Characterization of Est-SSR markers related to <i>Colletotrichum fructicola</i> infection in strawberry (<i>Fragaria</i> ×<i>ananassa</i> Duchase)

<i>Colletotrichum fructicola</i> causes strawberry anthracnose, which results in considerable economic losses in quality and production in Asia. However, the molecular mechanism of strawberry infection with <i>C. fructicola</i> is still poorly understood. Here, we employed RNA-Seq technology to mine the strawberry transcriptome for EST-SSRs (Expressed Sequence Tag–Simple Sequence Repeats) following <i>C. fructicola</i> infection. Fortunately, we detected 3019 potential EST-SSRs from the transcriptomic data of cv. Jiuxiang. The seven commonly occurring repeat motifs were A/T (278), GAA/TTC (263), GAG/CTC (215), AAG/CTT(188), GGA/TCC (163), AGA/TCT (153) and AGG/CCT (153). We identified 31, 84 and 129 differentially expressed EST-SSR-containing sequences corresponding to 24, 72 and 96 Hpi, while 13 DE-EST-SSRs -containing sequences were differentially expressed and common for all the three time points. Furthermore, we identified allele polymorphisms for some DE-EST-SSRs among several resistant and susceptible strawberry varieties and wild species. The EST-SSRs in our research were related to the reported QTL resistance loci in strawberry which are differentially expressed after <i>C. fructicola</i> infection and have allele polymorphisms in different strawberry varieties and wild species. These provide a clue for utilisation of the EST-SSRs in marker-assisted breeding to improve anthracnose-resistant breeding in future.