First report of cotton leafroll dwarf virus in cotton fields of South Carolina

Authors: WANG, HEHE - Clemson University; GREENE, JEREMY - Clemson University; MUELLER, JOHN - Clemson University; CONNER, KASSIE - Auburn University; JACOBSON, ALANA - Auburn University

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/10/2020
Publication Date: 7/6/2020
Citation: Wang, H., Greene, J., Mueller, J., Conner, K., Jacobson, A. 2020. First report of cotton leafroll dwarf virus in cotton fields of South Carolina. Plant Disease. 104(9):2532. https://doi.org/10.1094/PDIS-03-20-0635-PDN.
DOI: https://doi.org/10.1094/PDIS-03-20-0635-PDN

Interpretive Summary: A survey was conducted for Cotton leafroll dwarf virus (CLRDV) in South Carolina after it was detected by Auburn University in sentinel plots in Blackville during 2019. CLRDV symptomatic plants were collected from 10 counties and disease incidence was assessed from each field. Disease incidence was estimated to range from 5 to 25% based on visual assessment of symptoms from 17 fields. Samples were transported to the virology lab at Clemson, RNA was extracted, cDNA was synthesized, and samples were processed through PCR targeting the coat protein of the virus. 79% of the samples tested positive for CLRDV, representing all 10 counties surveyed. Positive samples were further analyzed by amplifying three additional regions of the virus genome for confirmation. Representative amplicons (6) were sequenced and analyzed with BLASTn for identification. The sequences were identified as CLRDV and matched to isolates from AL. These sequences were deposited in GenBank. This is the first report of CLRDV infecting cotton in South Carolina.

Technical Abstract: Cotton leafroll dwarf virus (CLRDV, family Luteoviridae, genus Polerovirus) was recently reported in cotton (Gossypium hirsutum L.) plants affected by cotton leafroll dwarf disease (CLRDD) in the United States (Alabama, Georgia, Kansas, Mississippi, and Texas). From July to September 2019, a CLRDV survey was conducted in 10 counties (Aiken, Anderson, Barnwell, Calhoun, Chester, Clarendon, Darlington, Florence, Sumter, and York) representing the cotton-growing areas in South Carolina. The CLRDD-like symptoms observed in the fields included pronounced rugosity, curling, and distortion of leaves, reddening of the petioles and leaves, brittle leaves when handled, shortened internodes and stunting, and a reduction in boll set. The disease incidence across 17 fields was estimated to range from 5 to 25% based on visual assessment of symptoms. From each county, leaf/petiole samples from two to four cotton plants showing CLRDD-like symptoms were collected from one to two fields and tested in the lab for the presence of CLRDV by RT-PCR. RNA was extracted from each plant sample using Qiagen RNeasy Plant Mini kits 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 segment of ORF3 to ORF5. Positive and negative controls were included in each run, and PCR products were examined by gel electrophoresis. Twenty-six samples (78.8%) out of 33 tested produced the expected PCR bands. The positive samples were derived from cultivars DeltaPine 1646 B2XF and Phytogen 430 W3FE, and they spanned all 10 surveyed counties. All positive samples were further amplified with three additional primer pairs specifically designed to detect CLRDV: CLRDV-RdRpF2/CLRDV-RdRpR1, amplifying a 770-bp region of ORF1 to ORF2; AL674F/AL1407R, amplifying a 733-bp portion of ORF0 to ORF1; and CLPOF/CLPOR, amplifying a 783-bp fragment spanning ORF0. DNA bands of the expected sizes were obtained with each primer pair as examined by agarose gel electrophoresis. The PCR products for one Barnwell County sample (all four primer pairs) and the CLPOF/CLPOR-specific products from one sample each from Anderson and Sumter Counties were directly sequenced. After removing the primer sequences, the partial CLRDV sequences from the three samples were deposited in GenBank (MN651102 to MN651107). All six sequences showed very high nucleotide identities to corresponding sequences of CLRDV isolates from Alabama based on BLASTn analysis (98.9 to 100%; 98 to 100% query coverage). To our knowledge, this is the first report of CLRDV infecting cotton in South Carolina. CLRDD could negatively impact the cotton industry in South Carolina and other cotton-producing states due to its potential to reduce yield. Future research is needed to quantify the impact of the virus on cotton production in the United States and to identify strategies for minimizing the potential economic losses.