Abstract
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.
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This work was supported by Natural Science Fund of China (No. 31701964).
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10528_2019_9912_MOESM1_ESM.tif
Preliminary screening of polyacrylamide gel electrophoresis patterns of amplified polymorphic primers (partial). a b c and d were amplified by primers UgRFsr57622, UgRFsr94149, UgRFsr40142 and UgRFsr54608, respectively. Lanes 1–24 were red-flowered hybrids from the cross of Pink Princess × Pink Beauty and lanes 25–50 were white-flowered hybrids from the same cross used for RNA-Seq. Lanes 50–70 were red-flowered hybrids from the cross of combinations (Pink Princess × Honeoye, Pretty Beauty × Honeoye, Pink Princess × Pretty Beauty) and lanes 70–90 were white-flowered hybrids from the same cross of combinations used for molecular marker identification. Supplementary material 1 (TIFF 912 kb)
10528_2019_9912_MOESM3_ESM.xlsx
The Number of genes with Gene ontology classification of the red-flowered strawberry. Supplementary material 3 (XLSX 12 kb)
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Ding, Y., Xue, L., Guo, Rx. et al. De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry. Biochem Genet 57, 607–622 (2019). https://doi.org/10.1007/s10528-019-09912-6
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DOI: https://doi.org/10.1007/s10528-019-09912-6