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Identification and characterization of SSR markers of Guadua chacoensis (Rojas) Londoño & P.M. Peterson and transferability to other bamboo species.
3 Biotech ( IF 2.6 ) Pub Date : 2020-05-29 , DOI: 10.1007/s13205-020-02268-4
Márcia D Rossarolla 1 , Tiago C Tomazetti 1 , Leila N Vieira 2 , Miguel P Guerra 1, 3 , Gustavo H F Klabunde 4 , Ramon F Scherer 4 , Rosete Pescador 1 , Rubens O Nodari 1
Affiliation  

The aim of this study was to develop simple sequence repeat (SSR) markers for genetic studies on G. chacoensis, as well as to evaluate their transferability to other bamboo species. Genomic DNA was isolated from G. chacoensis and its partial sequencing was used to find SSR loci. The obtained sequencing data were de novo assembled using the software CLC Genomics Workbench® 8.0v. The SSR loci primers were identified and designed with the software SSRLocator. The selected markers were validated using 56 plants sampled in seven populations from southern Brazil. The markers with potential polymorphism were selected and fluorescently labeled for characterization by capillary electrophoresis. In total, 92 SSR loci were found in G. chacoensis contigs. Suitable primers were designed for 70 SSR loci, and the remaining 22 SSR loci did not have sequences for primer development. Out of 35 selected SSR markers, after PCR optimization, 10 with high polymorphism potential were characterized. These loci can be used in genetic analyses of G. chacoensis and all of them were successfully transferred to other bamboo species. Non-polymorphic loci require further tests with additional plants, from different populations, to identify possibilities of their use.



中文翻译:

番石榴(Guadua chacoensis(Rojas)Londoño&PM Peterson)的SSR标记的鉴定和表征以及对其他竹种的转移性。

这项研究的目的是开发简单序列重复(SSR)标记,用于遗传学对chacoensis的遗传研究,并评估其向其他竹种的转移性。从cha.ensis分离出基因组DNA,并将其部分测序用于发现SSR基因座。所获得的测序数据是从头使用软件CLC基因组学工作台组装® 8.0V。用软件SSRLocator鉴定并设计了SSR基因座引物。使用来自巴西南部七个种群的56种植物对所选标记进行了验证。选择具有潜在多态性的标记,并对其进行荧光标记,以通过毛细管电泳进行表征。在chacoensis中总共发现了92个SSR基因座重叠群。针对70个SSR基因座设计了合适的引物,而其余的22个SSR基因座没有用于引物开发的序列。在优化的35个SSR标记中,PCR优化后,鉴定出10个具有高多态性的潜力。这些基因座可用于Chacoensis的遗传分析,并将所有基因座成功转移到其他竹种中。非多态位点需要对来自不同种群的其他植物进行进一步测试,以确定其使用可能性。

更新日期:2020-05-29
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