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首页> 外文期刊>Journal of the American Society for Horticultural Science >Strawberry GenBank-derived and genomic simple sequence repeat (SSR) markers and their utility with strawberry, blackberry, and red and black raspberry.
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Strawberry GenBank-derived and genomic simple sequence repeat (SSR) markers and their utility with strawberry, blackberry, and red and black raspberry.

机译：草莓GenBank衍生的基因组简单序列重复（SSR）标记及其在草莓，黑莓以及红黑莓上的实用性。

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摘要

Although simple sequence repeat (SSR) markers have been developed for species in the closely related genera Fragaria L. (strawberry) and Rubus L. (raspberry and blackberry), the number of SSRs available is insufficient for genetic mapping. Our objective was to use and compare multiple approaches for developing additional SSRs for Fragaria and Rubus. The approaches included: the development of SSRs from GenBank sequences from species of varied relatedness to Fragaria and Rubus and identified with two different data-mining methods (BLAST and SSRIT); the evaluation of some previously published SSRs designed from related species; and the development of SSRs from a genomic library made from F. xananassa Duschene ex Rozier 'Earliglow'. When an SSR was developed from a known gene sequence, the location of the repeat in the gene was determined to evaluate the effect on amplification and polymorphism detection. Cross-generic amplification between closely related Fragaria and Rubus as well as transference from species of varied relatedness to Fragaria and Rubus also was evaluated and indicated limited transference within the subfamily Rosoideae. However, development of SSRs for Fragaria and Rubus from Rosa L. (rose) and Rosaceae genera outside Rosoideae was not efficient enough to be practical for new map development. SSRIT was superior to BLAST for identifying GenBank sequences containing repeats. SSRs developed from repeats found in either the 5'UTR (80% polymorphic) or 3'UTR (85% polymorphic) were most likely to detect polymorphisms, compared with those developed from coding regions (30%). SSRs developed from the genomic library were only slightly superior to GenBank-derived SSRs in their ability to detect polymorphisms.
机译：尽管已经为紧密相关的草莓属（Fragaria L.（strawberry））和Rubus L.（Raspberry and Blackberry）中的物种开发了简单序列重复（SSR）标记，但是可用的SSR数量不足以进行遗传作图。我们的目标是使用和比较多种方法来为草莓和悬钩子开发额外的SSR。这些方法包括：从GenBank序列开发与草莓和悬钩子具有不同相关性的SSR，并用两种不同的数据挖掘方法（BLAST和SSRIT）进行鉴定;对一些以前发表的，由相关物种设计的SSR的评价;并由Rozier'Earliglow'的F. xananassa Duschene制造的基因组文库开发SSR。当从已知的基因序列开发出SSR时，将确定基因中重复序列的位置，以评估对扩增和多态性检测的影响。还评估了密切相关的草莓和悬钩子之间的跨属种扩增，以及与草莓和悬钩子的各种相关性物种的转移，并表明在蔷薇科中的转移有限。但是，从蔷薇科和蔷薇科的蔷薇科和野蔷薇属的草莓和SSRs的开发效率不足，无法用于新的地图开发。 SSRIT在鉴定包含重复序列的GenBank序列方面优于BLAST。与在5'UTR（80％多态性）或3'UTR（85％多态性）中发现的重复序列形成的SSR相比，从编码区（30％）形成的SSR最有可能检测出多态性。从基因组文库开发的SSR在检测多态性方面仅略高于GenBank衍生的SSR。

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