of primers were randomly selected to amplify nine different types of spinach materials, of which 38 pairs showed polymorphism. Using UPGMA to do cluster analysis, nine spinach materials were clustered into three categories. In this study, SSR loci with rich polymorphism were obtained by analyzing the SSR locus information of spinach transcriptome and developing its molecular markers. This study provided the basis for genetic diversity analysis, genetic map construction and molecular marker assisted breeding of spinach Basic information.