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Molecular variation and expansion of a rice black-streaked dwarf virus population based on analysis of segment 1 in Jining, China

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Abstract

To analyze the variation in rice black-streaked dwarf virus (RBSDV) in an area with high incidence of maize rough dwarf disease (MRDD), the RBSDV S1 segment in a collection of 100 maize isolates (sample population A100) from Jining, Shandong Province, was sequenced. An additional 21 maize and rice isolates (subpopulation B21) that were sampled from nine other geographic locations in China in 2012 and 2013 were used as a control. A total of 914 nucleotide mutations, including 239 singleton variable and 675 parsimony-informative sites were detected among the segment 1 (S1) sequences from A100. A total of 614 nucleotide mutation sites including 164 singleton variable and 450 parsimony-informative sites were detected among the S1 sequences from B21, while 97.55 % of the parsimony-informative sites from B21 were also detected in A100. The nucleotide sequence diversities of A100 (π = 0.0479) and B21 (π = 0.0396) were significantly different (P = 0.0002) but showed similar trends. Phylogenetic analysis showed that the 121 RBSDV isolates could be classified into two groups based on their S1 sequences, independent of subpopulation, with a combination of host species and locations. A100 and B21 were under the same level of negative and purifying selection, with Ka/Ks ratios of 0.0337 and 0.0369, respectively. The combined RBSDV population, including 121 isolates, was expanding, with negative values for Tajima’s D, Fu and Li’s D, and Fu and Li’s F in both A100 and B21, except Tajima’s D in A100. Based on S1, the RBSDV population in China has long-term phytogeographic stability, and there do not appear to be any newly-emerging strains.

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Acknowledgments

Plant samples were provided by Xiaomin Kong, Jianhua Yuan, Zhaodong Meng, Qi Sun, Tao Guo, Zhaowen Sun, Jie Shi, Wenyue Tong, Xiaohua Han, and Shuanggui Tie, whom we would like to thank for their kind assistance. This study was funded by the National Hi-Tech Research Program and Development Program of China (2012AA101104), the International Cooperation Program of Ministry of Science and Technology (2014DFG31690), the Science and Technology Program of Beijing (D141100005014003) and the Agricultural Science and Technology Innovation Program at CAAS. Author Jianfeng Weng has received research grants from the Chinese Academy of Agricultural Sciences. This article does not contain any studies with human participants or animals performed by any of the authors.

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Authors and Affiliations

  1. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China

    Yu Zhou, Zhuanfang Hao, Degui Zhang, Mingshun Li, Hongjun Yong, Shihuang Zhang, Xinhai Li & Jianfeng Weng

  2. College of Agronomy, Northeast Agricultural University, Mucai Street, Xiangfang District, Harbin, Heilongjiang, China

    Yu Zhou & Zhenhua Wang

  3. Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu, China

    Qingchang Meng, Yanping Chen & Jirong Wu

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  1. Yu Zhou
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Correspondence to Xinhai Li or Jianfeng Weng.

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Zhou, Y., Meng, Q., Chen, Y. et al. Molecular variation and expansion of a rice black-streaked dwarf virus population based on analysis of segment 1 in Jining, China. Arch Virol 161, 3435–3443 (2016). https://doi.org/10.1007/s00705-016-3052-z

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