Scientia Agricultura Sinica ›› 2013, Vol. 46 ›› Issue (19): 4075-4081.doi: 10.3864/j.issn.0578-1752.2013.19.013

• PLANT PROTECTION • Previous Articles     Next Articles

Identification of Viruses from Potato Planted in Winter in Guangxi by Small RNA Deep Sequencing

 SONG  Jing-Jing-1, MENG  Jiao-Rong-12, ZOU  Cheng-Wu-3, LI  Pu-3, WANG  Zhi-Qiang-2, CHEN  Bao-Shan-23   

  1. 1.College of Agriculture, Guangxi University, Nanning 530004
    2.State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004
    3.College of Life Science and Technology, Guangxi   University, Nanning 530004
  • Received:2013-04-03 Online:2013-10-01 Published:2013-06-04

PDF

773

Cited

4

Abstract: 【Objective】The objective of this study is to identify viruses infecting potato planted in winter in Guangxi for establishing a future healthy potato seed program and better disease control in the field. 【Method】One hundred and nine samples with viral disease-like symptoms were collected from potato plants in the fields in 2012 and subject to initial ELISA screening before they were pooled and analyzed by small RNA deep sequencing. Viruses identified by small RNA sequencing were validated by virus-specific RT-PCR from selected groups of samples.【Result】Potato leafroll virus (PLRV), Potato virus A (PVA), Potato virus H (PVH), Potato virus M (PVM), Potato virus S (PVS), Potato virus Y (PVY), and Potato spindle tuber viroid (PSTVd) were detected in the samples and PVS was found to have a rich genetic diversity.【Conclusion】Potato planted in winter in Guangxi were infected with many viruses including two viruses and a viroid that had not been reported in the region before. Thus, a virus-free healthy potato seed program is needed in urgency.

Key words: small RNA deep sequencing , Guangxi , potato planted in winter , viruses disease

[1]Jeffries G J. FAO/IPGRI Technical Guidelines for the Safe Movement of Potato Germplasm: No 19, Potato. Rome: Food and Agriculture Organization of the United Nations, 1998: 33-96.

[2]Salazar L. Potato viruses after the XXth century: effects, dissemination and their control. Material Participants in Pyongyang Intern, Scientific Simp, on Potato, Pyongyang, DPRK, 2003: 35-42.

[3]高艳玲, 张威, 白艳菊, 申宇, 范国权, 耿宏伟, 刘玮婷. 马铃薯主产区病毒病发生情况调查分析. 植物保护, 2011, 37(3): 149-151.

Gao Y L, Zhang W, Bai Y J, Shen Y, Fan G Q, Geng H W, Liu W T. Investigation and analysis of viral diseases in main potato production areas. Plant Protection, 2011, 37(3): 149-151. (in Chinese)

[4]方中达. 植病研究方法. 3版. 北京: 中国农业出版社, 1998: 283-298.

Fang Z D. Research Methods of Plant Pathology. 3rd ed. Beijing: China Agriculture Press, 1998: 283-298. (in Chinese)

[5]谢联辉. 普通植物病理学. 北京: 科学出版社, 2006: 274-282.

Xie L H. General Plant Pathology. Beijing: Science Press, 2006: 274-282. (in Chinese)

[6]徐秉良, 曹克强. 植物病理学. 北京: 中国林业出版社, 2012: 126-127.

Xu B L, Cao K Q. Plant Pathology. Beijing: China Forestry Press, 2012: 126-127. (in Chinese)

[7]Banttari E E, Goodwin P H. Detection of potato viruses S, X, and Y by enzyme-linked immunosorbent assay on nitrocellulose membranes (dot-ELISA). Plant Disease, 1985, 69(3): 202-205.

[8]Lin N S, Hsu Y H, Hsu H T. Immunological detection of plant viruses and a mycoplasmalike organism by direct tissue blotting on nitrocellulose membranes. Phytopathology, 1990, 80(9): 824-828.

[9]Makkouk K M, Comeau A. Evaluation of various methods for the detection of barley yellow dwarf virus by the tissue-blot immunoassay and its use for virus detection in cereals inoculated at different growth stages. European Journal of Plant Pathology, 1994, 100(1): 71-80.

[10]Makkouk K, Kumari S. Molecular diagnosis of plant viruses. Arab Journal of Plant Protection, 2006, 24(2): 135-138.

