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| 基于柿雌雄花芽转录组测序的SSR和SNP多态性分析 |
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杜改改1,2, 孙鹏1,2, 索玉静1,2, 韩卫娟1,2, 刁松锋1,2, 傅建敏1,2, 李芳东1,2
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| (1.国家林业局泡桐研究开发中心, 郑州 450003;2.中国林业科学研究院经济林研究开发中心, 郑州 450003) |
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| 摘要: |
| 为深入开发柿SSR和SNP分子标记，进而推动柿品种鉴定和遗传多样性等研究，以‘禅寺丸’柿的雌雄花芽转录组序列为基础，对SSR和SNP位点进行发掘。结果表明：转录组测序获得了154 741条unigene，其中有38.49% unigene在数据库中得到注释。利用MISA软件进行SSR位点的搜索，共得到44 304个SSR，包含83种重复基元，其中以A/T类型为主的单核苷酸重复所占的比例最高（20 006个，占47.63%），其次是以AG/CT类型为主的二核苷酸重复（16 055个，占38.23%），再次是以AAG/CTT类型为主的三核苷酸重复（5 402个，占12.87%）和以AAAG/CTTT类型为主的四核苷酸重复（500个，占1.19%）。在转录组得到的unigene中共发现SNP 405 685个，发生频率为1/253 bp。6种单核苷酸变异中，转换类型发生频率显著高于颠换类型，转换类型中的C/T（31.51%）和A/G（31.41%）发生频率最高，在颠换类型中A/T发生频率最高。柿SSR和SNP的位点是非常丰富的，可为柿遗传图谱构建、遗传多样性和亲缘关系研究提供丰富的基础数据信息。 |
| 关键词: 柿 转录组测序 SSR标记 重复基元 SNP |
| DOI：10.11841/j.issn.1007-4333.2017.10.05 |
| 投稿时间：2016-10-27 |
| 基金项目:青年科学基金项目（31500559）；中国林科院青年项目配套类（CAFYBB2016QB017）；河南省基础与前沿技术研究项目（152300410135） |
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| SSR and SNP polymorphism analysis based on persimmon (Diospyros kaki) transcriptome |
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DU Gaigai1,2, SUN Peng1,2, SUO Yujing1,2, HAN Weijuan1,2, DIAO Songfeng1,2, FU Jianmin1,2, LI Fangdong1,2
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| (1.China Paulownia Research Center, State Forestry Administration, Zhengzhou 450003, China;2.Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China) |
| Abstract: |
| The aim of this study was to develop SSR and SNP markers and promote the researches on varieties identification and genetic diversity in Diospyros kaki.The transcriptome of persimmon flowers were sequenced by RNA-Seq technology,and MISA and GATK3 software were used to explore the SSR and SNP loci.A total of 154 741 unigenes were detected,of which 38.49% were annoted according to datebases.And 44 304 SSRs occurred in 59 570 unigenes were identified,including 83 SSR repeat motifs.Mononucleotide repeats(20 006,47.63%) based on A/T accounted for great proportion in complete SSRs,dinucleotide repeats(16 055,38.23%) mainly on AG/CT ranked the second;and trinucleotide(5 402,12.87%)with the main type of AAG/CTT and tetranucleotide(500,1.19%)with the main type of AAAG/CTTT,ranked third and forth seperately.A total of 405 685 candidate SNP bit points were searched and the average appearance frequency was 1/253 bp,and the number of the conversion type was significantly highier than the transversion type.C/T and A/G belonged to conversion type occurred most frequently among 6 kinds of SNP types.Of all the tranversion types,A/T occurred most frequently.SSR and SNP loci were abundant in persimmon,the development of molecular marker would provide the basic information for genetic map structure,analysis of genetic diversity and identificaiton of relative relationships for Diospyros kaki. |
| Key words: Diospyros kaki trancriptome sequeucing SSR marker frequent motif SNP |
