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A novel set of single-copy nuclear gene markers in white oak and implications for species delimitation

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Abstract

Oaks have often been the focus of research on plant evolution owing to their propensity to intercross and their important role in ecology and economy. Compared with traditional molecular markers, such as amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs), multiple single-copy nuclear genes (SCNGs) are of greater utility in inferring evolutionary processes in oaks. Nineteen primer pairs were developed from expressed sequence tags (ESTs) of Quercus mongolica and Q. robur that could produce orthologous products in Chinese white oaks (section Quercus). These SCNG markers showed a moderate to high level of nucleotide polymorphism in 42 individuals of two closely related white oaks, Q. mongolica and Q. liaotungensis, and demonstrated high transferability across seven white oaks, four oaks from section Cerris, and one oak from section Lobatae. A phylogenetic tree based on these SCNGs provided resolution at deep nodes and robust support for delimiting populations of Q. mongolica and Q. liaotungensis; Bayesian analysis clustered individuals into their respective species with high probability and no admixture. When the same individuals were used, Bayesian clusters based on either 194 AFLPs or 19 SSRs gave comparable results, but one or several individuals respectively were identified as having admixed ancestry. This indicates that the hybridization rate between these two oaks may have been overestimated using SSR markers due to the occurrence of homoplasy. The SCNGs are powerful for species delimitation of white oaks, and these markers could be useful for future phylogenetics and phylogeography research in white oaks.

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Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (31270701, 31370398). We would like to thank Prof. Da-Yong Zhang from Beijing Normal University and Prof. Shou-Xian Li from Taiwan Normal University for their useful discussions and insightful comments in marker development and Dr. Fang Du from Beijing Forestry University for providing the sample of Q. aquifolioides and her help in marker development.

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Authors and Affiliations

  1. State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China

    Jun Chen, Yan-Fei Zeng & Jian-Guo Zhang

  2. Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China

    Jun Chen & Jian-Guo Zhang

  3. MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, China

    Wan-Jin Liao

  4. Beijing Key Laboratory of Cloud Computing Key Technology and Application, Beijing Computing Center, Beijing, China

    Peng-Cheng Yan

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  1. Jun Chen
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  2. Yan-Fei Zeng
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  3. Wan-Jin Liao
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  4. Peng-Cheng Yan
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  5. Jian-Guo Zhang
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Corresponding authors

Correspondence to Yan-Fei Zeng or Jian-Guo Zhang.

Additional information

Communicated by A. Kremer

Data archiving statement

All nucleotide sequences were deposited in GenBank with accession numbers KX599550-KX600473

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Chen, J., Zeng, YF., Liao, WJ. et al. A novel set of single-copy nuclear gene markers in white oak and implications for species delimitation. Tree Genetics & Genomes 13, 50 (2017). https://doi.org/10.1007/s11295-017-1130-3

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  • DOI: https://doi.org/10.1007/s11295-017-1130-3

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