Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica
Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica
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DOI：
10.1371/journal.pone.0221040
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发表时间：
2019-08-22
期刊：
影响因子：
3.7
通讯作者：
Wu, Wei
中科院分区：
文献类型：
--
作者：
Chen, Chen;Chen, Youjun;Wu, Wei
白芷是一种广泛种植的植物，具有多种用途，特别是在医学领域。然而，A.白芷新的地区，使品种之间难以区分。基于转录组分析的简单重复序列（SSR）对于构建遗传图谱和分析遗传多样性非常有用。这些结果也为利用分子标记辅助育种提供了依据。dahurica。我们根据转录组测序数据鉴定了33，724个基因SSR位点。共设计了114对SSR引物，并对它们的特异性和多样性进行了测试。最终筛选出非翻译区的10个SSR位点。第56话A对不同地区的白芷生态型进行了分析。SSR位点由2-8个等位基因组成，平均每个位点5.2个等位基因。多态信息含量值为0.6274-0.2702（平均值为0.4091），Shannon信息指数为1.3040-0.5618（平均值为0.8475）。因此，本研究中发现的10个新的SSR位点基本符合Harvey-Weinberg平衡，将有助于分析A. dahurica遗传关系本研究的结果证实了转录组数据库的潜在价值，为新的SSR标记的发展。
Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A. dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are very useful for constructing genetic maps and analyzing genetic diversity. They are also relevant for the molecular marker-assisted breeding of A. dahurica. We identified 33,724 genic SSR loci based on transcriptome sequencing data. A total of 114 primer pairs were designed for the SSR loci and were tested for their specificity and diversity. Ten SSR loci in untranslated regions were ultimately selected. Subsequently, 56 A. dahurica ecotypes collected from different regions were analyzed. The SSR loci comprised 2-8 alleles, with a mean of 5.2 alleles per locus. The polymorphic information content value and Shannon's information index were 0.6274-0.2702 (average of 0.4091) and 1.3040-0.5618 (average of 0.8475), respectively. Thus, the 10 novel SSRs identified in this study were almost in accordance with Harvey-Weinberg equilibrium and will be useful for analyzing A. dahurica genetic relationships. The results of this study confirm the potential value of transcriptome databases for the development of new SSR markers.