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Genetic evolutionary analysis of soybean mosaic virus populations from three geographic locations in China based on the P1 and CP genes

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Abstract

Soybean mosaic virus (SMV) is one of the major pathogens causing serious soybean losses. Little is known about the genetic structure and evolutionary biology of the SMV population in southwestern China. In this study, 29 SMV isolates were obtained from Sichuan Province, and the genomic regions encoding the first protein (P1) and coat protein (CP) were sequenced. Combined with SMV isolates from the southeastern and northeastern regions of China, the genetic and molecular evolution of SMV was studied. Recombination analysis revealed that intraspecific and interspecific recombination had occurred in the SMV population. A phylogenetic tree based on the P1 gene reflected the geographic origin of the non-interspecific recombinant SMV (SMV-NI), while a tree based on the CP gene did not. Though frequent gene flow of the SMV-NI populations was found between the southeastern and northeastern populations, the southwestern population was relatively independent. Genetic differentiation was significant between the SMV interspecific recombinant (SMV-RI) and the non-interspecific recombinant (SMV-NI) populations. It was interesting to note that there was an almost identical recombination breakpoint in SMV-RI and Watermelon mosaic virus (WMV). Population dynamics showed that SMV-RI might be in an expanding state, while the SMV-NI population is relatively stable.

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Abbreviations

SMV:

Soybean mosaic virus

BCMV:

Bean common mosaic virus

WMV:

Watermelon mosaic virus

SMV-RI:

Interspecific recombination of SMV

SMV-NI:

Non-interspecific recombination of SMV

P1:

First protein

CP:

Coat protein

NE:

Northeast

SE:

Southeast

SW:

Southwest

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Funding

This study was supported by grants from the National Key Research and Development Plan, Project No. 2017YFD0301704, 2018YFD0200700, and 2018YFD0201006; Sichuan Provincial Science and Technology Project, Project No. 2016NYZ0053; Research Foundation of Sichuan Provincial Education Department (035Z1038); and Scientific Research Foundation of Sichuan Provincial Science and Technology Department (2015NZ0040).

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Author notes

  1. Lei Zhang and Jing Shang contributed equally to this work.

Authors and Affiliations

  1. Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China

    Lei Zhang, Jing Shang, Qi Jia, Zhongqin Tang, Xiaoli Chang & Wenyu Yang

  2. College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China

    Lei Zhang, Jing Shang, Qi Jia, Hui Yang, Huanhuan Liu, Zhongqin Tang, Xiaoli Chang, Min Zhang & Wenming Wang

  3. National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, China

    Kai Li

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  1. Lei Zhang
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Zhang, L., Shang, J., Jia, Q. et al. Genetic evolutionary analysis of soybean mosaic virus populations from three geographic locations in China based on the P1 and CP genes. Arch Virol 164, 1037–1048 (2019). https://doi.org/10.1007/s00705-019-04165-5

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