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2025年8月13日 星期三
  2016, Vol. 24 Issue (11): 1688-1697    
  研究论文与报告 本期目录 | 过刊浏览 | 高级检索 |
菠菜转录组SSR位点分析及其分子标记的开发
潜宗伟1,陈海丽2,崔彦玲2
1. 北京市农林科学院蔬菜研究中心
2.
Analysis of the SSR Loci and Development of Molecular Markers in Spinacia oleracea Transcriptome
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摘要 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。
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潜宗伟
陈海丽
崔彦玲
关键词 菠菜转录组SSR标记    
Abstract:Single sequence repeat (SSR) has the advantages of high polymorphism and comparability, great reproducibility and co-dominance, and has been widely used in genetics and breeding of vegetable crops. In this study, the SSR loci information of spinach (Spinacia oleracea) was analyzed, the SSR molecular markers were developed and genetic diversity of different spinach materials were analyzed. The study used the high generation inbred lines 1012 as the test material, the spinach tissues of flowers, roots, stems and leaves were collected at the flowering stage, and the Illumina HiSeqTM 2500 technique was used to sequence the genes expression. A total of 44 796 unigenes were screened by using MISA software from Spinacia oleracea transcriptome, 2 045 SSR loci occurred in 1 940 unigenes, 1 835 unigenes contained a single SSR loci, 105 unigenes contained 2 or more than 2 SSR loci, and the frequency of these SSRs was 4.33%, and the mean distance was 19.81 kb. Among all SSR loci of Spinacia oleracea, mononucleotide, trinucleotide and tetranucleotide repeat were major types, accounting for 19%, 65% and 7% of the total SSR, respectively, and the repeat types of dinucleotide, pentanucleotide and hexanucleotide were lesser, and the distribution frequency of these types were 0.18%, 0.10% and 0.17%, accounting for 4%, 2% and 3% of the total SSR, respectively. The average repeat length was 21 bp, and the main repeat length was 18~24 bp, accounting for 93.55% of the total SSR, the secondly repeat length was 25~30 bp, accounting for 4.11% of the total SSR,and number of SSR repeat length at 31~39 bp and ≥40 bp were fewer. The main number of repeats was 6 and 7, accounting for 31.42% and 31.05%, the secondly number of repeats were >12 and 5, accounting for 19.17% and 8.41%, respectively, the number of repeats was 8~12. The mononucleotide repeat motif of A/T was the predominant repeat types, dinucleotide repeat motifs of GA/TC and AG/CT were the predominant repeat types, trinucleotide repeat motifs of CAA/TTG, GTT/AAC, GAA/TTC, TGT/ACA and GAT/ATC were the predominant repeat types. The repeat motifs of tetranucleotide, pentanucleotide and hexanucleotide were dispersed, each repeat motifs were relatively lower. All 218 primers of 2 199 SSR primers were selected randomly for PCR amplification using 9 Spinacia oleracea materials with different sources, including 38 SSR markers which performed polymorphical bands, accounting for 17.43% of the total test primers. The 9 materials were divided into 3 major groups by UPGMA, and the first major group included 4 materials, which were 11231, 1408, 1439 and 13190, the second major group included 2 materials, 1012 and 09248, and the third major group included 3 materials, 0928, 8301 and 1723. The SSR information and obtaining abundant polymorphisms SSR markers were studyed, which can be used for the genetic diversity, genetic mapping construction and molecular marker-assisted breeding in Spinacia oleracea.
Key wordsSpinacia oleracea    Transcriptome    SSR    Markers
收稿日期: 2016-05-27      出版日期: 2016-10-01
基金资助:科技部科技支撑项目;北京市财政专项
通讯作者: 崔彦玲     E-mail: cuiyanling@nercv.org
引用本文:   
潜宗伟 陈海丽 崔彦玲. 菠菜转录组SSR位点分析及其分子标记的开发[J]. , 2016, 24(11): 1688-1697.
链接本文:  
http://journal05.magtech.org.cn/Jwk_ny/CN/     或     http://journal05.magtech.org.cn/Jwk_ny/CN/Y2016/V24/I11/1688
 
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