Characterization of the mycoflora associated with cotton seeds (Gossypium hirsutum) and comparative evaluation of two methods for detecting infection by Colletotrichum species in Burkina Faso

Seeds are the primary agricultural input, and their sanitary quality directly influences crop establishment and yield.This study aimed to characterize the mycoflora associated with cotton seeds (Gossypium hirsutum) in Burkina Faso and to compare two detection methods for identifying infection by Colletotrichum species.A total of 132 seed samples collected from 11 provinces during the 2022/2023 and 2023/2024 agricultural seasons were analyzed using the blotting paper method.In addition, a seedling disease test was conducted on six selected samples to evaluate transmission from seeds to seedlings.The blotting paper method identified 37 fungal species distributed among 21 genera, with Fusarium oxysporum (100%), Aspergillus flavus (100%), Lasiodiplodia theobromae (99%), Phoma exigua (99%), and Rhizopus species (98%) as the most frequent species.Colletotrichum dematium was the most prevalent Colletotrichum spp., with a frequency of 29 %.The seedling disease test revealed 29 fungal species to 20 genera, with F. oxysporum (78%) and C. dematium (70%) as the most prevalent.The infection rate of Colletotrichum spp.detected by the seedling method was 20 to 60 times higher than that obtained using the blotting paper method.These results demonstrate that the seedling disease test is more effective for detecting Colletotrichum spp.and highlight the importance of method selection in cotton seed health evaluation.