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Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms

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Abstract

Black poplar (Populus nigra L.) is an economically and ecologically important tree species and an ideal organism for studies of genetic variation. In the present work, we use a candidate gene approach to infer the patterns of DNA variation in natural populations of this species. A total of 312 single nucleotide polymorphisms (SNPs) are found among 8,056 bp sequenced from nine drought-adaptation and photosynthesis-related gene loci. The median SNP frequency is one site per 26 bp. The average nucleotide diversity is calculated to be θW = 0.01074 and πT = 0.00702, higher values than those observed in P. tremula, P. trichocarpa and most conifer species. Tests of neutrality for each gene reveal a general excess of low-frequency mutations, a greater number of haplotypes than expected and an excess of high-frequency derived variants in P. nigra, which is consistent with previous findings that genetic hitchhiking has occurred in this species. Linkage disequilibrium is low, decaying rapidly from 0.45 to 0.20 or less within a distance of 300 bp, although the declines of r 2 are variable among different loci. This is similar to the rate of decay reported in most other tree species. Our dataset is expected to enhance understanding of how evolutionary forces shape genetic variation, and it will contribute to molecular breeding in black poplar.

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Acknowledgments

We thank Bronwyn Matheson (CSIRO Plant Industry, Australia) for her critical reading of the manuscript. This work was financially supported by the National Key Technology R&D Program for the Eleventh Five-Year-Plan of China (Grant No. 2006BAD01A15 and 2006BAD24B0403) and National Basic Research Program of China (973 program) (Grant No. 2009CB119107).

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  1. Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, 100091, WanShouShan, Beijing, The People’s Republic of China

    Yanguang Chu, Xiaohua Su, Qinjun Huang & Xianghua Zhang

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Chu, Y., Su, X., Huang, Q. et al. Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms. Genetica 137, 141–150 (2009). https://doi.org/10.1007/s10709-009-9371-1

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