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园艺学报 ›› 2016, Vol. 43 ›› Issue (9): 1816-1824.doi: 10.16420/j.issn.0513-353x.2016-0298

• 研究报告 • 上一篇    下一篇

菜薹转录组中SSR信息与可用性分析

李荣华1,王直亮1,陈静芳1,夏岩石1,郭培国1,*,张 华2,Kadambot Siddique3   

  1. (1广州大学生命科学学院,作物抗逆国际合作研究中心,广州 510006;2广州市农业科学院,广州 510308;3西澳大利亚大学农业研究所,WA 6009,澳大利亚)
  • 出版日期:2016-09-25 发布日期:2016-09-25

Analysis of SSR Information in Transcriptome and Their Usability in Flowering Chinese Cabbage

LI Rong-hua1,WANG Zhi-liang1,CHEN Jing-fang1,XIA Yan-shi1,GUO Pei-guo1,*,ZHANG Hua2,and Kadambot Siddique3   

  1. (1International Crop Research Center for Stress Resistance,College of Life Sciences,Guangzhou University,Guangzhou 510006,China;2Guangzhou Academy of Agricultural Sciences,Guangzhou 510308,China;3The Institute of Agriculture,The University of Western Australia,WA 6009,Australia)
  • Online:2016-09-25 Published:2016-09-25

摘要:

利用菜薹转录组分析检测到48 975条unigene(38.17 Mb)序列数据,运用MIcroSAtellite(MISA)工具发现其中具有1 ~ 6个核苷酸重复类型的SSR位点11 879个,SSR位点发生频率为1/3.2 kb(312.5/Mb)。6种SSR位点类型中主要为1 ~ 3个核苷酸重复,占总SSR位点数的99.01%,其中单、二和三核苷酸类型分别为41.11%、28.23%和29.67%。发现重复序列的基序58个,重复次数在5 ~ 23之间,其中出现频率高的基序主要有A/T、AG/CT、AT/AT、AC/GT、AAG/CTT和AGG/CCT。重复序列长度在10 ~ 60 bp之间,大多小于20 bp,大于20 bp的仅有7.9%(938个SSR位点)。设计出676对具有潜在多态性的SSR引物组合,从中随机抽取30对引物进行PCR扩增验证其可用性,发现22对引物在4份菜薹种质中的扩增产物条带清晰稳定,其中12对引物具有多态性。

关键词: 菜薹, 转录组, SSR, 可用性分析

Abstract:

In this study,SSR loci were mined from transcriptome sequencing data of flowering Chinese cabbage using the MIcroSAtellite identification tool(MISA). 11 879 SSR loci,including the types of 1–6 nucleotide repeats with occurring frequency of 1/3.2 kb(312.5/Mb),were discovered from 48 975 transcriptomic unigenes(38.17 Mb). The major types of SSR loci were 1–3 nucleotide repeats,accounted for 99.01% of the SSR loci,of which mono-,di- and tri- nucleotide repeats were 41.11%,28.23% and 29.67%,respectively. Fifty-eight repeat motifs with iteration numbers from 5 to 23 were identified,and the most abundant motifs were A/T,AG/CT,AT/AT,AC/GT,AAG/CTT and AGG/CCT. The lengths of repeat nucleotide sequences for all SSR loci ranged from 10 to 60 bp,with most below 20 bp,and only 7.9% (938 SSR loci)above 20 bp. A total of 676 pairs of SSR primers with the potential to produce polymorphism were designed;30 primer combinations were randomly selected for amplification tests,of which 22 primer pairs amplified unambiguously with reproducible amplicons and 12 primer combinations produced polymorphisms in four flower Chinese cabbage accessions. These results could provide the foundation for the development and application of SSR markers in flowering Chinese cabbage.

Key words: flowering Chinese cabbage, transcriptome, SSR, usability analysis

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