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Distribution and Genetic Diversity of Barley yellow striate mosaic virus in Northern China

YANG Fei1 ZHANG AiHong1 MENG FanSi1 HUO LiangZhan1 LI XiWang1 DI DianPing1 MIAO HongQin1

(1.Plant Protection Institute of Hebei Academy of Agricultural and Forestry Sciences/IPM Center of Hebei Province/Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, Hebei 071000)

【Abstract】[Objective] The objective of this study is to clarify the distribution and genetic diversity of Barley yellow striate mosaic virus (BYSMV) in major wheat production areas in northern China, and to provide a theoretical basis for the early warning, prevention and control of epidemic diseases. [Method] During 2008–2016, about 864 suspected virus-infected samples were collected from 66 districts in Hebei, Shandong, Jiangsu, Anhui, Henan, Shaanxi and Shanxi provinces and all the three viruses including BYSMV, Rice black-streaked dwarf virus (RBSDV) and Northern cereal mosaic virus (NCMV) were identified using one-step multiplex RT-PCR. L and N gene fragments of BYSMV were obtained by RT-PCR amplification and cloned, and then determined by nucleotide sequence analysis. The sequences were analyzed by softwares of MEGA, DnaSP, and PAML to elucidate the phylogenesis and genetic diversity of BYSMV isolates. [Result] A total of 336 samples collected from 48 districts in seven provinces were detected with BYSMV and the detection rate was 38.89%. The virus was mainly distributed in Shaanxi, Hebei, Shanxi and Shandong. In addition, it was also distributed in Henan and northern Anhui. Xuzhou and Pizhou in Jiangsu Province were only localized. The phylogenetic analysis showed that the population could be divided into two subgroups (I and II) based on fragments of L and N genes. The isolates in subgroup I were derived from all seven provinces, but the isolates in subgroup II were only from Shaanxi and Shanxi provinces. It was indicated that Iran isolate was related to the subgroup II isolates based on the phylogenesis of L gene sequence. The clustering of the isolates was related to their geographical origins, and not to the host plants or sampling dates. The genetic analysis by using 7 softwares of the RDP package showed that there was no evidence supporting the recombination. The selection pressure analysis showed that the ω (dN/dS) values varied from 0.02 to 0.19 which were far less than 1 within or between subgroups. It was indicated that the population was undergoing purifying selection. The haplotype diversity (Hd) values (0.909 09 and 0.995 24) of L and N gene fragments were greater than 0.5 and the nucleotide diversity (π) values (0.013 24 and 0.012 24) were higher than 0.005, indicating that there was a high level of genetic diversity in the population of BYSMV in China. The genetic differentiation based on L and N gene fragments showed that the fixation indices FST (0.322 01 and 0.373 26) of eastern and western subpopulations were greater than 0.25. The difference of statistical test was significant, which indicated that the BYSMV population in eastern and western regions was seriously differentiated. The Nm values (0.53 and 0.42) were less than 1, which indicated that the limited gene flow was the main reason of genetic differentiation. [Conclusion] BYSMV was widely distributed in the wheat production areas of northern China, and occurred in Hebei, Shandong, Jiangsu, Anhui, Henan, Shaanxi and Shanxi provinces on different levels. The population of BYSMV had a high level of genetic diversity in China, and there was a severe genetic differentiation between the eastern and western subpopulations.

【Keywords】 Barley yellow striate mosaic virus (BYSMV); phylogenesis; genetic diversity; selection pressure; genetic differentiation;

【DOI】

【Funds】 National Basic Research Program of China (973 Program) (2014CB138400) Open Fund of State Key Laboratory for Biology of Plant Diseases and Insect Pests (SKLOF201614)

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    References

    [1] CONTI M. Vector relationships and other characteristics of Barley yellow striate mosaic virus (BYSMV). Annals of Applied Biology, 1980, 95 (1): 83–92.

    [2] DI D P, ZHANG Y L, ZHANG A H, YAN C, YANG F, LU Y G, TIAN L Z, WANG X B, MIAO H Q. Identification of a virus transmitted by small brown planthopper in wheat. Acta Phytopathologica Sinica, 2016, 46 (4): 453–460 (in Chinese).

