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首页> 外文期刊>Biochemical Genetics >De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry
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De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry

机译：De Novo组装了红花草莓基因SSR标记的转录体分析及鉴定

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Red-flowered strawberry is a new ornamental flower derived from intergeneric hybridization (Fragaria x Potentilla). To date, few molecular markers have been reported for this plant. RNA sequencing provides a relatively fast and low-cost approach for large-scale detection of simple sequence repeats (SSRs). In the present study, we profiled the transcriptome of red-flowered strawberry by Illumina HiSeq 2500 to identify SSRs related to petal color. Based on 2 million clean reads of red and white flowers from red-flowered strawberry hybrids, we assembled 91,835 unigenes with an average length of 717 bp. After functional annotation and prediction, there were 47,058 unigenes; of these, 26,861 had a gene ontology annotation, with 14,264 SSR loci. Mononucleotide SSRs were the predominant repeat type (47.20%, n = 6724), followed by di- (32.50%, n = 4641), tri- (19.10%, n = 2729), tetra- (0.90%, n = 132), hexa- (0.2%, n = 21), and penta- (0.10%, n = 16) nucleotide repeats. The most frequent di-, tri-, and tetra-nucleotide repeats were AG/CT, AAG/CTT, and AAAG/CTTT, respectively. PCR amplification with 105 SSR primer pairs yielded four bands specific to red flowers, namely UgRFsr57622, UgRFsr94149, UgRFsr40142, and UgRFsr54608; corresponding 4 trait-specific markers were found to co-segregate with white and red flower color in hybrid population, demonstrating that the genic SSR marker is useful to discriminate between white and red flowers in strawberry. Markers to discriminate flower color in red-flowered strawberry will be useful for early selection of progeny and for breeding management.
机译：红花草莓是一种衍生自用于代际杂交的新装饰花（Fragaria x potentilla）。迄今为止，已经报道了这种植物的一些分子标记。 RNA测序提供了一种相对快速和低成本的方法，用于大规模检测简单序列重复（SSR）。在本研究中，我们通过Illumina Hiseq 2500探讨了红花草莓的转录组，以鉴定与花瓣颜色相关的SSR。根据红花草莓杂交种的200万清洁读取的红色和白花，我们组装了91,835个unigenes，平均长度为717 bp。功能辅助和预测后，有47,058个unigenes;其中，26,861具有基因本体注释，具有14,264个SSR基因座。单核苷酸SSR是主要的重复型（47.20％，n = 6724），其次是二 - （32.50％，n = 4641），三 - （19.10％，n = 2729），四 - （0.90％，n = 132） ，Hexa-（0.2％，n = 21）和五菌（0.10％，n = 16）核苷酸重复。最常见的二核，三核苷酸重复分别是Ag / CT，AAG / CTT和AAAG / CTTT。 PCR扩增用105 SSR引物对产生四个特异于红色花朵的条带，即UGRFSR57622，UGRFSR94149，UGRFSR40142和UGRFSR54608;发现相应的4个特异性标记用白色和红色花色共分离在杂种群中，表明基因SSR标记可用于区分草莓中的白色和红色花朵。用于区分红花草莓中花色的标记对于早期选择后代和育种管理是有用的。

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