Morphological and Molecular Characterization of Calonectria ilicicola Causing Black Root Rot on Soybean

Abstract

Black root rot symptoms observed on soybean (Glycine max L.) were investigated to identify the causal agent and characterize its morphological and molecular attributes. Field surveys in affected soybean-growing regions revealed chlorosis, stunted growth, root necrosis, and progressive plant wilting under high soil moisture conditions. Fungal isolates recovered from diseased root tissues produced slow-growing, white to buff colonies that later developed dark pigmentation on potato dextrose agar. Microscopic examination revealed cylindrical conidiophores bearing septate, cylindrical conidia consistent with Calonectria ilicicola. Pathogenicity tests conducted under controlled greenhouse conditions successfully reproduced black root rot symptoms on healthy soybean seedlings, confirming virulence and fulfilling Koch’s postulates. Molecular identification using ITS rDNA, β-tubulin, and histone H3 gene sequences confirmed the isolates as C. ilicicola, showing high sequence similarity with reference strains in global databases. Phylogenetic analysis placed all isolates within a distinct, well-supported clade corresponding to C. ilicicola, with limited intraspecific variation among regional populations. Observed minor nucleotide polymorphisms suggest possible adaptation to local soil and climatic conditions. Disease development was strongly associated with poorly drained soils and extended periods of high soil moisture, which favored pathogen survival and infection. The study highlights the increasing significance of C. ilicicola as a soil-borne pathogen in soybean production systems and emphasizes the need for early detection and integrated disease management strategies. Adoption of crop rotation, resistant cultivars, and improved soil drainage is recommended to reduce disease incidence and mitigate yield losses in soybean-growing regions.