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[1]李娜,姚民,梅兰菊,等.基于山桐子转录组序列的SSR分子标记开发[J].应用与环境生物学报,2017,23(05):952-958.[doi: 10.3724/SP.J.1145.2016.10028]
 LI Na,YAO Min,MEI Lan ju,et al.Development of SSR molecular markers based on transcriptome sequencing of Idesia polycarpa Maxim.[J].Chinese Journal of Applied & Environmental Biology,2017,23(05):952-958.[doi: 10.3724/SP.J.1145.2016.10028]
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基于山桐子转录组序列的SSR分子标记开发()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
23卷
期数:
2017年05期
页码:
952-958
栏目:
生物活性化合物的发现与开发专栏
出版日期:
2017-10-25

文章信息/Info

Title:
Development of SSR molecular markers based on transcriptome sequencing of Idesia polycarpa Maxim.
作者:
李娜姚民梅兰菊廖望陈放唐琳
四川大学生命科学学院,生物资源与生态环境教育部重点实验室 成都 610064
Author(s):
LI Na YAO Min MEI Lan ju LIAO Wang CHEN Fang & TANG Lin**
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
关键词:
山桐子转录组SSR分子标记遗传多样性
Keywords:
Idesia polycarpa Maxim. transcriptome SSR molecular marker gennetic diversity
分类号:
Q949.759.303
DOI:
10.3724/SP.J.1145.2016.10028
摘要:
为研究山桐子遗传多样性,对山桐子转录组数据进行分析,开发SSR分子标记技术. 将山桐子高通量转录组测序获得的84 213条Unigene进行简单重复序列(SSR)位点挖掘和分析,并结合引物验证,初步证明其可行性. 通过软件分析,共获得含SSR位点的序列数23 077,出现频率为27.40 %,涉及序列数量为29 953条,发生频率为35%. SSR序列中包括1 620种重复基元类型,其中单核苷酸、二核苷酸和三核苷酸为优势重复类型,SSR位点数分别为9 782(32.67%)、6 921(23.11%)和5 420(18.10%). 单核苷酸中A/T类型比例最高,为9 630(32.15%),二核苷酸和三核苷酸中以类型AG/CT(4 679;15.62%)和AAG/CCT(1 220;1.53%)为主. SSR位点重复次数差别较大,主要是3次(4 748;15.70%),其次为6次(3 707;12.25%)和5次(3 475;11.60%). 运用多态性分析的方式初步验证SSR位点在不同地区山桐子标记中的可行性. 同时,利用Primer 5.0进行引物设计,随机筛选100对引物进行验证,31对引物可以扩增出条带,19对引物扩增出预期大小的条带,8对引物能特异性区分宜宾、资阳、宁强、成都4个不同地区的山桐子. 本研究通过分析山桐子高通量转录组序列的SSR信息,筛选出8对引物验证不同地区山桐子的遗传多样性,将有助于山桐子基因挖掘、分子标记育种和资源保护等后续工作的开展. (图6 表4 参26)
Abstract:
SSR (simple sequence repeat) molecular markers were used for species identification and genetic diversity of Idesia polycarpa Maxim. This method provided bases of resource development and protection of I. polycarpa, and was developed based on transcriptome sequencing. A total of 84 213 unigenes obtained by transcriptome sequencing were used to explore SSR, and it was feasible to develop molecular markers of I. polycarpa by primers analysis. 29 953 SSR were identified through software analysis, and the frequency was 35.0%. Meanwhile, the number of sequences involved in these SSR was 23 077 accounting for 27.40%. The repeat types of SSR were 1 620. Among them, mononucleotide, dinucleotide and trinucleotide type were dominant types, and the number of SSR was 9 782 (32.67%), 6 921 (23.11%), and 5 420 (18.10%), respectively. Additionally, the dominant repeat type was A/T, AG/CT and AAG/CTT, and the distribution frequency was 32.15%, 15.62% and 1.53%. SSR repeat frequency was largely different, among which, the type which repeated 3 times was the most, accounting for 15.70%, followed by 6 times (12.25%) and 5 times (11.60%). Here, we proved initially that it was feasible to develop molecular markers of I. polycarpa by polymorphism analysis. Meanwhile, a total of 100 primer pairs were randomly selected to be verified by PCR and among them 31 pairs of primers were able to amplify products. 19 pairs of primers can amplify expected products, 8 pairs of primers could distinct the areas of Yibin, Ziyang, Ningqiang and Chengdu. By SSR of high-throughput transcriptome sequencing of I. polycarpa, the study selected 8 primers which were amplied to identify the genetic diversity of I. polycarpa in different areas. The SSR markers will benefit candidate gene mining, marker-assisted breeding and resources protection of I. polycarpa.

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更新日期/Last Update: 2017-10-25