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Genetic diversity and population structure of rice stripe virus in China

Tai-Yun Wei^1,

Jin-Guang Yang^1,

Han-Xin Lin^1,

¹ Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
² Key Laboratory of Agricultural Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, PR China

Correspondence
Han-Xin Lin
hanxinl{at}yahoo.com
or
linhan{at}mcmaster.ca
Lian-Hui Xie
xielh{at}fjau.edu.cn

Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997–2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.

These authors contributed equally to this paper.

Present address: Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada.

A supplementary table listing geographical location, collection year, GenBank accession numbers and rice variety of RSV isolates, and associated supplementary references are available with the online version of this paper.