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Characterization of masson pine (Pinus massoniana Lamb.) microsatellite DNA by 454 genome shotgun sequencing

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Abstract

Microsatellites (simple sequence repeats, SSRs) are important genetic markers in tree breeding and conservation. Here we utilized high-throughput 454 sequencing technology to mine microsatellites from masson pine (MP) genomic DNA. First, we analyzed the characteristics of SSRs in all nonredundant MP reads (genome survey sequences, GSSs) and compared them with loblolly pine (LP) GSSs and BACs (bacterial artificial chromosome clone sequences), and three other nonconiferous species GSSs. Second, a set of MP GSS–SSR primer pairs were designed. There were extremely low overall GSS–SSR densities (28 SSR/Mb) in MP when compared with LP (48 SSR/Mb) and the other species. AT, AAT, AAAT, and AAAAAT were the richest motifs in di-, tri-, tetra-, and hexanucleotides, respectively. Two hundred forty GSS–SSR primer pairs were designed in total, and 20 novel polymorphic markers were identified using three populations (two natural and one clonal seed orchard) as evaluating samples. These markers should be useful for future MP population genetics studies.

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Fig. 1
Fig. 2

Abbreviations

GSS:

Genome survey sequence

Mb:

Megabase

SSR:

Simple sequence repeat

BAC:

Bacterial artificial chromosome clone sequence

MP:

Masson pine

LP:

Loblolly pine

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Acknowledgments

This work was supported by the National High Technology Research and Development Program of China (2006AA100109) and A Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). We thank two anonymous reviewers for their insightful comments on previous versions.

Data Archiving Statement

The twenty novel SSR sequences (GenBank accession No.: KC146070- KC146089) were uploaded on NCBI (http://www.ncbi.nlm.nih.gov/nuccore/?term=microsatellite+sequences+pinus+massoniana);

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Authors and Affiliations

  1. Key Laboratory of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, 210037, China

    Tian-Dao Bai, Li-An Xu, Meng Xu & Zhang-Rong Wang

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  1. Tian-Dao Bai
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  2. Li-An Xu
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  3. Meng Xu
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  4. Zhang-Rong Wang
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Corresponding author

Correspondence to Li-An Xu.

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Communicated by P. Ingvarsson

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Bai, TD., Xu, LA., Xu, M. et al. Characterization of masson pine (Pinus massoniana Lamb.) microsatellite DNA by 454 genome shotgun sequencing. Tree Genetics & Genomes 10, 429–437 (2014). https://doi.org/10.1007/s11295-013-0684-y

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