    [3] DI D P, ZHANG Y L, YAN C, YAN T, ZHANG A H, YANG F, CAO X L, LI D W, LU Y G, WANG X B, MIAO H Q. First report of Barley yellow striate mosaic virus on wheat in China. Plant Disease, 2014, 98 (10): 1450.

    [4] CONTI M. Investigation on a bullet-shaped virus of cereals isolated in Italy from planthoppers. Journal of Phytopathology, 1969, 66 (3): 275–279.

    [5] GREBER R S. Maize sterile stunt—a delphacid transmitted rhabdovirus affecting some maize genotypes in Australia. Australian Journal of Agricultural Research, 1982, 33 (1): 13–23.

    [6] LOCKHART B E L, EL-MAATAOUI M, CARROLL T W, LENNON A M, ZASKE S K. Identification of Barley yellow striate mosaic virus in Morocco and its field detection by enzyme immune assay. Plant Disease, 1986, 70 (12): 1113–1117.

    [7] IZADPANAH K, EBRAHIM-NESBAT F, AFSHARIFAR A R. Barley yellow striate mosaic virus as the cause of a major disease of wheat and millet in Iran. Journal of Phytopathology, 1991, 131 (4): 290–296.

    [8] MAKKOUK K M, BERTSCHINGER L, CONTI M, BOLAY N, DUSUNCELI F. Barley yellow striate mosaic rhabdovirus naturally infects cereal crops in the Anatolian Plateau of Turkey. Journal of Phytopathology, 1996, 144 (7/8): 413–415.

    [9] MAKKOUK K, KUMARI S G, GHULAM W, ATTAR N. First record of Barley yellow striate mosaic virus affecting wheat SummerNurseries in Syria. Plant Disease, 2004, 88 (1): 83.

    [10] DUMÓN A D, ARGÜELLO-CARO E B, ALEMANDRI M V, BAINOTTI C, MATTIO M F, RODRÍGUEZ S M, DEL VAS M, TRUOL G. Identification and biological characterization of Barley yellow striate mosaic virus (BYSMV): A new wheat disease in Argentina. Tropical Plant Pathology, 2011, 36 (6): 374–382.

    [11] YAN T, ZHU J R, DI D P, GAO Q, ZHANG Y L, ZHANG A H, YAN C, MIAO H Q, WANG X B. Characterization of the complete genome of Barley yellow striate mosaic virus reveals a nested gene encoding a small hydrophobic protein. Virology, 2015, 478: 112–122.

    [12] ALMASI R, AFSHARIFAR A, NIAZI A, PAKDEL A, IZADPANAH K. Analysis of the complete nucleotide sequence of the polymerase gene of Barley yellow striate mosaic virus–Iranian isolate. Journal of Phytopathology, 2010, 158 (5): 351–356.

    [13] ROOSSINCK M J. Mechanisms of plant virus evolution. Annual Review of Phytopathology, 1997, 35: 191–209.

    [14] DRAKE J W, HOLLAND J J. Mutation rates among RNA viruses. Proceedings of the National Academy of Sciences of the United States of America, 1999, 96 (24): 13910–13913.

    [15] WEI T Y, YANG J G, LIAO F R, GAO F L, LU L M, ZHANG X T, LI F, WU Z J, LIN Q Y, XIE L H, LIN H X. Genetic diversity and population structure of Rice stripe virus in China. Journal of General Virology, 2009, 90 (4): 1025–1034.

    [16] WU B, BLANCHARD-LETORT A, LIU Y, ZHOU G, WANG X, ELENA S F. Dynamics of molecular evolution and phylogeography of Barley yellow dwarf virus—PAV. PLoS ONE, 2011, 6 (2): e16896.

    [17] YIN X, ZHENG F Q, TANG W, ZHU Q Q, LI X D, ZHANG G M, LIU H T, LIU B S. Genetic structure of Rice black-streaked dwarf virus populations in China. Archives of Virology, 2013, 158 (12): 2505–2515.

