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Development and Characterization of Intron-Flanking EST-PCR Markers in Rubber Tree (Hevea brasiliensis Muell. Arg.)

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Abstract

With a long-term goal of constructing a linkage map enriched with gene-specific markers in rubber tree (Hevea brasiliensis Muell. Arg.), we utilized rubber tree ESTs associated with tapping panel dryness (TPD) to develop intron-flanking PCR markers. After downloading and assembling the rubber tree ESTs associated with TPD, we predicted the exon/exon junction sites (E/E) by aligning rubber tree transcripts with the genomic sequences of castor bean (Ricinus communis L.). Based on the predicted E/E, the primers flanking intron(s) and no intron were designed. Compared with the markers designed by conventional method, the PCR success rate of the markers designed with the predicted E/E increased 28-30%, whereas the polymorphism rate of intron-flanking EST-PCR markers was approximately 3.43-fold increase. Therefore, the intron-flanking marker was more polymorphism-generating efficient than the markers designed by conventional methods. In addition, analyzing the polymorphic information content (PIC) among Hevea germplasm showed that the polymorphism of wild rubber tree accessions was higher than one of cultivated rubber tree clones and Hevea species. This study enriches the categories and numbers of molecular markers in rubber tree, and the markers developed in this research will have a wide application in DNA fingerprinting, marker-assisted selection and genetic mapping in rubber tree. This research also indicates that it is possible to develop intron-flanking EST-PCR markers of rubber tree with castor bean genome as reference sequences, which provides new insights into developing intron-flanking EST-PCR markers for rubber tree or other plant species without genomic information.

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Acknowledgments

This research was supported by Ministry of Agriculture Opening Project Fund of Key Laboratory of Rubber Biology/State Key Laboratory Breeding Base of Cultivation & Physiology for Tropical Crops (KLOF1103), National Natural Science Foundation of China (30960310), Fundamental Research Funds for Rubber Research Institute, CATAS (1630022011024), Natural Science Foundation of Hainan Province (310072), and Modern Agricultural Industry R&D System of China (nycytx-34-GW1-2). We also thank the National Rubber Tree Germplasm Repository, Rubber Research Institute, CATAS to provide all the Hevea germplasm.

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Authors and Affiliations

  1. Key Open Laboratory of Rubber Biology, Ministry of Agriculture/State Key Laboratory Breeding Base of Cultivation & Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, China

    Dejun Li, Zhi Deng & Xianghong Liu

  2. Institute of Biological Science and Technology, College of Agriculture, Hainan University, Haikou, 570228, China

    Zhihui Xia & Junmei Dong

  3. College of Agriculture, Hainan University, Haikou, 570228, China

    Xianghong Liu

  4. College of Life Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China

    Fuying Feng

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  1. Dejun Li
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  2. Zhihui Xia
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  3. Zhi Deng
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  4. Xianghong Liu
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  5. Junmei Dong
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Correspondence to Dejun Li or Fuying Feng.

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Dejun Li and Zhihui Xia contributed equally to this work.

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Li, D., Xia, Z., Deng, Z. et al. Development and Characterization of Intron-Flanking EST-PCR Markers in Rubber Tree (Hevea brasiliensis Muell. Arg.). Mol Biotechnol 51, 148–159 (2012). https://doi.org/10.1007/s12033-011-9449-8

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