De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry.

De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry.
Biochem Genet. 2019 Mar 01;:
Authors: Ding Y, Xue L, Guo RX, Luo GJ, Song YT, Lei JJ
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 ...

Source: Biochemical Genetics - February 28, 2019 Category: Genetics & Stem Cells Authors: Ding Y, Xue L, Guo RX, Luo GJ, Song YT, Lei JJ Tags: Biochem Genet Source Type: research