Scientia Agricultura Sinica ›› 2013, Vol. 46 ›› Issue (15): 3125-3133.doi: 10.3864/j.issn.0578-1752.2013.15.006

• PLANT PROTECTION • Previous Articles     Next Articles

Detection and Molecular Variation of Potato virus Y CP Gene in China

 GAO  Fang-Luan-1, SHEN  Jian-Guo-2, SHI  Feng-Yang-1, FANG  Zhi-Guo-1, XIE  Lian-Hui-1, ZHAN  Jia-Sui-1   

  1. 1.Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002
    2.Inspection & Quarantine Technology Center, Fujian Exit-Entry Inspection and Quarantine Bureau, Fuzhou 350001
  • Received:2013-01-25 Online:2013-08-01 Published:2013-05-16

PDF

878

Abstract: 【Objective】 The objectives of this study are to investigate the occurrence of Potato virus Y (PVY) disease in China, to develop fast and accurate PVY detection methods and to understand sequence variations in PVY CP gene.【Method】ELISA method was used to detect the infected leaf samples randomly collected from 14 provinces (municipalities) in China during 2011 and 2012. A subsample of the infected leaves was examined using a transmission electron microscope. CP gene of PVY was amplified by reverse-transcription polymerase chain reaction (RT-PCR) using a pair of degenerate primers designed from the conserved regions of published CP gene sequences. Sequence variation was analyzed and phylogenetic tree was re-constructed using Bayesian inference method.【Result】ELISA revealed that 220 out of the 691 samples assayed were infected with PVY. The pin-wheel inclusion bodies were visualized clearly under the transmission electron microscope in the subsamples of ELISA-positive leaves. RT-PCR amplifications of the 14 ELISA-positive subsamples randomly selected from different provinces (municipalities) all generated an expected fragment of ≈800 bp in size. CP genes in the selected 14 subsamples shared more than 88% nucleotide identity with the reported sequences in other PVY strains. Among the 14 CP gene sequences in the subsamples, 29 polymorphic sites were detected, including 6 parsimony informative and 23 singleton variable sites. Some of the sequence variations were geography-specific. Bayesian inference of phylogenetic trees revealed that 14 PVY isolates were in the same branch with reference PVYN:O strains, suggesting that the 14 PVY isolates analyzed in this study shared high homology with PVYN:O strain.【Conclusion】CP gene in PVY is highly conserved but some geographical variation in sequences exists. The results reported in this manuscript provide useful insights in understanding the evolution of PVY, the epidemiology and control of PVY disease in potato.

Key words: Potato virus Y , ELISA , coat protein gene (CP gene) , molecular variation , Bayesian inference method

[1]胡新喜, 何长征, 熊兴耀, 刘明月, 宋勇, 聂先舟. 马铃薯Y病毒研究进展. 中国马铃薯, 2009, 23(5): 293-300.

Hu X X, He C Z, Xiong X Y, Liu M Y, Song Y, Nie X Z. Progress on Potato virus Y . Chinese Potato Journal, 2009, 23(5): 293-300. (in Chinese)

[2]Glais L, Tribodet M, Kerlan C. Genomic variability in Potato potyvirus Y (PVY): evidence that PVYNW and PVYNTN variants are single to multiple recombinants between PVYO and PVYN isolates. Archives of Virology, 2002, 147: 363-378.

[3]Nolte P, Whitworth J L, Thornton M K, McIntosh C S. Effect of seedborne Potato virus Y on performance of Russet Burbank, Russet Norkotah, and Shepody potato. Plant Disease, 2004, 88(3): 248-252.

[4]Whitworth J L, Nolte P, McIntosh C, Davidson R. Effect of Potato virus Y on yield of three potato cultivars grown under different nitrogen Levels. Plant Disease, 2006, 90(1): 73-76.

[5]Beczner L, Horváth J, Romhányi I, Förster H. Studies on the etiology of tuber necrotic ringspot disease in potato. Potato Research, 1984, 27: 339-352.

[6]Ohshima K, Sako K, Hiraishi C, Nakagawa A, Matsuo K, Ogawa T, Shikata E, Sako N. Potato tuber necrotic ringspot disease occurring in Japan: its association with Potato virus Y necrotic strain. Plant Disease, 2000, 84(10): 1109-1115.

[7]孙琦, 张春庆. PVYN与PVYO病毒RT-PCR快速检测体系研究. 中国农业科学, 2005, 38(1): 213-216.

Sun Q, Zhang C Q. Studies on the methods of detecting PVYN and PVYO by RT-PCR. Scientia Agricultura Sinica, 2005, 38(1): 213-216. (in Chinese)

[8]Ogawa T, Tomitaka Y, Nakagawa A, Ohshima K. Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison with North American and European populations. Virus Research, 2008, 131: 199-212.

[9]Nie B H, Singh M, Murphy A, Sullivan A, Xie C H, Nie X Z. Response of potato cultivars to five isolates belonging to four strains of Potato virus Y. Plant Disease, 2012, 96(10): 1422-1429.

