Characterization and cross-species transferability of EST-SSR markers developed from the transcriptome of Dysosma versipellis (Berberidaceae) and their application to population genetic studies
Characterization and cross-species transferability of EST-SSR markers developed from the transcriptome of Dysosma versipellis (Berberidaceae) and their application to population genetic studies
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从 Dysosma versipellis（小檗科）转录组开发的 EST-SSR 标记的表征和跨物种可转移性及其在群体遗传学研究中的应用
DOI：
10.1007/s11032-014-0134-z
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发表时间：
2014-12-01
影响因子：
3.1
通讯作者：
Qiu, Ying-Xiong
中科院分区：
文献类型：
--
作者：
Guo, Rui;Mao, Yun-Rui;Qiu, Ying-Xiong
八角莲属（Dysosma）为小檗科（Berberidaceae）多年生草本植物，有7种，是传统中药“鬼酒“的主要原料。“尽管八角莲在生态和经济上具有重要意义，但由于分子标记的缺陷，八角莲的分子研究一直滞后。本研究利用cDNA文库技术构建了D.使用Illumina HiSeq（TM）2000测序系统对小麦叶进行测序。从5760万个读段中总共组装了44,855个非冗余的unigenes，并在4,536个unigenes中鉴定了5,167个表达序列标签-简单序列重复序列（EST-SSR）。三核苷酸基序是最常见的类型，频率为43.7%（2，260）。在5，167个EST-SSR中，成功设计了1，050对引物。随机选取80对SSR标记进行验证，其中19对为真型SSR标记，其中14对能可靠地扩增出12个个体的多态性条带。versipellis。这14个EST-SSR标记表现出较高的平均遗传多样性（例如，N（A）= 6.29; H（E）= 0.528）。versipellis种群，也可转移到几乎所有其他八角莲属物种，除了一个标记（4而不是6个物种）。最后，选择了11个多态性标记，为深入了解D. versipellis及其姐妹种D.多花。遗传距离和结构分析确定了两个遗传聚类基本一致，与目前的物种分类。这些结果表明，所检测的EST-SSR标记可用于未来的种群遗传学研究。versipellis和D.多花。
Dysosma (Berberidaceae), which comprises seven herbaceous perennial species, has long been used as main sources of a traditional Chinese medicine, "Guijiu." Despite its ecological and economic importance, molecular research of Dysosma has lagged behind because of the shortcoming of molecular markers. In this study, a cDNA library of D. versipellis leaves was sequenced using the Illumina HiSeq (TM) 2000 sequencing system. A total of 44,855 nonredundant unigenes were assembled from 57.6 million reads, and 5,167 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified in 4,536 unigenes. Trinucleotide motifs were the most common type, with a frequency of 43.7 % (2,260). Among the 5,167 EST-SSRs, 1,050 primer pairs were successfully designed. After selecting 80 of these pairs at random for further validation, 19 pairs were identified as true-to-type SSR loci, and 14 of those could reliably amplify polymorphic bands from 12 individuals of D. versipellis. These 14 EST-SSR markers showed high average genetic diversity (e.g., N (A) = 6.29; H (E) = 0.528), when surveyed across four D. versipellis populations, and were also transferable to almost all other Dysosma species, excepting one marker (four instead of six species). Finally, 11 polymorphic markers were chosen to provide insights into the population structure of D. versipellis and its presumed sister species, D. pleiantha. Both genetic distance and structure analyses identified two genetic clusters largely congruent with the current species classification. These findings indicate that the EST-SSRs examined can be used with confidence in future population genetic studies of both D. versipellis and D. pleiantha.