Development of Simple Sequence Repeat Markers from De Novo Assembled Transcriptomes of Pumpkins

Pumpkin (Cucurbita spp.) is one of the major vegetable crops grown worldwide. The number of simple sequence repeat (SSR) markers in pumpkins lags far behind the requirement of genetic analysis. Transcriptomes generated from different genotypes provide valuable sequence resources for molecular marker development. In this study, transcriptomes from the roots of C. maxima and C. moschata inbred lines suffering salinity stress were separately de novo assembled. The assembled unigenes were aligned between the two genotypes to in silico screen the polymorphic SSR loci. A total of 328 putatively polymorphic SSR loci were identified. Of which, 211 loci that is suitable to the primer design were selected for polymorphic validation by polymerase chain reaction amplification and electrophoresis analysis. A total of 110 SSR markers exhibited polymorphism among 65 pumpkin varieties with the mean polymorphism information content value of 0.34. Cluster analysis showed that these SSR markers distinctly classified the pumpkin varieties into different groups according to their genetic backgrounds at species level. The SSR markers developed in this study provided valuable supplements to the available genetic tools of pumpkins.