Abstract
With the development of high-throughput sequencing techniques, transcriptome sequencing projects which provide valuable resources for designing simple sequence repeat (SSR) primers have been carried out for many plants. However, the utility of SSRs for molecular breeding depends on genome-wide distribution and coverage, as well as moderately high allelic variability, in the available SSR library. In this study, we characterized the exonic SSRs developed from the publicly available Populus genome as a case study to determine their value for molecular breeding. As expected, our results confirmed that microsatellites occurred approximately three times less often in coding regions than in non-coding regions. Mutability test also showed that exonic SSRs contained less allelic variability than intronic SSRs. More importantly, exonic SSRs were unevenly distributed both among and within chromosomes. Large exonic SSRs deserts were observed on several chromosomes. Differential selection between paralogous chromosomes, at the gene level, appears to be responsible for these SSR deserts, though the mechanisms that cause chromosome-specific SSR deserts are not known. This work provides ample evidence that the candidate gene approach based on unigenes identified from transcribed sequences may not be the best strategy to identify highly polymorphic SSRs.
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Acknowledgments
We thank Han Jingling, Zhenghong Liu and Faying Yuan at Nanjing Forestry University for their help in sample collection. Special thanks go to the editor and anonymous reviewers for their help in formulating the revision. Funds for this research were provided by Natural Science Foundation of China (30971609) and Forestry Nonprofit Project (200904002). This work is also supported by the US DOE BioEnergy Science Center. The BioEnergy Science Center is a US Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science.
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11032_2010_9413_MOESM1_ESM.xls
Table 1. Distribution test of exonic SSRs in the 2-Mb sliding windows along the Populus chromosomes. The valid reading length is the length of A, T, G, C designation in each window. Distribution test is performed by the Poisson calculation at P ≤ 0.05 and P ≤ 0.01 significance levels. “**+” Significantly overabundant at P ≤ 0.01; “*+” significantly overabundant at P ≤ 0.05; “**−” significantly sparse at P ≤ 0.01; “*−” significantly sparse at P ≤ 0.05 (XLS 78 kb)
11032_2010_9413_MOESM2_ESM.xls
Table 2. Exploring the loss of exonic SSR repeat motifs on the paralogous segments between chromosome I and chromosome III. Note: The two chromosomes share two duplicated segments; lines without shadow correspond to exonic SSRs in the upper duplicated region on chromosome I, whereas lines in gray shadow correspond to the exonic SSRs in the lower duplicated region on chromosome I (XLS 201 kb)
11032_2010_9413_MOESM3_ESM.xls
Table 3. Summary of primer information and amplification results in SSR variability test. In this table, the primer name is designated as “P” followed by “number of chromosome ID”, followed by “_”, and ends with “the start base of left primer”. Columns I to AF contain the amplification results of the tested primer pairs. In these columns, “M/M” stand for the missing data; “No amp” stand for no amplification products. The corresponding gene model and their definition are listed in the last two columns (XLS 165 kb)
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Li, S., Yin, T., Wang, M. et al. Characterization of microsatellites in the coding regions of the Populus genome. Mol Breeding 27, 59–66 (2011). https://doi.org/10.1007/s11032-010-9413-5
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DOI: https://doi.org/10.1007/s11032-010-9413-5