基于RNA-seq的崇左金花茶EST-SSR标记开发  

Development of EST-SSR Markers in Camellia chuongtsoensis Based on RNA-seq

作　　者：邵阳[1] 范文[1] 黄连冬 高继银[3,4] 李昕骥 张文驹[1] 

机构地区：[1]复旦大学生命科学学院生物多样性科学研究所生物多样性与生态工程教育部重点实验室,上海200438 [2]广西南宁市金花茶公园,南宁530022 [3]广东棕榈风景园林科学研究院,中山528416 [4]中国林业科学研究院亚热带林业研究所,富阳311400

出　　处：《复旦学报（自然科学版）》2015年第6期761-767,共7页Journal of Fudan University：Natural Science

基　　金：国家自然科学基金(31270407)

摘　　要：本研究分析了崇左金花茶（Camellia chuongtsoensis）转录组水平的EST-SSR特征.从崇左金花茶转录组数据组装获得的35 410个Unigene中,共鉴定出2-7不同核苷酸重复类型的SSR位点7 754个,分别分布于6 394条序列中,其中1 121个Unigene具有两个以上的位点.在转录组中SSR位点出现频率为21.90%,分布密度为1/3.6kb;在所有重复单元中,二碱基微卫星占主要优势,占SSR位点总数的61.3%.利用Primer 3.0设计引物,共计3 303条Unigene成功设计出引物.随机选择10对SSR引物,对一个崇左金花茶群体进行扩增多态性分析,8对引物能够扩增出符合预期大小的PCR片段,其中4对引物成功检测出多态.以上结果表明,转录组数据能够提供丰富的SSR位点,用于快速高效地开发SSR引物,所开发的引物可为崇左金花茶遗传多样性的研究以及种质资源的鉴定与保护等方面提供分子基础.In this study, the EST-SSR makers of Camellia chuongtsoensis S. Y. Liang et L. D. Huang were characterized on the transcriptome level. From 35410 Unigenes assembled by the transcriptome data of C. chuongtsoensis, 7754 SSR loci （di to hepta-nucleotide repeats） were identified from 6394 sequences, among which 1121 Unigenes had more than two loci. The frequency of SSR loci on the transcriptome level was 21.90 %, and the density of distribution was on average 1/3. 6 kb. Dinucleotide repeats predominated with an occurrence frequency of 61.3%. A total of 3303 Unigenes could be designed for EST-SSR markers. We randomly selected 10 primer pairs and tested them in a population of C. chuongtsoensis and 8 pairs of them successfully produced the expected PCR bands, among which 4 were found to be polymorphic. These results illustrate that transcriptome data can be used to develop the SSR markers rapidly and efficiently, and these SSR markers are a powerful resource for further applications in the study of C. chuongtsoensis such as the analysis of genetic diversity and the identification and protection of germ plasm resources.

关 键 词：崇左金花茶 简单重复序列 转录组 RNA-SEQ 

分 类 号：Q948[生物学—植物学]