[10]Ogawa T, Nakagawa A, Hataya T, Ohshima K. The genetic structure of populations of Potato virus Y in Japan; Based on the analysis of 20 full genomic sequences. Journal of Phytopathology, 2012, 160: 661-673.

[11]Wang F, Wu Y H, Gao Z L, Zhou B G, Guo L. First report of Potato virus Y in Kalimeris indica in China. Plant Disease, 2012, 96(12): 1827-1828.

[12]谢思, 易图永, 肖启明. 马铃薯Y病毒的株系分化及检测方法研究进展. 中国农学通报, 2011, 27(5): 40-43.

Xie S, Yi T Y, Xiao Q M. Research progress in strains differentiation and detection research of Potato virus Y. Chinese Agricultural Science Bulletin, 2011, 27(5): 40-43. (in Chinese)

[13]高秀妍, 高艳玲, 耿宏伟, 张威, 范国权, 白艳菊, 吕文河, 蒋希峰. 马铃薯Y病毒黑龙江分离物株系鉴定. 中国马铃薯, 2009, 23(1): 11-14.

Gao X Y, Gao Y L, Geng H W, Zhang W, Fan G Q, Bai Y J, Lü W H, Jiang X F. Identification of a Potato virus Y isolate from Heilongjiang. Chinese Potato Journal, 2009, 23(1): 11-14. (in Chinese)

[14]吴志明, 董志茹, 刘小娟, 温春秀, 谢晓亮, 张庆良. 马铃薯Y病毒河北分离物外壳蛋白基因序列分析和株系鉴定. 园艺学报, 2005, 32: 324-326.

Wu Z M, Dong Z R, Liu X J, Wen C X, Xie X L, Zhang Q L. Coat protein gene sequence analysis and identification of a Potato virus Y Hebei isolate. Acta Horticulturae Sinica, 2005, 32: 324-326. (in Chinese)

[15]陈士华, 刘晓磊, 张晓婷, 吴兴泉. 中国部分马铃薯产区马铃薯Y病毒 (PVY)的株系分化与鉴定. 河南农业大学学报, 2011, 45(5): 548-551.

Chen S H, Liu X L, Zhang X T, Wu X Q. Study on the PVY strain differentiation and identification of some potato producing areas in China. Journal of Henan Agricultural University, 2011, 45(5): 548-551. (in Chinese)

[16]谢联辉, 林奇英. 植物病毒学. 3版. 北京: 中国农业出版社, 2011: 154-155.

Xie L H, Lin Q Y. Plant Virology. 3rd ed. Beijing: China Agriculture Press, 2011: 154-155. (in Chinese)

[17]Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 2009, 25(11): 1451-1452.

[18]Larkin M A, Blackshields G, Brown N P, Chenna R, McGettigan P A, McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D, Gibson T J, Higgins D G. Clustal W and Clustal X version 2.0. Bioinformatics, 2007, 23(21): 2947-2948.

[19]Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 2007, 56(4): 564-577.

[20]Nylander J A A. MrModeltest v2.3. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, 2008.

[21]Ronquist F, Teslenko M, van der Mark P, Ayres D L, Darling A, Hohna S, Larget B, Liu L, Suchard M A, Huelsenbeck J P. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 2012, 61(3): 539-542.

[22]Hu X, Karasev A V, Brown C J, Lorenzen J H. Sequence characteristics of Potato virus Y recombinants. Journal of General Virology, 2009, 90: 3033-3041.

[23]Chikh Ali M, Maoka T, Natsuaki K T, Natsuaki T. The simultaneous differentiation of Potato virus Y strains including the newly described strain PVYNTN-NW by multiplex PCR assay. Journal of Virological Methods, 2010, 165: 15-20.

[24]Quenouille J, Vassilakos N, Moury B. Potato virus Y: a major crop pathogen that has provided major insights into the evolution of viral pathogenicity. Molecular Plant Pathology, 2013, DOI: 10.1111/mpp.12024.

[25]吴祖建, 高芳銮, 沈建国. 生物信息学分析实践. 北京: 科学出版社, 2010: 158-159.

Wu Z J, Gao F L, Shen J G. Bioinformatics Analysis Practice. Beijing: Science Press, 2010: 158-159. (in Chinese)

[26]黄原. 分子系统发生学. 北京: 科学出版社, 2012: 323-324.

Huang Y. Molecular Phylogenetics. Beijing: Science Press, 2012: 323-324. (in Chinese)

[27]Hall B G. Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Molecular Biology and Evolution, 2005, 22(3): 792-802.

