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园艺学报 ›› 2020, Vol. 47 ›› Issue (4): 759-768.doi: 10.16420/j.issn.0513-353x.2019-0589

• 研究报告 • 上一篇    下一篇

韭菜全长转录组SSR信息分析及分子标记开发

李延龙,张华敏*,崔蕴刚,陈建华,吕爱芹,李纪军,李艺潇   

  1. 平顶山市农业科学院,河南省韭菜工程技术研究中心,河南平顶山 467001
  • 出版日期:2020-04-25 发布日期:2020-04-25
  • 基金资助:
    国家现代农业产业技术体系建设专项资金项目(CARS-24-A-11)

Analysis on SSR Information in Full-length Transcriptome and Development of Molecular Markers in Allium tuberosum

LI Yanlong,ZHANG Huamin*,CUI Yungang,CHEN Jianhua,Lü Aiqin,LI Jijun,and LI Yixiao   

  1. Pingdingshan Academy of Agricultural Sciences,Henan Chinese Chive Engineering Technology Research Center,Pingdingshan,Henan 467001,China
  • Online:2020-04-25 Published:2020-04-25

摘要: 利用MISA软件筛选韭菜(Allium tuberosum)全长转录组测序获得的49 876条(大于500 bp)转录本序列(89.44 Mb),共检测出13 111个SSR位点,分布在10 332条转录本中,SSR出现频率为26.29%,平均分布距离为6.82 kb。在搜索的6种SSR位点类型中,1 ~ 3个核苷酸重复类型占主要地位,占总SSR位点数的98.74%,其中单核苷酸、二核苷酸和三核苷酸重复类型分别为66.55%、12.52%、19.67%。发现重复序列的基序有103个,其中二核苷酸和三核苷酸重复类型中出现频率高的基序有AC/GT(2.54%)、CA/TG(2.29%)、GAA/TTC(1.85%)和AAG/CTT(1.60%)。重复序列的长度在10 ~ 289 bp之间,其中小于20 bp的有11 128个(84.88%),大于20 bp的有1 983个(15.12%)。根据这些SSR位点,共设计出3 311对SSR引物,在随机选取的208对引物中有164对(78.85%)能进行有效扩增,其中39对引物在24份韭菜种质资源中表现出多态性。利用多态性引物SSR41,鉴定出‘马蔺韭’ב791’后代中的6株有性生殖后代。以上结果表明,基于韭菜全长转录组测序开发的SSR标记可以为韭菜的遗传多样性分析、种质资源鉴定和有性生殖后代筛选提供充足可靠的标记来源。

关键词: 韭菜, 全长转录组, SSR, 无融合生殖

Abstract: Based on 49 876 transcripts(> 500 bp,89.44 Mb)obtained by full-length transcriptome sequencing of Allium tuberosum,13 111 SSR loci distributed in 10 332 transcripts were detected by MISA software. The frequency of these SSR loci was 26.29% and the average distribution distance was 6.82 kb. Among the six types of SSR loci searched,1–3 nucleotide repeats were dominant and accounted for 98.74% of the total SSR loci,of which mono-,di- and tri-nucleotide repeats were 66.55%,12.52%,and 19.67%,respectively. There are 103 detected repeat motifs,of which AC/GT(2.54%),CA/TG(2.29%),GAA/TTC(1.85%)and AAG/CTT(1.60%)were high frequency repeat motifs in dinucleotide and trinucleotide repeats. The lengths of repeat nucleotide sequences for all SSR loci ranged from 10 bp to 289 bp,of which 11 128(84.88%)were less than 20 bp,and 1 983(15.12%)were larger than 20 bp.According to these SSR loci,a total of 3 311 pairs of SSR primers were designed. Two hundred and eight pairs of primers were randomly selected for amplification tests,164 pairs of primers(78.85%)could amplify clear band effectively,and 39 pairs of primers showed polymorphism in 24 Allium tuberosum germplasm resources. Using the polymorphism primer SSR41,six sexual reproductive progenies from‘Malinjiu’ב791’were successfully identified. These results indicated that the SSR markers developed from the full-length transcriptome sequencing of Allium tuberosum could provide sufficient and reliable markers for analysis of genetic diversity,identification of germplasm resources and screening of sexual reproduction progeny of Allium tuberosum.

Key words: Allium tuberosum, full-length transcriptome, SSR, apomixis

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