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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Publications at this Location » Publication #425964
Research Project: Identify and Characterize Resistance to Soybean Pathogens and Pests

Location: Soybean/maize Germplasm, Pathology, and Genetics Research

Title: Low diversity of isolates of Calonectria ilicicola, the causal agent of red crown rot of soybean, detected across Illinois

Author
item Clough, Steven
item Herman, Theresa
item McCoppin, Nancy
item Karki, Hari
item BRADLEY, CARL - University Of Kentucky
item CAMILETTI, BORIS - University Of Illinois Urbana-Champaign

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/5/2026
Publication Date: 1/7/2026
Citation: Clough, S.J., Herman, T.K., Mccoppin, N.K., Karki, H.S., Bradley, C., Camiletti, B.X. 2026. Low diversity of isolates of Calonectria ilicicola, the causal agent of red crown rot of soybean, detected across Illinois. Plant Disease. https://doi.org/10.1094/PDIS-07-25-1424-SC.
DOI: https://doi.org/10.1094/PDIS-07-25-1424-SC

Interpretive Summary: Red Crown Rot was first reported in Illinois in 2018, but its spread was not known. By sampling across the State of Illinois in 2022, 2023, and 2024, the disease was detected, and 79 isolates of the pathogen were verified from 44 fields across 17 counties. By amplifying 7 genomic regions and sequencing these regions, it was shown that the pathogen isolates collected across the state have very little genetic variation and indicate that the pathogen is not the same as the isolate(s) previously described in the Southeast US infecting soybean, peanut, blueberry and other crops.

Technical Abstract: Red crown rot (RCR) of soybean, caused by Calonectria ilicicola, is new to the US Midwest. It was first reported from a 2018 soybean field in western Illinois, and later from the neighboring states of Kentucky (2021 field), Indiana (2023 field) and Missouri (2024 field). Illinois has seen the most reported cases—various fields in 34 counties as of the end of the 2024 growing season. To determine the diversity and spread of C. ilicicola in Illinois, RCR-symptomatic soybean plants were collected across 44 fields from 18 Illinois counties and 79 C. ilicicola isolates were purified from lower stems. To examine the genetic diversity of these isolates, seven genetic regions were targeted for PCR amplicon sequence comparisons. The DNA sequences of the amplicons from act, cmdA, his3, tef1 and tub2 were identical to all. However, the ITS and IGS amplicons each revealed one single nucleotide polymorphism (SNP). Additionally, the PCR amplicon sequences were compared to amplicons from historical isolates collected between 1970 and 1988 in the Southeastern United States from peanut, blueberry, and soybean hosts. Sequence polymorphisms were found for all PCR amplicons (except cmdA) from the Southeastern U.S. isolates compared to the Illinois isolates, and these amplicon sequences were identical in all Southeastern U.S. isolates regardless of collection location or year. These results show that Illinois from 2018-2024 have low diversity and are most likely not due to the spread of the isolate(s) previously found in the Southeastern U.S.