[28]Yang Z, Rannala B. Molecular phylogenetics: principles and practice. Nature Reviews. Genetics, 2012, 13: 303-314.
[1] LI ZhiLing,LI XiangJu,CUI HaiLan,YU HaiYan,CHEN JingChao. Development and Application of ELISA Kit for Detection of EPSPS in Eleusine indica [J]. Scientia Agricultura Sinica, 2022, 55(24): 4851-4862.
[2] ZHANG FengXi,XIAO Qi,ZHU JiaPing,YIN LiHong,ZHAO XiaLing,YAN MingShuai,XU JinHua,WEN LiBin,NIU JiaQiang,HE KongWang. Preparation and Identification of Monoclonal Antibodies to P30 Protein and Establishment of Blocking ELISA to Detecting Antibodies Against African Swine Fever Virus [J]. Scientia Agricultura Sinica, 2022, 55(16): 3256-3266.
[3] YuXin LIANG,JianXiang WU,XiaoYu LI,ChunYu ZHANG,JiChao HOU,XuePing ZHOU,YongZhi WANG. Mapping of Epitopes and Establishment of Rapid DAS-ELISA for Potato Virus Y Coat Protein [J]. Scientia Agricultura Sinica, 2021, 54(6): 1154-1162.
[4] LI ZiTeng,CAO YuHan,LI Nan,MENG XiangLong,HU TongLe,WANG ShuTong,WANG YaNan,CAO KeQiang. Molecular Variation and Phylogenetic Relationship of Apple Scar Skin Viroid in Seven Cultivars of Apple [J]. Scientia Agricultura Sinica, 2021, 54(20): 4326-4336.
[5] QU XiaoLing,JIAO YuBing,LUO JianDa,SONG LiYun,LI Ying,SHEN LilLi,YANG JinGuang,WANG FengLong. Cloning of Nicotiana benthamiana NAC062 and Its Inhibitory Effect on Potato Virus Y Infection [J]. Scientia Agricultura Sinica, 2021, 54(19): 4110-4120.
[6] Xiao WEI,Qi ZHANG,Wen ZHANG,Hui LI,PeiWu LI. Improving the Sensitivity of ELISA by Large-Capacity Reaction System of Aflatoxigenic Fungi-Biomarker in Agro-products [J]. Scientia Agricultura Sinica, 2020, 53(7): 1473-1481.
[7] HuiMin HU,XueFeng PAN,Heng YANG,Chen CHEN,YinJi CHEN. Wheat Gluten, Gliadins and Glutenin Content Changes During Germination Based on the Methods of R5 ELISA and RP-HPLC [J]. Scientia Agricultura Sinica, 2020, 53(6): 1247-1255.
[8] MingYue GONG,XiaoTian DUAN,TingTing YU,Jie WANG,LiLi SHEN,Ying LI,MingHong LIU,YongLiang LI,HongKun LÜ,SongBai ZHANG,JinGuang YANG. Cloning of Hsc70-2 and Its Promoting Effect on Potato virus Y Infection in Nicotiana benthamiana [J]. Scientia Agricultura Sinica, 2020, 53(4): 771-781.
[9] WANG Fang, FENG Yu, ZHANG Ge, JIANG Hui, ZHU Liang-quan, DING Jia-bo. Development of Indirect ELISA for Antibody of Brucella abortus [J]. Scientia Agricultura Sinica, 2016, 49(9): 1818-1825.
[10] SHEN Lin-lin, ZOU Wen-chao, GAO Fang-luan, ZHAN Jia-sui. Strain Composition of Potato virus Y in Fujian Province Detected with the Concatenated Sequence Approach [J]. Scientia Agricultura Sinica, 2016, 49(20): 3918-3926.
[11] CHEN Zhe, SONG Ge, ZHOU Xue-ping, WU Jian-xiang. Preparation and Application of Monoclonal Antibodies Against Watermelon mosaic virus (WMV) [J]. Scientia Agricultura Sinica, 2016, 49(14): 2711-2724.
[12] CHEN Rui, FAN Xue-zheng, ZHU Yuan-yuan, ZOU Xing-qi, XU Lu, ZHANG Qian-yi, WANG Qin, ZHAO Qi-zu. Prevalence Study and Phylogenetic Analysis of Bovine Viral Diarrhea Virus in Free-Roaming Beef Cattle in Western China [J]. Scientia Agricultura Sinica, 2016, 49(13): 2635-2641.
[13] LU Hui-xiang, Lü Chang-wen, WU Zheng-dan, LUO Kai, YIN Wang, YANG Hang, WANG Ji-chun, ZHANG Kai. Development of Detection Method for Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV) Through Fluorescence Quantitative RT-PCR [J]. Scientia Agricultura Sinica, 2016, 49(1): 90-102.
[14] GAO Fang-luan, CHANG Fei, SHEN Jian-guo, XIE Lian-hui, ZHAN Jia-sui. Complete Genome Analysis of a PVYNTN-NW Recombinant Isolate from Yulin of China [J]. Scientia Agricultura Sinica, 2015, 48(2): 270-279.
[15] JIN Xin, ZHANG Man, FAN Yan-ru, WANG Pei, YANG Yin-feng. Effects of Saccharomyces cerevisiae on the Expression of SBD-1 in Cultured Ruminal Epithelial Cells of Sheep [J]. Scientia Agricultura Sinica, 2015, 48(19): 3910-3918.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd