| 引用本文: | 王忠良,丁燏,许尤厚,简纪常,鲁义善,王蓓,陈刚,吴灶和.基于转录组数据的马氏珠母贝EST-SSR 位点的信息分析及其多态性检测.海洋与湖沼,2015,46(3):687-693. |
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| 基于转录组数据的马氏珠母贝EST-SSR 位点的信息分析及其多态性检测 |
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王忠良1,2, 丁燏1,3, 许尤厚4, 简纪常1,3, 鲁义善1,3, 王蓓1,3, 陈刚1,2, 吴灶和3,5
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1.广东海洋大学水产学院 湛江 524088;2.广东海洋大学南海水产经济动物增养殖重点实验室 湛江 524088;3.广东省水产经济动物病原生物学及流行病学重点实验室湛江 524088;4.广西北部湾海洋生物多样性养护重点实验室(钦州学院) 钦州 535000;5.仲恺农业工程学院 广州 510225
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| 摘要: |
| 为获得稳定可靠的马氏珠母贝SSR 分子标记, 本文利用MISA 软件对转录组测序数据进行了大规模的EST-SSR 标记发掘, 并分析了位点信息及其多态性。结果表明, 马氏珠母贝转录组测序所获得的74007 条Unigenes 中检测出9872 个EST-SSR 位点, 位点出现频率为13.34%, 平均每5102 bp含有1 个SSR 位点。在转录组SSR 中共有132 种重复基元类型, 其中单核苷酸重复基元为主要类型,占SSR 总数的81.46%; 单核苷酸重复以A/T 基序为主, 占SSR 总数的71.27%。基于筛选的SSR 序列, 应用Primer3 软件进行引物的批量设计, 共为5922 条EST-SSR 序列成功设计出17766 对引物。随机选择80 对引物对EST-SSR 多态性进行检测, 共有62 对引物成功扩增出稳定条带, 占引物总数的77.5%; 其中, 17 对EST-SSR 引物表现出个体多态性, 多态性比率为27.42%。以上研究为马氏珠母贝遗传多样性、遗传图谱构建及分子辅助育种研究提供了有效工具, 对于马氏珠母贝种质资源保护、优良品种培育和珍珠养殖业的健康发展均具有重要意义。 |
| 关键词: 马氏珠母贝 简单重复序列 转录组 分子标记 |
| DOI：10.11693/hyhz20141200361 |
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| 基金项目:国家自然科学基金项目, 31202023 号; 广东海洋大学优秀青年骨干教师特别资助计划, 2014001 号; 广西北部湾海洋生物多样性养护重点实验室(钦州学院)开放课题, 2015KB05 号。 |
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| POLYMORPHISM OF EST-SSRs FROM PINCTADA MARTENSII BASED ON TRANSCRIPTOME DATASETS |
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WANG Zhong-Liang1,2, DING Yu1,3, XU You-Hou4, JIAN Ji-Chang1,3, LU Yi-Shan1,3, WANG Bei1,3, CHEN Gang1,2, WU Zao-He3,5
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1.Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China;2.Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal, Regular High Education Institute of Guangdong Province, Zhanjiang 524088, China;3.Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China;4.Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou University, Qinzhou 535000, China;5.Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
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| Abstract: |
| To enrich the SSR markers from the pearl oyster Pinctada martensii, the EST-SSRs (expressed sequence tag-derived-simple sequence repeats) were developed on a large scale based on the transcriptome sequencing data using program MISA, and polymorphism of SSRs were analyzed and characterized. The results indicate that 9872 EST-SSRs were recognized from 74007 unigenes generated from the transcriptome datasets, accounting for 13.34% of the total unigenes (one EST-SSR per 5102 bp sequence on average). In addition, 132 types of repeat motifs were classified in all EST-SSRs, of which the type of mono-nucleotide repeat was dominant (81.46%), and A/T was the most abundant mono-nucleotide motif (71.27%). Based on the identified SSRs, 17766 pairs of primer sets were designed from 5922 unigenes using program Primer 3. Eighty pairs of primer were randomly selected for PCR amplification to analyze the polymorphism of EST-SSRs, and 62 primers were amplified successfully, among which 17 were polymorphic and the polymorphic rate was 27.42%. These results will provide a useful tool for studies in genetic diversity, genetic map construction and molecular assisted breeding of P. martensii, and be of great importance in genetic resource conservation, stock breeding of P. martensii and sound development of the pearls culture. |
| Key words: Pinctada martensii simple sequence repeat transcriptome molecular marker |
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