Red-flowered strawberry is a new ornamental flower derived from intergeneric hybridization (Fragaria × 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.

中文翻译：

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De Novo组装的转录组分析和红花草莓中SSR标记的鉴定。

红花草莓是一种新的观赏花卉，来源于属间杂交（草莓属 × 委陵菜属））。迄今为止，尚未报道该植物的分子标记。RNA测序为大规模检测简单序列重复（SSR）提供了一种相对快速且低成本的方法。在本研究中，我们通过Illumina HiSeq 2500分析了红色草莓的转录组，以鉴定与花瓣颜色相关的SSR。根据200万条从红色开花草莓杂种上读取的红色和白色花朵的清晰读数，我们组装了91,835个单基因，平均长度为717 bp。经过功能注释和预测，共有47,058个单基因。其中26,861个具有基因本体注释，其中包含14,264个SSR位点。单核苷酸SSR是主要的重复类型（47.20％，n  = 6724），其次是di-（32.50％，n  = 4641），tri-（19.10％，n （＝ 2729），四-（0.90％，n  ＝ 132），六-（0.2％，n  ＝ 21）和五-（0.10％，n  ＝ 16）核苷酸重复。最常见的二，三和四核苷酸重复序列分别是AG / CT，AAG / CTT和AAAG / CTTT。用105对SSR引物进行PCR扩增，产生了四个对红色花朵特有的条带，分别是UgRFsr57622，UgRFsr94149，UgRFsr40142和UgRFsr54608；在杂种群体中发现了相应的4个性状特异性标记与白色和红色花朵颜色共分离，表明基因SSR标记可用于区分草莓中的白色和红色花朵。区分红色花朵草莓中花朵颜色的标记对于后代的早期选择和育种管理很有用。