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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC IMPROVEMENT OF SUGARCANE BY CONVENTIONAL AND MOLECULAR APPROACHES Title: Molecular characterization and phylogenetic analysis of sugarcane yellow leaf virus isolates from China

Authors
item Gao, San-Ji -
item Lin, Yi-Hua -
item Pan, Yong-Bao
item Damaj, Mona -
item Wang, Qin-Nan -
item Mirkov, T Erik -
item Chen, Ru-Kai -

Submitted to: Virus Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 7, 2012
Publication Date: July 3, 2012
Repository URL: http://handle.nal.usda.gov/10113/58973
Citation: Gao, S., Lin, Y.-H., Pan, Y.-B., Damaj, M.B., Wang, Q., Mirkov, T., Chen, R. 2012. Molecular characterization and phylogenetic analysis of sugarcane yellow leaf virus isolates from China. Virus Genes. 45:340-349. DOI 10:1007/s11262-012-0774-1.

Interpretive Summary: Sugarcane yellow leaf disease (YLD) is found in all sugarcane growing areas in the world causing a yield reduction in cane and sugar production. The causal agent of YLD is a virus by its scientific name of sugarcane yellow leaf virus (SCYLV). This study was conducted to survey the distribution of the SCYLV across five major sugarcane production provinces in China. Leaf samples from 22 varieties showing YLD symptoms were collected and presence of the SCYLV in the leaf samples were detected by both immunological and nucleic acid-based laboratory methods. In addition, the whole or partial viral nucleotide sequences were amplified by a molecular gene amplification method called RT-PCR. These sequences were compared with other reported SCYLV sequences available from the GenBank database. The results showed that the real-time RT-PCR method is the most sensitive for SCYLV detection. Fourteen new Chinese SCYLV strains were confirmed to belong to one taxonomic group named BRA, although several other Chinese strains of SCYLV reported earlier belonged to PER (3 strains) or CHN1 (2 strains). This indicated that at least three taxonomic groups of SCYLV were causing the YLD in China. In addition, a Florida strain was found to belong to HAW group and a Louisiana strain belonged to BRA group. Another significant finding was a deletion of 49 nucleotides in the SCYLV strain CHN-GD3 locating at a position previously reported to be highly unstable. These results will help improve the efficiency of SCYLV detection in sugarcane fields and add some new knowledge to the biology of the virus.

Technical Abstract: Sugarcane yellow leaf virus (SCYLV), the causal agent of sugarcane yellow leaf disease (YLD), was first reported in China in 2006. In order to determine the distribution existence of SCYLV in major sugarcane-growing provinces in China, leaf samples were collected from 22 sugarcane clones (Saccharum spp. hybrids) showing YLD symptoms and subjected to SCYLV diagnosis by reverse transcriptase PCR (RT-PCR), real-time RT-PCR, and serological methods. The complete genomic sequence of a Chinese SCYLV isolate CHN-FJ1 (5,879 nt) and partial genomic sequences (2,915 nt) of 13 other Chinese SCYLV isolates from this study were amplified, cloned and sequenced. The complete genomic sequence of CHN-FJ1 shared a high similarity value (98.8%-99.1%) with the isolates of BRA genotype and low similarity (86.1%-86.9%) with the two isolates of CHN1 genotype. Based on either the full or partial genomic sequences, the genetic diversity of these 14 Chinese SCYLV isolates was assessed along with 33 reported SCYLV isolates from the GenBank database representing worldwide origins. Phylogenetic analysis demonstrated that all the 14 Chinese isolates were clustered together in the BRA genotype group with seven other reported isolates. In addition, five reported Chinese SCYLV isolates were grouped in either genotype PER or genotype CHN1. Therefore, we speculated that at least three SCYLV genotypes (BRA, CHN1, and PER) were associated with YLD in China. Interestingly, a 49-nt deletion was found in the genomic sequence of CHN-GD3 isolate, locating in the middle of the ORF1 adjacent to the overlap between ORFs 1 and 2. This location was previously reported as one of the recombination breakpoints in the Luteoviridae family.

Last Modified: 11/24/2014
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