GENETIC IMPROVEMENT OF FRUIT CROPS THROUGH FUNCTIONAL GENOMICS AND BREEDING
Location: Appalachian Fruit Research Laboratory: Innovative Fruit Production, Improvement and Protection
Title: Characterization of the partial RNA1 and RNA2 3' untranslated region of tomato ringspot virus isolates from North America
Submitted to: Canadian Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 21, 2010
Publication Date: February 24, 2011
Citation: Li, R., Mock, R.G., Fuchs, M., Halbrendt, J., Howell, B., Liu, Z. 2011. Molecular characterization of the partial RNA1 and RNA2 3' untranslated region of tomato ringspot virus isolates from North America. Canadian Journal of Plant Pathology. DOI: 10.1080/07060661.2011.536648.
Interpretive Summary: Tomato ringspot virus can infect a wide range of host species including apple, peach, cherry, plum, blueberry, and raspberry, and is a major disease for fruit production. This virus is endemic to both the west and east coast of the U.S. Recently, we analyzed and sequenced 18 ToRSV isolates from various locations in the U.S and identified a highly conserved region in ToRSV genome. A new and sensitive detection method based on the result of this study has been developed and tested, and can be used for practical detection and survey of ToRSV virus in orchards.
The 3' non-translated regions (NTRs) of RNA1 and RNA2 of Tomato ringspot virus (ToRSV) are long and virtually identical. In this study, sequences containing most of the 3’ NTRs (1168-1265 bp) were determined from 18 ToRSV isolates collected from fruit trees, small fruits, and grapevines in North America. In pairs, comparisons of these sequences with those of two ToRSV isolates available from GenBank showed that the majority of these isolates had identities of 95.1-100% at this region. Most genetic variations occurred as point mutations and 1-bp insertions and/or deletions. Phylogenetic analysis showed that 17 of the 20 isolates grouped together in a major cluster, three isolates grouped into two other distinct clusters, and genetic divergences among three clusters ranged from 11.8% to 23.8%. No correlation was found between the 3'-NTR sequences and symptom expressions, natural hosts, or geographic origins. RT-PCR using primers designed within the highly conserved 3'-NTR regions was more sensitive than the previously reported 'U1/D1' primer. It was the only primer able to detect all 18 ToRSV isolates plus two field samples in our tests, which can serve as a practical tool for sensitive detection and survey of a wide spectrum of ToRSV isolates, as well as their infection and disease development in orchards.