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中国农学通报

中国农学通报 ›› 2019, Vol. 35 ›› Issue (28): 38-43.doi: 10.11924/j.issn.1000-6850.casb18050026

所属专题： 生物技术

• 生物技术科学 • 上一篇    下一篇

香蕉根系转录组SSR位点信息分析

王静毅, 刘菊华, 王卓, 金志强, 徐碧玉   

  1. 中国热带农业科学院热带生物技术研究所
  • 收稿日期:2018-05-08 修回日期:2019-09-04 接受日期:2018-07-24 出版日期:2019-10-14 发布日期:2019-10-14
  • 通讯作者: 徐碧玉
  • 基金资助:
    海南省重点研发计划项目“香蕉新品种选育的分子标记技术研发与应用”(ZDYF2018097)；国家现代农业产业技术体系项目“国家香蕉产 业技术体系”(CARS-31)。

Bioinformatic Analysis of Simple Sequence Repeat (SSR) Loci in Banana (Musa acuminata L.) Root Transcriptome

  • Received:2018-05-08 Revised:2019-09-04 Accepted:2018-07-24 Online:2019-10-14 Published:2019-10-14

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摘要： 分析香蕉根系转录组中的SSR位点信息，并设计SSR引物，为开发新的分子标记奠定基础。利用MISA工具对香蕉根系转录组unigene序列进行SSR检索。从25158条unigene中共发现4663个SSR，分布在3820条unigene序列中，出现频率为18.53%，平均每7.77 kb含有1个SSR位点，共有58种重复基元。香蕉根系转录组中，二、三核苷酸重复基元所占比例最大，分别为40.50%和40.63%；二者分别以AG/CT和AGG/CCT重复基元为主，分别占该重复基元的88.03%和30.83%。SSR重复次数以5~9次为主，基序长度主要分布于12~20 bp，平均长度为18.80 bp。香蕉根系转录组SSR位点频率、密度较高，类型多样，在香蕉遗传多样性研究及分子标记辅助育种中有较大应用潜能。

关键词: 车前属, 车前属, 车前, 大车前, 平车前, 种子生物学

Abstract: In order to establish new molecular markers and design SSR primers, the SSR motifs were identified based on the root transcriptome sequencing of Musa acuminata. SSR loci in unigene sequences were identified with the MISA software. A total of 4,663 SSRs were identified from 25,158 banana root unigene sequences, and these SSRs were distributed in 3,820 unigenes in the examined sequences. The frequency of SSRs accounted for 18.53% of all unigenes, and the average distribution distance of SSRs was 7.77 kb. Fifty-eighty kinds of repeat motifs were found. Among them, the most abundant motifs were the di-, and tri-nucleotide repeats, accounting for 40.50% and 40.63% of all SSRs, respectively. AG/CT and AGG/CCT are the superior repeat motifs of di-, and tri-nucleotide, accounting for 88.03% and 30.83%, respectively. Most of the repeat numbers of the SSRs were from 5 to 9, and the length of the motifs mainly ranged from 12 to 20 bp, with the average of 18.80 bp. The SSR loci in the banana root transcriptome had high frequency, and density of distribution, and various types, which can be applied in genetic diversity and marker-assisted breeding in banana.