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Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis

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Abstract

The para rubber tree is the most widely cultivated tree species for producing natural rubber (NR) latex. Unfortunately, rubber tree characteristics such as a long life cycle, heterozygous genetic backgrounds, and poorly understood genetic profiles are the obstacles to breeding new rubber tree varieties, such as those with improved NR yields. Recent evidence has revealed the potential importance of controlling microRNA (miRNA) decay in some aspects of NR regulation. To gain a better understanding of miRNAs and their relationship with rubber tree gene regulation networks, large genomic DNA insert-containing libraries were generated to complement the incomplete draft genome sequence and applied as a new powerful tool to predict a function of interested genes. Bacterial artificial chromosome and fosmid libraries, containing a total of 120,576 clones with an average insert size of 43.35 kb, provided approximately 2.42 haploid genome equivalents of coverage based on the estimated 2.15 gb rubber tree genome. Based on these library sequences, the precursors of 1 member of rubber tree-specific miRNAs and 12 members of conserved miRNAs were successfully identified. A panel of miRNAs was characterized for phytohormone response by precisely identifying phytohormone-responsive motifs in their promoter sequences. Furthermore, the quantitative real-time PCR on ethylene stimulation of rubber trees was performed to demonstrate that the miR2118, miR159, miR164 and miR166 are responsive to ethylene, thus confirmed the prediction by genomic DNA analysis. The cis-regulatory elements identified in the promoter regions of these miRNA genes help augment our understanding of miRNA gene regulation and provide a foundation for further investigation of the regulation of rubber tree miRNAs.

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Acknowledgments

The plant materials used in BAC and fosmid library construction were provided by Ms. Kanikar Teerawatanasuk, CRRC-Rubber Research Institute of Thailand (CRRC-RRIT), Department of Agriculture. We would like to express special gratitude to Ms. Samaporn Teeravechyan, National Center for Genetic Engineering and Biotechnology (BIOTEC) (Thailand) for her help in English editing. This work was supported by BIOTEC, RRIT, and Mahidol University.

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Authors and Affiliations

  1. Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Rd, Rajthewee, Bangkok, 10400, Thailand

    Supanath Kanjanawattanawong & Jarunya Narangajavana

  2. National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Rd, Klong 1, Klong Luang, Pathum Thani, 12120, Thailand

    Sithichoke Tangphatsornruang, Panthita Ruang-areerate, Duangjai Sangsrakru, Supannee Poopear & Suthasinee Somyong

  3. Institute of Molecular Bioscience, Mahidol University, Nakhon Pathom, 73170, Thailand

    Kanokporn Triwitayakorn

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  1. Supanath Kanjanawattanawong
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  2. Sithichoke Tangphatsornruang
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  3. Kanokporn Triwitayakorn
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  8. Jarunya Narangajavana
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Correspondence to Suthasinee Somyong or Jarunya Narangajavana.

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Communicated by S. Hohmann.

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Kanjanawattanawong, S., Tangphatsornruang, S., Triwitayakorn, K. et al. Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis. Mol Genet Genomics 289, 921–933 (2014). https://doi.org/10.1007/s00438-014-0862-0

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