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Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus

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Abstract

The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative’s species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

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Abbreviations

BES:

Citrus clementina BAC end sequences

GSSs:

Genome survey sequences

GO:

Gene ontology

SSR:

Simple sequences repeat

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Acknowledgments

We are grateful to Dr. Yun-Jiang Cheng for discussing on the sampling strategy. This research was financially supported by the Ministry of Science and Technology of China (Nos. 2011CB100600, 2011AA100205) and the national NSF of China.

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Authors and Affiliations

  1. Key Laboratory of Horticultural Plant Biology (MOE), National Center of Citrus Breeding, Huazhong Agricultural University, 430070, Wuhan, People’s Republic of China

    Manosh Kumar Biswas, Lijun Chai, Qiang Xu, Wenwu Guo & Xiuxin Deng

  2. Center of Molecular Biodiversity, Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113, Bonn, Germany

    Christoph Mayer

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  1. Manosh Kumar Biswas
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  2. Lijun Chai
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  3. Christoph Mayer
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  4. Qiang Xu
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  5. Wenwu Guo
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  6. Xiuxin Deng
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Correspondence to Xiuxin Deng.

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Biswas, M.K., Chai, L., Mayer, C. et al. Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus. Mol Biol Rep 39, 5373–5386 (2012). https://doi.org/10.1007/s11033-011-1338-5

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