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Development, characterization and utilization of GenBank microsatellite markers in Phyllostachys pubescens and related species

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Abstract

Public sequence databases provide a rapid, simple and cost-effective source of microsatellite markers. We analyzed 1,532 bamboo (Phyllostachys pubescens) sequences available in public domain DNA databases, and found 3,241 simple sequence repeat (SSR) loci comprising repeats of two or more nucleotides in 920 genomic survey sequences (GSSs) and 68 cDNA sequences. This corresponded to one SSR per 336 bp of GSS DNA and one SSR per 363 bp of cDNA. The SSRs consisted of 76.6 and 74.5% dinucleotide repeats, 20.0 and 22.3% trinucleotide repeats, and 3.4 and 3.2% higher-number repeats in the GSS DNA and cDNA sequences, respectively. The repeat motif AG/CT (or GA/TC) was the most abundant. Nineteen microsatellite markers were developed from Class I and Class II SSRs, showing that the limited polymorphism in Ph. pubescens cultivars and provenances could be attributed to clonal propagation of the bamboo plant. The transferability of the microsatellites reached 75.3%, and the polymorphism of loci successfully transferred was 66.7% for six additional Phyllostachys species. Microsatellite PBM014 transferred successfully to all six species, showed rich polymorphism, and could serve as species-specific alleles for the identification of Phyllostachys interspecies hybrids.

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Acknowledgments

We gratefully acknowledge C Chen of Fujian Agriculture and Forestry University and G Liao of the Jiangxi Forestry Research Institute for providing the materials on provenances and hybrids, and K Zheng of the China National Rice Research Institute for reviewing the manuscript and providing helpful suggestions. This work was financially supported by grants from the National Natural Science Foundation of China (grant no. 30371181 to DQ Tang) and the Talents Program of the Natural Science Foundation of Zhejiang Province (grant no. R303420 to DQ Tang).

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Authors and Affiliations

  1. Key Lab for Modern Silvicultural Technology of Zhejiang Province, Zhejiang Forestry University, 311300, Lin’an, Zhejiang Province, People’s Republic of China

    Ding-Qin Tang, Jiang-Jie Lu, Wei Fang & Ming-Bing Zhou

  2. Eastwin Life Science Inc, 100085, Beijing, People’s Republic of China

    Shan Zhang

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  1. Ding-Qin Tang
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  2. Jiang-Jie Lu
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Correspondence to Ding-Qin Tang.

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Tang, DQ., Lu, JJ., Fang, W. et al. Development, characterization and utilization of GenBank microsatellite markers in Phyllostachys pubescens and related species. Mol Breeding 25, 299–311 (2010). https://doi.org/10.1007/s11032-009-9333-4

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