Low diversity of isolates of <i>Calonectria ilicicola</i> , the causal agent of red crown rot of soybean, detected across Illinois

Red crown rot (RCR) of soybean, caused by Calonectria ilicicola, is new to the Midwest region of the United States, first identified in 2018 in western Illinois, and later in the neighboring states of Kentucky (2021), Indiana (2022) and Missouri (2024). 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 isolates collected from 2018 to 2024 showed low diversity and are most likely not due to the spread of the isolate(s) previously found in the Southeastern U.S.