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

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Abstract

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.

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Acknowledgements

This work was supported by the Agricultural Biotechnology Developmental Program (Nos. 114061-3, 115076-2 and 116091-3) Grants from the Ministry of Agriculture, Food and Rural Affairs and KRIBB Research Initiative Program to HS Cho.

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Authors and Affiliations

  1. Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea

    Won Yong Jung, Sang Sook Lee, Hyun Ji Park, Suk-Yoon Kwon, Jae-Heung Jeon, Hyun-Soon Kim & Hye Sun Cho

  2. Animal Material Engineering, Gyeongnam National University of Science and Technology, Jinju, 52725, Korea

    Won Yong Jung & Chul Wook Kim

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  1. Won Yong Jung
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Correspondence to Hyun-Soon Kim or Hye Sun Cho.

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11816_2016_421_MOESM4_ESM.tif

Figure S1. Coverage distribution of H. tuberosus transcripts against integrated representative transcripts, as revealed by BLAST analysis. a Comparison of integrated RTs and H. tuberosus loci. b Comparison of integrated RTs and H. tuberosus ESTs using sequence similarity searches. (TIFF 588 kb)

11816_2016_421_MOESM5_ESM.tif

Figure S2. Length distribution of assembled representative transcripts from the transcriptomes of the three cultivars. A comparison of the distribution of assembled representative transcript lengths from the three cultivars is shown. The length of the assembled transcripts vs. number of transcripts is shown. (TIFF 178 kb)

11816_2016_421_MOESM6_ESM.tif

Figure S3. Validation of cultivar-specific gene expression in the three cultivars. a The expression patterns of cultivar-specific genes from the three cultivars are shown. Total RNAs from three cultivars of leaves and tubers were analyzed using RT-PCR. b Expression of anthocyanin-related genes in the tubers of the three cultivars. Expression of HtActin7 was used an internal standard. An aliquot of each RT-PCR mixture was electrophoresed on a 1% agarose gel and visualized by ethidium bromide staining. (TIFF 534 kb)

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Jung, W.Y., Lee, S.S., Park, H.J. et al. Comparative transcriptome profiling and SSR marker identification in three Jerusalem artichoke (Helianthus tuberosus L.) cultivars exhibiting phenotypic variation. Plant Biotechnol Rep 10, 447–461 (2016). https://doi.org/10.1007/s11816-016-0421-8

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