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Title: Genetic diversity of Sweet potato begomoviruses in the United States and identification of a natural recombinant between Sweet potato leaf curl virus and Sweet potato leaf curl Georgia virus

Author
item ZHANG, SHUOCHENG - Alcorn State University
item Ling, Kai-Shu

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/29/2010
Publication Date: 6/2/2011
Citation: Zhang, S., Ling, K. 2011. Genetic diversity of Sweet potato begomoviruses in the United States and identification of a natural recombinant between Sweet potato leaf curl virus and Sweet potato leaf curl Georgia virus. Archives of Virology. 156(6):955-968.

Interpretive Summary: The United States produced 966,785 metric tons of sweetpotatoes in 2009 with a total value of $410 million. One major limitation in sweetpotato production is cultivar decline, likely due to the cumulative effect of virus infection on this vegetatively propagated crop. Sweet potato leaf curl is an emerging disease which could results in significant yield losses (10-80%) to many sweetpotato cultivars. Although, this disease has been shown to be caused by a number of begomoviruses in other parts of world, its genetic diversity in the United State has not been thoroughly characterized. In the present study, we sequenced a large number of field collected isolates from both South Carolina and Mississippi and identified 10 distinct genotypes. Although, majority of field isolates (50/52) were related to Sweet potato leaf curl virus (SPLCV), a novel species was identified in South Carolina. A natural recombinant isolated from Mississippi was shown to consist of sequences from both SPLCV and Sweet potato leaf curl Georgia virus. The knowledge of greater genetic diversity of begomoviruses on sweetpotato will likely have a major impact on PCR–based virus detection and on disease management practice through breeding for virus resistance.

Technical Abstract: In the United States, two sweetpotato begomoviruses, Sweet potato leaf curl virus (SPLCV) and Sweet potato leaf curl Georgia virus (SPLCGV) were previously identified in Louisiana. In recent years, at least seven additional sweetpotato begomoviruses have been identified in other parts of the world. In an effort to determine the genetic diversity and distribution of sweetpotato begomoviruses in the U.S., we focused our efforts on molecular characterization of field collected begomovirus isolates in two states (Mississippi and South Carolina). Using rolling-circle amplification, a total of 52 clones in full-genome were obtained and sequenced. Initial inspection of a sequence alignment revealed a strong genetic diversity among the U.S. isolates, which were assigned in 10 genotypes. The majority of the isolates (50/52) in eight genotypes were shown to be closely related to SPLCV. Among them, four genotypes from South Carolina with 91-92% sequence identity to the type member of SPLCV were considered as a new strain; whereas four other genotypes from Mississippi with >95% sequence identity to SPLCV were considered variants. In addition, a novel begomovirus species was identified after comparative sequence analysis of the isolate [US:SC:646B-9] from South Carolina with <89% of sequence identity to all known begomoviruses, hence a provisional name Sweet potato leaf curl South Carolina virus (SPLCSCV) is proposed. Moreover, a natural recombinant consisting of two distinct parental genomic sequences from SPLCV and SPLCGV was identified in the sample [US:MS:1B-3] from Mississippi. Two recombinant breakpoints were identified, one in the origin of replication and the other in between AC2 and AC4. The knowledge of greater genetic diversity of begomoviruses on sweetpotato will likely have a major impact on PCR–based virus detection and on disease management practice through breeding for virus resistance.