First report of cotton leafroll dwarf virus in cotton plants affected by cotton leafroll dwarf disease in North Carolina

Authors: THIESSEN, LINDSEY - North Carolina State University; SCHAPPE, TYLER - North Carolina State University; ZACCARON, MARCIO - Auburn University; CONNER, KASSIE - Auburn University; KOEBERNICK, JENNY - Auburn University; JACOBSON, ALANA - Auburn University; HUSETH, ANDERS - North Carolina State University

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2020
Publication Date: 10/8/2020
Citation: Thiessen, L., Schappe, T., Zaccaron, M., Conner, K., Koebernick, J., Jacobson, A., Huseth, A. 2020. First report of cotton leafroll dwarf virus in cotton plants affected by cotton leafroll dwarf disease in North Carolina. Plant Disease. 104(12):3275. https://doi.org/10.1094/PDIS-02-20-0335-PDN.
DOI: https://doi.org/10.1094/PDIS-02-20-0335-PDN

Interpretive Summary: During the 2019 growing season, cotton plants in North Carolina were observed to have virus-like symptoms including leaf rugosity, leaf curling, and shortened upper internodes, consistent with cotton leafroll dwarf disease (CLRDD) associated with cotton leafroll dwarf virus (CLRDV). Sentinel plots planted on June 17, 2019, at the Sandhills Research Station in Moore County, NC, exhibited CLRDD symptoms, and disease incidence was estimated at 75% on a 0.1-ha field. Cotton aphids (Aphis gossypii), the reported vector of CLRDV, were detected on plants throughout the growing season. Samples (n = 24) were collected from sentinel plots on September 20, 2019, to test for CLRDV through PCR at Auburn University. Each sample represented five symptomatic plants collected from a single plot. RNA was extracted from the samples, cDNA was synthesized, and PCR was performed targeting the coat protein region of the genome. Seven CLRDV-positive samples were further amplified with two additional primer sets targeting other regions of the genome for confirmation. The amplicons were sequenced and analyzed with BLASTn for identification. The best matches for all sequences in this study were derived from CLRDV with 99.2 to 100% identity for all genome segments. From symptomatic samples (14), the isolated virus was confirmed as CLRDV in several cotton varieties. CLRDD is a newly named disease of cotton in the United States that was first reported in Alabama, Georgia, Mississippi, and Texas. Although the virus has been reported with variable impacts, losses can be extensive in some fields that are affected. North Carolina produced over one million bales of cotton in 2019, and given reported losses among fields with high disease incidence, CLRDV has the potential to significantly reduce cotton yield and quality for the state if it becomes widespread. This is the first report of CLRDV in NC.

Technical Abstract: During the 2019 growing season, cotton (Gossypium hirsutum L.) plants in North Carolina were observed to have virus-like symptoms including leaf rugosity, leaf curling, and shortened upper internodes, consistent with cotton leafroll dwarf disease (CLRDD) associated with cotton leafroll dwarf virus (CLRDV, family Luteoviridae, genus Polerovirus). Sentinel plots planted on June 17, 2019, at the Sandhills Research Station in Moore County, NC, exhibited CLRDD symptoms, and disease incidence was estimated at 75% on a 0.1-ha field. Cotton aphids (Aphis gossypii), the reported vector of CLRDV, were detected on plants throughout the growing season. Samples (n = 24) were collected from sentinel plots on September 20, 2019, to test for CLRDV through reverse transcription PCR. Each sample represented five symptomatic plants collected from a single plot. Total RNA was extracted from the petiole tissue of each sample using a Qiagen RNeasy Plant Mini kit, following the manufacturer’s recommendations. The cDNA was synthesized using a SuperScript IV first-strand synthesis system and amplified with CLRDV-specific PCR primers CLRDV3675F/Pol3982R targeting a 310-bp genome segment of ORF3-5. Seven CLRDV-positive samples were further amplified with two additional primer sets specifically designed to detect CLRDV: AL674F/AL1407R, targeting a 733-bp portion of the ORF0-ORF1, and CLPOF/CLPOR, amplifying an 880-bp fragment spanning the ORF0. Nucleotide BLAST searches showed that the best matches for all sequences in this study were derived from CLRDV with a range of pairwise identity of 99.2 to 100% for all genome segments. From symptomatic samples (n = 14), the isolated virus was confirmed as CLRDV in several cotton varieties, including Deltapine 1646 B2XF, Phytogen 480 W3FE, Stoneville 5471 GLTP, and Nextgen 5711 B3XF. CLRDD is a newly named disease of cotton in the United States that was first reported in Alabama, Georgia, Mississippi, and Texas. Although the virus has been reported with variable impacts, losses can be extensive in some fields that are affected. North Carolina produced over one million bales of cotton in 2019, and given reported losses among fields with high disease incidence, CLRDV has the potential to significantly reduce cotton yield and quality for the state if it becomes widespread.