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Development and mapping of functional expressed sequence tag-derived simple sequence repeat markers in a rubber tree RRIM600 × PB217 population

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Abstract

Sets of polymorphic expressed sequence tag–simple sequence repeat (EST-SSR) markers from the rubber tree (Hevea brasiliensis) have been published by many researchers, but none has been specifically developed to study latex and wood yield traits. In this study, a total 10,321 rubber tree EST sequences, generated from suppression subtractive hybridization-cDNA libraries of bark and latex of high- and low-yielding clones, were used as sources for SSR searching. A total of 432 EST-SSR loci were identified and it was possible to design primer pairs for a subset of 298 EST-SSRs. The highest proportion of EST-SSRs was represented by dinucleotide repeats (46.6 %), followed by trinucleotide repeats (44.3 %). Based on BLASTX analysis, 234 ESTs (80 %) showed similarity to genes in NCBI databases and could be divided into 120 putative proteins with known function and 114 unknown proteins. To enhance the resolution of an existing linkage map from previous work on a rubber tree RRIM600 × PB217 population, 69 EST-SSR markers from the above set were tested to be integrated into the reference genetic map. The enriched map of 18 linkage groups spanned 2054.2 cM in length, showed an average genetic distance of 4.3 cM between adjacent markers, and included 63 new EST-SSR markers. The enhanced map from this study provides a basis for comparative mapping using PCR-based markers and identification of expressed genes possibly affecting important traits of interest.

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Abbreviations

DNRs:

Dinucleotide repeats

EST:

Expressed sequence tag

SSRs:

Simple sequence repeats

TNRs:

Trinucleotide repeats

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Acknowledgments

This research was supported by Rubber Research Institute of Thailand (RRIT), Department of Agriculture, the Thailand Research Fund (TRF) Grant No. MRG5180088 with Faculty of Science, Mahidol University and a grant from Mahidol University, Thailand.

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Authors and Affiliations

  1. Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand

    Kanlaya Nirapathpongporn & Jarunya Narangajavana

  2. Rubber Research Institute of Thailand (RRIT), Bangkok, Thailand

    Kanlaya Nirapathpongporn & Kanikar Teerawattanasuk

  3. Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand

    Panida Kongsawadworakul & Unchera Viboonjun

  4. Institut de Recherche pour le Développement (IRD), Montpellier, France

    Hervé Chrestin

  5. Agricultural Research for Development (CIARD), Montpellier, France

    Marc Segiun & André Clément-Dement

Authors
  1. Kanlaya Nirapathpongporn
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  2. Panida Kongsawadworakul
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  3. Unchera Viboonjun
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  4. Kanikar Teerawattanasuk
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  5. Hervé Chrestin
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  6. Marc Segiun
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  7. André Clément-Dement
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  8. Jarunya Narangajavana
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Correspondence to Jarunya Narangajavana.

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Nirapathpongporn, K., Kongsawadworakul, P., Viboonjun, U. et al. Development and mapping of functional expressed sequence tag-derived simple sequence repeat markers in a rubber tree RRIM600 × PB217 population. Mol Breeding 36, 39 (2016). https://doi.org/10.1007/s11032-016-0461-3

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  • DOI: https://doi.org/10.1007/s11032-016-0461-3

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