Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptome
Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptome
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DOI：
10.56093/ijas.v90i5.104330
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发表时间：
2020-09
期刊：
影响因子：
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通讯作者：
Yijing Gao;Hui Zhou;Junxian Liu;Jingchao Lei;W. Duan;Cuifang Yang;Shane Zhou;Xiang Li;
中科院分区：
文献类型：
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作者：
Yijing Gao;Hui Zhou;Junxian Liu;Jingchao Lei;W. Duan;Cuifang Yang;Shane Zhou;Xiang Li;
利用表达序列标签（EST）数据库开发的微卫星或简单重复序列（SSR）是一种经济有效的工具，可用于在功能水平上进行遗传研究。在这里，一个新的甘蔗数据库的转录组从我们的品种，GT 35，SSR的存在进行了检查。为了测试EST衍生的SSR标记的实用性，总共鉴定了51个新的EST-SSR，其可能用作来自没有冗余SSR阳性EST的潜在遗传标记，所述SSR阳性EST通过BLACKS与NCBI甘蔗EST数据库中可用的序列未作图。利用筛选到的51个EST-SSR标记，对广西农业科学院甘蔗研究所2013年种植和收集的21个甘蔗基因型进行了多态性分析。结果表明，该群体的等位基因数在5-36个之间，平均为16.8个，多态信息含量在0.74 ~ 0.95之间，平均为0.92。对斑茅和楠仁的平均转移率分别为23.9%和34.4%。用聚类分析方法分析了它们建立亲缘关系的能力，结果表明，它们的主要类群与分类学上的分类是一致的。新的EST-SSR标记的开发将对遗传分析和育种具有重要意义。
Microsatellites, or simple sequence repeats (SSR), developed by expressed sequence tag (EST) databases is an economical and efficient tools that can be used to perform genetic investigations at a functional level. Here, a new sugarcane database of transcriptome from our variety, GT35, was examined for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 51 new EST-SSRs were identified for possible use as potential genetic markers from no redundant SSR-positive ESTs, which were unmapped with the sequences available in the NCBI’EST database of sugarcane by BLASTN. Polymorphisms of the identified 51 EST-SSR markers were evaluated in 21 sugarcane genotypes, planted and collected in 2013 at Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences (SRI-GXAAS) in China. High polymorphisms were detected in terms of number of alleles ranging from 5-36 with an average of 16.8 per locus and polymorphism information content values ranging from 0.74 to 0.95 with a mean of 0.92. Average transferability to Erianthus arundinaceus and Narenga porphyrocoma was 23.9% and 34.4%, respectively. The ability to establish genetic relationship was analyzed by cluster analysis, the result of which revealed that the major grouping was in accordance with taxonomical classification. The development of new EST-SSR markers presented in this work will have important implications for genetic analysis and breeding.