Comparative transcriptome profiling and SSR marker identification in three Jerusalem artichoke (Helianthus tuberosus L.) cultivars exhibiting phenotypic variation

Jerusalem artichoke (Helianthus tuberosus L.), a plant of the Asteraceae family, is widely cultivated for its multiple pharmacological properties and is being developed as a renewable feedstock, as well as a source of biofuels and biochemicals for industrial applications. Despite its nutritional benefits and economic potential, transcriptomic and genomic information is scarce. In the present study, we performed phenotypic characterization and RNA-Seq analysis of three Jerusalem artichoke cultivars, Purple Jerusalem artichoke (PJA), Hindung Jerusalem artichoke (HJA) and Dafeng Jerusalem artichoke (DJA). The cultivars exhibited obvious differences in their responses to drought, high salinity and oxidative stress, as well as morphological variations. The PJA cultivar had the highest concentration of anthocyanin, and the DJA cultivar had the strongest tolerance to environmental stresses among the three cultivars. Based on the three assembled transcriptomes, we identified 2435, 3283 and 3657 putative cultivar-specific transcripts from leaf and tuber tissues in cultivars PJA, HJA and DJA, respectively, which enlarges the pool of transcriptomes available for Jerusalem artichoke. We also detected 11,319, 13,190 and 12,717 potential cultivar-specific simple sequence repeats (SSRs) from the transcriptomic data for, PJA, HJA and DJA, respectively. In addition, five SSRs were identified as candidate molecular markers for cultivar identification, as determined by genomic PCR analysis. Our comparative RNA-Seq analysis and de novo transcriptome assemblies constitute a comprehensive transcriptome resource and provide essential sequence information for identifying Jerusalem artichoke cultivars. These results should therefore be useful for future gene discovery, molecular studies and agricultural improvement of this important non-model species.