Remarkably high internal transcribed spacer haplotype diversity of the fungal select agent Coniothyrium glycines discovered throughout its range in Sub-Saharan Africa

Authors: Koch Bach, Rachel; MURITHI, HARUN - Orise Fellow; Slocum, Clint; COYNE, DANNY - International Institute Of Tropical Agriculture (IITA); Clough, Steven

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2024
Publication Date: 4/19/2024
Citation: Koch Bach, R.A., Murithi, H.M., Slocum, C.R., Coyne, D., Clough, S.J. 2024. Remarkably high internal transcribed spacer haplotype diversity of the fungal select agent Coniothyrium glycines discovered throughout its range in Sub-Saharan Africa. Phytopathology. https://doi.org/10.1094/PHYTO-09-23-0315-KC.
DOI: https://doi.org/10.1094/PHYTO-09-23-0315-KC

Interpretive Summary: Coniothyrium glycines is a fungus that causes a disease of soybean called red leaf blotch in Africa. The disease can be so severe it reduces soybean yield by half. However, nothing is known about the genetic diversity of C. glycines, which limits our ability to assess the fungus' ability to overcome disease control practices. Therefore, we collected 108 C. glycines samples from six countries in eastern and southern Africa. A DNA fingerprint was made of each of the samples, and showed that there were 23 unique DNA groups. This research is important because it provides the first DNA fingerprints of this important foreign pathogen in its endemic range. It also shows regions of Africa that should be monitored because the prospects of rapid pathogen evolution are highest there. The results of this work will be used by plant pathologists and regulatory officials to assess the risks posed by this pathogen to US agriculture.

Technical Abstract: Red leaf blotch of soybean, caused by the fungus Coniothyrium glycines, is a foliar disease characterized by blotching, necrosis, and defoliation, which has only been reported from Africa. The species is listed as a Select Agent by the Federal Select Agent Program due to its potentially devastating impacts to soybean production should it spread to the U.S. Despite its potential import, very few isolates are available for study. Herein, we obtained 96 new C. glycines isolates from six soybean-producing countries throughout sub-Saharan Africa. Along with 12 previously collected ones, we sequenced each at the internal transcribed spacer (ITS) region. Between all isolates, we identified a total of 28 single nucleotide polymorphisms and 23 haplotypes. One hypothesis to explain the tremendous diversity uncovered at the ITS—which is generally conserved within a species—is that our current species concept of C. glycines is too broad, and that there may be multiple species that cause RLB. Zambia contained the highest haplotype diversity, a significant fraction of which remains unsampled. Most haplotypes were specific to a single country, except for two, which were found in Zambia and either neighboring Mozambique or Zimbabwe. This geographic specificity indicates that the ITS region may be useful in identifying source populations or routes of transmission should this pathogen spread beyond Africa. The observed geographic partitioning of this pathogen is likely the result of millions of years of replication on little-studied native hosts, given that soybean has only been cultivated in Africa since the early 1900s. Keywords: ascomycete; biogeography; evolution; foreign pathogens; fungal barcode; legumes