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Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis)

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Abstract

Genomic simple sequence repeat (SSR) markers are particularly valuable in studies of genetic diversity, evolution, genetic linkage map construction, quantitative trait loci tagging, and marker-assisted selection because of their multi-allelic nature, reproducibility, co-dominant inheritance, high abundance, and extensive genome coverage. The traditional methods of SSR marker development, such as genomic-SSR hybrid screening and microsatellite enrichment, have the disadvantages of high cost and complex operation. The selectively amplified microsatellite method is less costly and highly efficient as well as being simple and convenient. In this study, 252 sequences with SSRs were cloned from the rubber tree (Hevea brasiliensis) genome from which 258 SSR loci were obtained. The average repeat number was six. There were only 10 (3.9%) mononucleotide, trinucleotide, and pentanucleotide repeats, whereas the remaining 248 (96.1%) were dinucleotide repeats, including 128 (49.6%) GT/CA repeats, 118 (45.7%) GA/CT repeats, and 2 (0.8%) AT/TA repeats. A total of 126 primer pairs (see ESM) were successfully designed of which 36 primer pairs generated polymorphic products from 12 accessions of the cultivated species, 4 related species, and 3 species of the family Euphorbiaceae. In addition, investigations based on four genomic SSRs (GAR4, ACR22, CTR25, and GTR28) by cloning and sequencing provided evidence for cross-species/genera applicability, and homologous sequences were obtained from the rubber tree and Euphorbiaceae. Further analysis about the variation of the flanking regions of the four markers was carried out.

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Acknowledgments

This work was supported by the National Nonprofit Institute Research Grant of CATAS-ITBB (ITBBZD0715). We wish to express our faithful thanks to Yanling Xiao (Hainan University). Many thanks also go to Bennett and Bettina’s friendly and critical reading of this article.

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Authors and Affiliations

  1. Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, 4 Xueyuan Street, Longhua District, Haikou, 571101, Hainan, People’s Republic of China

    Fei Yu, Su-Ping Feng & Jing-Yi Wang

  2. Key Laboratory of Rubber Biology of Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People’s Republic of China

    Wei-Guo Li

  3. Key Laboratory of Tropical Horticulture Plant Resources and Genetic Improvement, Ministry of Education, Agricultural College, Hainan University, 58 Renmin Avenue, Haikou, 570228, Hainan, People’s Republic of China

    Fei Yu & Jing-Yi Wang

  4. Qiongzhou University, Sanya, 572002, Hainan, People’s Republic of China

    Su-Ping Feng & Yao-Ting Wu

  5. School of Life Science, Nantong University, No. 999, East Waihuan Road, Nantong, 226007, Jiangsu, People’s Republic of China

    Bao-Hua Wang

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  1. Fei Yu
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Correspondence to Yao-Ting Wu.

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Communicated by J. Bennett.

A contribution to the Special Issue: Plant Biotechnology in Support of the Millennium Development Goals.

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Yu, F., Wang, BH., Feng, SP. et al. Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis). Plant Cell Rep 30, 335–344 (2011). https://doi.org/10.1007/s00299-010-0908-7

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  • DOI: https://doi.org/10.1007/s00299-010-0908-7

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