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首页> 外文期刊>Journal of the American Society for Horticultural Science >Development and Application of Genic Simple Sequence Repeat Markers from the Transcriptome of Loquat
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Development and Application of Genic Simple Sequence Repeat Markers from the Transcriptome of Loquat

机译：Lo转录组基因组简单序列重复标记的开发与应用

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摘要

Deep transcriptome sequencing allows for the acquisition of large-scale microsatellite information, and it is especially useful for genetic diversity analysis and mapping in plants without reference genome sequences. In this study, a total of 14,004 simple sequence repeats (SSRs) were mined from 10,511 unigenes screening of 63,608 nonredundant transcriptome unigenes in loquat (Eriobotryajaponica) with a frequency of 22 SSR loci distributed over 100 unigenes. Dinucleotide and trinucleotide repeat SSRs were dominant, accounting for 20.62%, and 42.1% of the total, respectively. Seventy primer pairs were designed from partial SSRs and used for polymerase chain reaction (PCR) amplification. Of these primer pairs, 54 exhibited amplification and 33 were polymorphic. The number of alleles at these loci ranged from two to 17, and the polymorphism information content values ranged from 0.24 to 0.89. We tested the transferability of 33 SSR polymorphic primer pairs in apple and pear, and the transferability rates in these two species were 90.9% and 87.9%, respectively. A high level of marker polymorphism was observed in apple [Malus xdomestica (66.7%)], whereas a low level was observed in pear [Pyrus sp. (51.5%)]. In addition, the PCR products from seven SSR primer pairs were selected for sequence analysis, and 89.2% of the fragments were found to contain SSRs. SSR motifs were conserved among loquat, apple, and pear. According to our sequencing results for real SSR loci, approximate to 12,490 SSR loci were present in these loquat unigenes. The cluster dendrogram showed a distinct separation into different groups for these three species, indicating that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the species of Maloideae in the Rosaceae. The results of our identified SSRs should be useful for genetic linkage map construction, quantitative trait locus mapping, and molecular marker-assisted breeding of loquat and related species.
机译：深度转录组测序可获取大规模的微卫星信息，对于在没有参考基因组序列的植物中进行遗传多样性分析和作图特别有用。在这项研究中，从10（Eriobotryajaponica）的63,608个非冗余转录组单基因的10,511个单基因中筛选出总共14,004个简单序列重复（SSR），频率为22个SSR基因座，分布在100个单基因上。二核苷酸和三核苷酸重复SSRs占主导地位，分别占总数的20.62％和42.1％。从部分SSR设计了70对引物，并用于聚合酶链反应（PCR）扩增。在这些引物对中，有54个表现出扩增，而33个是多态性。这些基因座处的等位基因数目范围为2至17，多态性信息含量值范围为0.24至0.89。我们测试了33个SSR多态性引物对在苹果和梨中的转移能力，这两个物种的转移率分别为90.9％和87.9％。在苹果[Malus xdomestica（66.7％）]中观察到高水平的标记多态性，而在梨[Pyrus sp。梨中观察到低水平的标记多态性。 （51.5％）]。此外，从七个SSR引物对中选择PCR产物进行序列分析，发现89.2％的片段含有SSR。 SR，苹果和梨中的SSR主题是保守的。根据我们对真实SSR基因座的测序结果，这些lo单基因中大约存在12,490个SSR基因座。簇状图显示了这三个物种的明显不同，这表明这些SSR标记可用于评估蔷薇科中丙二烯科之间及其内部的遗传关系和多样性。我们鉴定出的SSRs的结果应可用于and连锁及相关物种的遗传连锁图谱构建，数量性状基因座定位以及分子标记辅助育种。

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