Large-scale development of EST-SSR markers in sponge gourd via transcriptome sequencing

Abstract

Sponge gourd is a versatile vegetable that can be used as a household cleaning product, industrial material and medicine, and possesses anti-human immunodeficiency virus activity. In the current study, a large dataset composed of 77,858 unigenes derived from the sponge gourd transcriptome was assembled. Of all unigenes, 52,113 (66.93 %) had significant similarity to known proteins from NCBI non-redundant, Swiss-Prot, Clusters of Orthologous Group and Kyoto Encyclopedia of Genes and Genomes databases. Based on these generated sequences, we identified 12,932 putative simple sequence repeats (SSRs) and successfully designed 8,523 high-quality SSR primer pairs. Six hundred and forty-one primer pairs were randomly selected to be verified among S1174 [Luffa acutangula (L.) Roxb.], 93075 [L. cylindrica (L.) Roem.] and their hybrid F1. The result showed that 494 (77.07 %) exhibited successful amplification, of which 201 (40.69 %) revealed polymorphism between S1174 and 93075. Fifty polymorphic expressed sequence tag (EST)-SSRs were used to genotype 60 sponge gourd accessions. Cluster analysis revealed two major clusters, one comprising 42 accessions of L. acutangula and the other 18 accessions belonging to L. cylindrica. Transferability of the 77 polymorphic EST-SSR markers was investigated in six other cucurbits: pumpkin, cucumber, wax gourd, bitter gourd, bottle gourd and chieh-qua, and the percentage of cross-genus amplification was 85.90, 83.33, 83.33, 79.49, 75.64 and 74.36 %, respectively. This indicated that EST-SSRs in sponge gourd could well be applied to other cucurbits. These transcriptome shotgun assembly sequences and EST-SSR data are of great value for the discovery of novel genes and for marker-assisted selection in sponge gourd.