    [18] HIGGINS C M, CHANG W L, KHAN S, TANG J, ELLIOTT C, DIETZGEN R G. Diversity and evolutionary history of Lettuce necrotic yellows virus in Australia and New Zealand. Archives of Virology, 2016, 161 (2): 269–277.

    [19] KLERKS M M, LINDNER J L, VAŠKOVA D, ŠPAK J, THOMPSON J R, JELKMANN W, SCHOEN C D. Detection and tentative grouping of Strawberry crinkle virus isolates. European Journal of Plant Pathology, 2004, 110: 45–52.

    [20] PAPPI P G, MALIOGKA V I, AMOUTZIAS G D, KATIS N I. Genetic variation of Eggplant mottled dwarf virus from annual and perennial plant hosts. Archives of Virology, 2016, 161 (3): 631–639.

    [21] TAMURA K, STECHER G, PETERSON D, FILIPSKI A, KUMAR S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 2013, 30 (12): 2725–2729.

    [22] MARTIN D P, MURRELL B, GOLDEN M, KHOOSAL A, MUHIRE B. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution, 2015, 1 (1): vev003.

    [23] MARTIN D, RYBICKI E. RDP: detection of recombination amongst aligned sequences. Bioinformatics, 2000, 16 (6): 562–563.

    [24] PADIDAM M, SAWYER S, FAUQUET C M. Possible emergence of new geminiviruses by frequent recombination. Virology, 1999, 265 (2): 218–225.

    [25] SMITH J M. Analyzing the mosaic structure of genes. Journal of Molecular Evolution, 1992, 34 (2): 126–129.

    [26] MARTIN D P, POSADA D, CRANDALL K A, WILLIAMSON C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Research and Human Retroviruses, 2005, 21 (1): 98–102.

    [27] POSADA D, CRANDALL K A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proceedings of the National Academy of Sciences of the United States of America, 2001, 98 (24): 13757–13762.

    [28] GIBBS M J, ARMSTRONG J S, GIBBS A J. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics, 2000, 16 (7): 573–582.

    [29] BONI M F, POSADA D, FELDMAN M W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics, 2007, 176 (2): 1035–1047.

    [30] YANG Z H. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 2007, 24 (8): 1586–1591.

    [31] SWANSON W J, VACQUIER V D. The rapid evolution of reproductive proteins. Nature Reviews Genetics, 2002, 3 (2): 137–144.

    [32] SWANSON W J, NIELSEN R, YANG Q F. Pervasive adaptive evolution in mammalian fertilization proteins. Molecular Biology and Evolution, 2003, 20 (1): 18–20.

    [33] YANG Z H, NIELSEN R, GOLDMAN N, PEDERSEN A M K. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 2000, 155 (1): 431–449.

    [34] YANG Z H, WONG W S W, NIELSEN R. Bayes empirical bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution, 2005, 22 (4): 1107–1118.

    [35] LIBRADO P, ROZAS J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 2009, 25 (11): 1451–1452.

    [36] QIU W F, YANG L, MEI R H, LIN Z L, CAI Z N. Studies on a rosette disease of wheat I distribution, symptoms and losses. Acta Phytophylacica Sinica, 1979, 6 (1): 11–16 (in Chinese).

    [37] DUAN X F, DI D P, ZHANG A H, MIAO H Q. Molecular detection and identification of the pathogen causing wheat rosette stunt disease in the north of China. Acta Phytopathologica Sinica, 2013, 43 (1): 91–94 (in Chinese).

    [38] MOYA A, HOLMES E C, GONZÁLEZ-CANDELAS F. The population genetics and evolutionary epidemiology of RNA viruses. Nature Reviews Microbiology, 2004, 2 (4): 279–288.

This Article

ISSN:0578-1752

CN: 11-1328/S

Vol 51, No. 02, Pages 279-289

January 2018

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Article Outline

Abstract

  • 0 Introduction
  • 1 Materials and methods
  • 2 Results
  • 3 Discussion
  • 4 Conclusions
  • References