文献类型：期刊文献

中文题名：马尾松转录组SSR序列特征分析及其分子标记开发

英文题名：Characterization Analysis of SSR Sequences in the Transcriptome of Pinus massoniana and Its Molecular Marker Development

作者：陈晓明[1,2] 李魁鹏[2] 陈博雯[2] 刘青华[1] 周志春[1]

第一作者：陈晓明

机构：[1]中国林业科学研究院亚热带林业研究所;[2]广西林业科学研究院

年份：2018

卷号：16

期号：19

起止页码：6407-6414

中文期刊名：分子植物育种

外文期刊名：Molecular Plant Breeding

收录：CSTPCD;;北大核心:【北大核心2017】；CSCD:【CSCD2017_2018】；

基金：中国林业科学研究院中央级公益性科研院所基本科研业务费专项资金项目(CAFYBB2017ZA001-2);国家自然科学基金(31470670);广西自然科学基金(2014GXNSFBA118106);浙江省农业(林木)新品种选育重大科技专项重点课题(2016C02056-4);江西省林业科技创新专项资金项目(201703)共同资助

语种：中文

中文关键词：马尾松;转录组;SSR;分子标记;序列特征

外文关键词：Pinus massoniana;Transcriptome;SSR;Molecular marker;Sequence characteristic

分类号：S3

摘要：为了开发马尾松SSR标记,本研究利用MISA软件对马尾松转录组测序获得的148 186条Unigene (序列总长约91 449.7 kb)进行全面分析,共搜索获得6 611个SSR位点,分布在6 003条Unigene上,SSR发生频率为4.05%,平均每13.83 kb出现1个SSR,结果发现单核苷酸重复出现的频率占总SSR的53.60%;二核苷酸为23.46%;三核苷酸为21.33%。通过对含SSR的Unigene的GO分析,显示生物过程包含的Unigene占40.60%;细胞组分包含的Unigene占35.45%,分子功能包含的Unigene占23.95%;转录组中有724个Unigene可被注释到110个KEGG通路中,其中被注释到新陈代谢的Unigene最多有312个,其次是遗传信息处理类有183个。根据含SSR的Unigene序列共设计了4 247对SSR引物,并随机挑选30对SSR引物进行PCR扩增验证,其中12对引物能够扩增出目标条带,引物的有效性为40%。本研究结果表明,马尾松转录组测序获得的Unigene序列可作为SSR标记开发的有效来源,所开发的SSR标记为马尾松的遗传图谱构建、分子标记辅助育种等研究提供丰富可靠的标记。
In order to develop SSR markers in Pinus massoniana （PM）, MISA software was used in this study to comprehensively analyze 148 186 unigenes （the total length of the sequence was about 91 449.7 kb） obtained from the transcriptome sequencing of Pinus massoniana. A total of 6 611 SSRs which distributed in 6 003 unigenes were identified, with the frequency of SSRs occurrence of 4.05%, and the average density of distribution was one SSR per 13.83 kb. The result showed that the repetition rate of mononucleotide, dinucleotide and trinucleotide accounted for 53.60%, 23.46% and 21.33% of the total SSR, respectively. GO classification analysis of the SSR-containing unigenes revealed that up to 40.60% unigenes belonged to biological process, followed by 35.45% in cellular component and 23.95% in molecular function. 724 unigenes in the transcriptome could be annotated into 110 KEGG pathways, of which up to 312 unigeneswere annotated to metabolism pathways, followed by 183 to genetic information processing pathways. 4 247 pairs of primers were designed based on the sequences of the SSR-containing unigenes. Moreover, 30 pairs of primers were selected randomly for PCR amplification validation. Among them, 12 pairs of primers could amplify target bands, and the effectiveness of these primers was 40%. These results indicated that the unigenes generated from the transcriptome sequencing of Pinus massoniana could be used as an effective source for SSR markers development. The developed SSR markers in this study could provide more reliable markers for the genetic map construction and molecular marker assisted breeding in Pinus massoniana.