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Molecular detection, genetic diversity and distribution of Sugarcane yellow leaf virus genotypes in China

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Abstract

A total of 332 sugarcane leaf samples were collected from seven provinces in China during 2010 to 2013. RT-PCR was performed using the YLS111/YLS462 primers to detect the causal pathogen Sugarcane yellow leaf virus (SCYLV) causing yellow leaf disease in sugarcane. The incidence of SCYLV infection ranged from 24 to 38 % depending on geographic areas. A new primer pair (P0-R3/P0-F2) was designed to prime the amplification of a 968-nucleotide (nt) fragment from SCYLV-positive samples. The fragment contained a partial 5′ untranslated region, the complete ORF0 encoding P0, and a partial ORF1. A phylogenetic analysis of 141 P0 fragment sequences (937 nt) worldwide showed that all SCYLV isolates were clustered into eight genotypes. The 107 SCYLV isolates collected in this study were classified into three genotypes (BRA, HAW, and CHN3), of which the BRA genotype (102/107) was the most prevalent and was detected in all evaluated locations. One isolate (1/107) of genotype HAW was found in Hainan province. Four isolates (4/107) of the genotype CHN3 were observed in Guangxi, Guizhou and Hainan provinces. These findings help understand the genotypic diversity and distribution of SCYLV isolates in China.

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Acknowledgments

This research was supported by a grant from the National Natural Science Foundation of China (31170345) and an Earmarked Fund from the China Agriculture Research System (CARS-20-2-4). The authors wish to express sincere thanks to the scientists in CARS for collecting the sugarcane leaf samples. We also thank Yong-Bao Pan at the USDA-ARS, Sugarcane Research Unit, Houma, LA, USA for critically review of the manuscript.

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    Authors and Affiliations

    1. Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

      Yi-Hua Lin, Xiao-Bin Wu, Ying-Hang Liu, Sheng-Hua Xiao, Ru-Kai Chen, Hua-Ying Fu & San-Ji Gao

    2. Laboratory of Plant Virology, South China Agricultural University, Guangzhou, Guangdong, 510642, China

      Guo-Hui Zhou

    3. Guangxi Collaborative Innovation Center of Sugarcane Industry, Guangxi University, Nanning, Guangxi, 530004, China

      Ru-Kai Chen & San-Ji Gao

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    1. Yi-Hua Lin
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    Correspondence to Ru-Kai Chen or San-Ji Gao.

    Additional information

    Section Editor: Alice Nagata

    Yi-Hua Lin and Xiao-Bin Wu contributed equally to this work.

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    Supplementary Table S1

    Sources of sugarcane yellow leaf virus (SCYLV) P0 fragment sequences used in this study. (DOC 220 kb)

    Supplementary Figure S1

    Phylogenetic tree based on the multiple sequence alignment among the nucleotide sequences of a 771-nt P0 gene from 141 sugarcane yellow leaf virus (SCYLV) isolates (107 from this study marked with an asterisk plus 34 from the GenBank database). The tree was constructed using the neighbor-joining (NJ) method and the Kimura 2-parameter substitution model with bootstrap resampling of 1000 replications. Isolates of the BRA genotype were condensed as a triangle. (DOCX 255 kb)

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    Lin, YH., Wu, XB., Liu, YH. et al. Molecular detection, genetic diversity and distribution of Sugarcane yellow leaf virus genotypes in China. Trop. plant pathol. 40, 200–207 (2015). https://doi.org/10.1007/s40858-015-0037-5

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