[11]Barker H, McGeachy K D, Toplak N, Gruden K, Zel J, Browning I. Comparison of genome sequence of PVY isolates with biological properties. American Journal of Potato Research, 2009, 86(3): 227-238.

[12]Schaad N W, Frederick R D. Real-time PCR and its application for rapid plant disease diagnostics. Canadian Journal of Plant Pathology, 2002, 24(3): 250-258.

[13]Kogovšek P, Gow L, Pompe-Novak M, Gruden K, Foster G D, Boonham N, Ravnikar M. Single-step RT real-time PCR for sensitive detection and discrimination of Potato virus Y isolates. Journal of Virological Methods, 2008, 149(1): 1-11.

[14]Schuster S C. Next-generation sequencing transforms today's biology. Nature Methods, 2008, 5(1): 16-18.

[15]Li R, Gao S, Hernandez A G, Wechter W P, Fei Z, Ling K S. Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS One, 2012, 7(5): e37127.

[16]Wu Q F, Luo Y J, Lu R, Lau N, Lai E C, Li W X, Ding S W. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proceedings of the Natural Academy of Sciences of the United States of America, 2010, 107(4): 1606-1611.

[17]Adams I P, Glover R H, Monger W A, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Molecular Plant Pathology, 2009, 10(4): 537-545.

[18]Al Rwahnih M, Daubert S, Golino D, Rowhani A. Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology, 2009, 387(2): 395-401.

[19]Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F, Burgyan J. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One, 2009, 4(11): e7686.

[20]陈保善, 蒙姣荣, 蔡健和, 王华生, 陈景成, 韦相贤. 2005年玉林市冬种马铃薯病毒病调查. 广西植保, 2006, 19(2): 1-2.

Chen B S, Meng J R, Cai J H, Wang H S, Chen J C, Wei X X. Investigation of Potato viruses planted in winter of Yulin in 2005. Plant Protection of Guangxi, 2006, 19(2): 1-2. (in Chinese )

[21]李芝芳. 中国马铃薯主要病毒图鉴. 北京: 中国农业出版社, 2004: 25-69.

Li Z F. Field Guide of Major Potato Virus in Chinese. Beijing: China Agriculture Press, 2004: 25-69. (in Chinese )

[22]Duarte P D S G, Galvino-Costa S B F, Ribeiro S R R D P, Figueira A D R. Complete genome sequence of the ?rst Andean strain of potato virus S from Brazil and evidence of recombination between PVS strains. Archives of Virology, 2012, 157: 1357-1364.

[23]Rose D G. Some properties of an unusual isolate of potato virus S. Potato Research, 1983, 26: 49-62.

[24]Dolby C A, Jones R A C. Occurrence of the Andean strain of potato virus S in imported potato material and its effects on potato cultivars. Plant Pathology, 1987, 36: 381-388.

[25]Foster G D, Meehan B M, Mills P R. A comparison of the nucleotide sequence homologies between isolates of the Andean and ordinary strains of Potato virus S and their relationship to other carlaviruses. Virus Genes, 1990, 4(3): 257-260.
[1] SHU JingTing,SHAN YanJu,JI GaiGe,ZHANG Ming,TU YunJie,LIU YiFan,JU XiaoJun,SHENG ZhongWei,TANG YanFei,LI Hua,ZOU JianMin. Relationship Between Expression Levels of Guangxi Partridge Chicken m6A Methyltransferase Genes, Myofiber Types and Myogenic Differentiation [J]. Scientia Agricultura Sinica, 2022, 55(3): 589-601.
[2] TANG YaFei,PEI Fan,LI ZhengGang,SHE XiaoMan,YU Lin,LAN GuoBing,DENG MingGuang,HE ZiFu. Identification of Viruses Infecting Peppers in Guangdong by Small RNA Deep Sequencing [J]. Scientia Agricultura Sinica, 2019, 52(13): 2256-2267.
[3] RAO Gui-bo, ZHONG Ya-ting, OUYANG Kang, MA Ling, HUANG Hong-mei, WU Jian-min. Analysis of Evolutionary Time of Porcine Endogenous Retrovirus in Guangxi Bama Mini-pigs [J]. Scientia Agricultura Sinica, 2015, 48(4): 778-787.
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