大蒜转录组简单重复序列标记分析与分子标记开发

doi:10.3969/j.issn.1004-1524.2020.09.10

浙江农业学报 ›› 2020, Vol. 32 ›› Issue (9): 1615-1625.DOI: 10.3969/j.issn.1004-1524.2020.09.10

大蒜转录组简单重复序列标记分析与分子标记开发

刘新雨¹, 田洁^1,2,*

1.青海大学农林科学院/青海省蔬菜遗传与生理重点实验室,青海西宁 810016;
2.青海大学省部共建三江源生态与高原农牧业国家重点实验室,青海西宁 810016

收稿日期:2020-04-09 出版日期:2020-09-25 发布日期:2020-10-10
通讯作者: *田洁,E-mail:tiantian8092001@163.com
作者简介:刘新雨(1999—),女,山东聊城人,本科生,主要从事蔬菜生理研究。E-mail:lxy061112@163.com
基金资助:
国家自然科学基金(31760568,31960590);青海省科技厅重点实验室项目(2020-ZJ-Y02);2019年度中国科学院“西部之光”人才培养计划;青海大学农科拔尖创新人才科研训练项目(NKX201805)

Analysis of simple sequence repeats in transcriptome of garlic (Allium sativum L.) and development of molecular markers

LIU Xinyu¹, TIAN Jie^1,2,*

1. Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China;
2. State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China

Received:2020-04-09 Online:2020-09-25 Published:2020-10-10

摘要/Abstract

摘要： 为探明大蒜转录组简单重复序列标记(SSR)的特征,开发适合大蒜育种的SSR引物,利用MISA软件对大蒜转录组序列进行SSR位点检测与信息分析,并通过PCR扩增检测引物的有效性和多态性。结果表明:大蒜转录组测序获得444 865条unigenes,共鉴定出141 132个SSR位点,出现频率为31.72%,平均每3.45 kb出现1个SSR位点。单核苷酸和二核苷酸为SSR位点中优势类型,分别占总SSR的68.02%和24.12%;SSR位点共有82种重复基序,以A/T和AT/AT数量较多,占总SSR位点的65.02%和12.37%。利用Primer 3.0共设计出125 616对SSR引物,在随机选取的14对引物中有12对引物能够有效扩增,其中6对引物在35份大蒜资源中表现出多态性,扩增共得到26条多态性条带,每对引物平均产生4.33条条带。UPGMA分析显示,在遗传相似系数0.756 9处,35份大蒜资源可被分成5大类群。综上所述,利用大蒜转录组数据进行SSR分子标记开发能够获得较高频率的SSR位点,且开发的SSR标记可用性强。

关键词: 大蒜, 转录组, 简单重复序列标记, 多态性

Abstract: In order to investigate features of SSR sequence and develop SSR primers of Allium sativum for garlic breeding, MISA software was used to detect the SSR loci and analyse the SSR information of the garlic transcriptome sequence in this study. The effectiveness and polymorphism of primers were determined by PCR amplification. The results showed that 444 865 unigenes were obtained from garlic transcriptome sequencing. A total of 141 132 SSR loci were identified, the occurrence frequency was 31.72%, the average distribution distance was 3.45 kb. The major repeat motifs were mononucleotide and dinucleotide, which accounted for 68.02% and 24.12%, respectively. 82 repeat motifs of SSR loci were identified, and the most abundant motifs were A/T and AT/AT,which accounted for 65.02% and 12.37%, respectively. A total of 125 616 pairs of SSR primers were designed by Primer 3.0, and 14 pairs of primers were randomly selected and amplified. There were 12 pairs of primers that were clearly amplified. Among them, 6 pairs showed rich polymorphism in 35 garlic germplasm. 26 polymorphic bands were obtained by using 6 pairs polymorphic primers, and the average polymorphic amplification band of each SSR primer was 4.33. According to the UPGMA analysis, 35 garlic germplasm resources were divided into 5 groups at the genetic similarity coefficient of 0.756 9. In conclusion, abundant SSR loci were obtained by development of SSR molecular markers in garlic transcriptome and SSR markers could be widely used.

Key words: Allium sativum L., transcriptome, simple sequence repeats, polymorphism

中图分类号:

S682.32

刘新雨, 田洁. 大蒜转录组简单重复序列标记分析与分子标记开发[J]. 浙江农业学报, 2020, 32(9): 1615-1625.

LIU Xinyu, TIAN Jie. Analysis of simple sequence repeats in transcriptome of garlic (Allium sativum L.) and development of molecular markers[J]. , 2020, 32(9): 1615-1625.

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大蒜转录组简单重复序列标记分析与分子标记开发

Analysis of simple sequence repeats in transcriptome of garlic (Allium sativum L.) and development of molecular markers

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