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United States Department of Agriculture

Agricultural Research Service

Title: Patterns of Polymorphism in Wheat Streak Mosaic Virus: Sequence Space Explored by a Clade of Closely Related Genotypes Rivals That Between the Most Divergent Strains

Authors
item Stenger, Drake
item Seifers, Dallas - KANSAS STATE UNIVERSITY
item French, Roy

Submitted to: Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 2, 2002
Publication Date: August 15, 2002
Citation: Stenger, D.C., Seifers, D.L., French, R.C. 2002. Patterns of polymorphism in wheat streak mosaic virus: sequence space explored by a clade of closely related genotypes rivals that between the most divergent strains. Virology 302:58-70.

Interpretive Summary: Genetic variation within the U. S. population of wheat streak mosaic virus (WSMV) was examined. Nucleotide sequencing revealed that WSMV isolates from the U. S. were closely related, yet distinguishable from one another by unique patterns of nucleotide substitutions. A phylogenetic analysis indicated that all WSMV isolates in the U. S. were descendent from a recent tcommon ancestor. Although pair wise divergence among U. S. isolates of WSMV was low (< 3.6%), total variation in the U. S. population (21.4%) rivaled that between two of the most divergent strains of WSMV: Sidney 81 from Nebraska and El Bat n 3 from Mexico (20%). Because over half of the variation within the U. S. population of WSMV was due to unique substitutions, each isolate appears to be evolving independently within the constraints of selection. Furthermore, the majority of substitutions were biased for silent substitutions that did not affect the encoded protein product, and these silent substitutions were randomly distributed throughout the region of the viral genome examined. The results suggest that much of the variation detected within the U. S. population of WSMV is neutral with respect to relative fitness. An estimate of the rate of divergence, calculated from previous studies, suggests that the present level of diversity within the U. S. population of WSMV arose in about a century, a time frame corresponding with establishment of wheat monoculture in the Great Plains.

Technical Abstract: Nucleotide (nt) sequence polymorphism within a collection of wheat streak mosaic virus isolates was examined. The coat protein (CP) cistron and flanking sequences were amplified by RT-PCR. Consensus sequences were compiled for each isolate from three clones per RT-PCR product. Among 59 consensus sequences, only two were identical. Clades A-C contained divergent isolates from Mexico (Clade A), Europe and Russia (Clade B), and Iran (Clade C). Fifty-four closely related isolates from the U. S. (51) Canada (1) and Turkey (2) comprised Clade D. Maximum pair-wise nt divergence within Clade D was 3.6%. In contrast, pair-wise nt divergence between two distantly related sequences (Sidney 81 of Clade D and El Bat n 3 of Clade A) was 20%. Nonetheless, total diversity within Clade D (21.4%) was of similar magnitude to that of the Sidney 81-El Bat n 3 pair. Patterns of polymorphism within Clade D and the Sidney 81-El Bat n 3 pair were remarkably similar with respect to synonymous, nonsynonymous, and non coding substitutions, as were the proportions of substitutions as a function of nt position within codons. The majority of substitutions within Clade D were silent. Nonsynonymous substitutions mostly occurred within a region of the CP cistron known to be "hypervariable" among and within species of the Potyviridae. In contrast, synonymous substitutions were randomly distributed throughout the coding region. As over half of the polymorphic sites within Clade D were of allele size class 1, the isolates appear to be evolving independently, within the constraints of selection. An estimate of the rate of divergence suggests that diversity within the U. S. population arose in about a century, a time frame corresponding to establishment of wheat monoculture in the Great Plains.

Last Modified: 10/23/2014
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