HUANG Qiong-lin,HE Rui,ZHAN Ruo-ting,et al.SSR Loci Information Analysis in Nervilia fordii Transcriptome[J].Northern Horticulture,2015,39(12):76-79.[doi:10.11937/bfyy.201512021]
南药青天葵转录组SSR位点信息分析
- Title:
- SSR Loci Information Analysis in Nervilia fordii Transcriptome
- 文章编号:
- 1001-0009（2015）12-0076-04
- Keywords:
- Nervilia fordii; SSR; loci information; transcriptome
- 分类号:
- R 282.71
- 文献标志码:
- A
- 摘要:
- 以青天葵全转录组测序获得的142 220条unigene为试材，采用MicroSAtellite（MISA）软件分析青天葵简单重复序列（simple sequence repeat，SSR）的分布频率和重复基元的类型等特征，利用Primer 5.0对符合鉴定要求的SSR基元进行引物设计，并通过SSRFinder校验SSR引物，以期为青天葵遗传多样性分析、分子标记辅助育种、遗传图谱绘制等种质资源研究提供参考依据。结果表明：在青天葵转录组共检测到分布在5 223条unigene上的5 684个SSR位点，SSR发生频率为3.67%，分布密度为1/13 kb。二核苷酸重复为青天葵SSR主要基元类型，其中AG/CT和AT/AT基序出现频率最高，占SSR总数的52.9%。设计筛选得到2 486条SSR引物。青天葵转录组SSR位点出现频率高、类型丰富、多态性潜能较高。
- Abstract:
- Taking 142 220 unigenes in Nervilia fordii transcriptome as materials to identify functional simple sequence repeat (SSR)，which would promote the researches on resource protection including genetic diversity，molecular breeding and genetic mapping of N.fordii. The distribution frequency of high flux transcriptome SSR and the basic characteristics of repeat motifs were analyzed using MicroSAtellite software，and then SSR primers were designed by Primer 5.0 software and validated by SSR Finder software The results showed that 5 684 SSR loci were acquired from 5 223 unigenes with an occurrence frequency of 3.67% and a density of 1/13 kb.Dinucleotide repeat was the main SSR type of N. fordii，and AG/CT and AT/AT exhibited the highest occurrence frequency (52.9%) among all SSR motifs.A total of 2 486 primer pairs were designed for marker development.
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备注/Memo
第一作者简介： 黄琼林（1986-），男，博士，讲师，研究方向为分子生物学。E-mail：perfecthql@163.com.责任作者： 何瑞（1972-），女，博士，研究员，博士生导师，研究方向为中药资源可持续利用与开发。E-mail:ruihe@gzucm.edu.cn.基金项目：教育部留学回国人员科研启动资助项目（教外司留［2009］1001号）；广东医学院博士学位人员科研启动资助项目（B2013017）。