AfricaRice and CIRAD elucidate the Fungal Species Complex causing severe Brown Spot disease in Farmers' Fields

Picture 1: Didier Tharreau and Geoffrey Onaga in a rice field in Gagnoa (Côte d’Ivoire). (Credit: AfricaRice)

Under the CGIAR Plant Health Initiative, scientists from CIRAD and AfricaRice recently conducted the first extensive study on brown spot disease causing species on rice in Côte d’Ivoire. The study was aimed at highlighting the importance of the varied species coexisting in one area and how their interactions potentially threaten rice production in Sub-Saharan Africa (SSA). Brown spot is widespread in rice-growing areas throughout the world and is recognized for its detrimental impact on both the quality and quantity of rice crops, resulting in losses of up to 90%. This is particularly true when the leaf spotting phase reaches extensive proportions, as was the case during the Great Bengal Famine of 1942.

A severe outbreak of brown spot in Côte d’Ivoire is currently causing critical concerns to rice farmers, and the rice industry in the entire West African region. Contrary to previous beliefs that brown spot was only associated with infertile soils and had insignificant effect on rice production, the current surge in severe infections, even in lowland irrigated areas, is causing panic. The disease is spread through seed and wind within and between rice fields. Infected plants have reduced grain filling and may exhibit discoloration. The disease is problematic due to the fact that the pathogen lives in the seeds for most of its lifecycle and has the capacity to persist on infected rice stubble and straw for an extended period of time.  Brown spot is primarily caused by Bipolaris oryzae, but there are other unidentified fungal species that are associated with brown spots on rice leaves. The lack of clarity in identifying these species is the main reason for their unknown status. Consequently, the identification of the species complex responsible for brown spot occurrence would enable the classification of these species and their associated lineages in SSA. This would help in assessing the risk to rice production and improving disease management and phytosanitary regulation.

In this study, scientists isolated species from infected leaves collected from six locations in Côte d'Ivoire (see Figure 1), resulting in 105 isolates from areas severely affected by brown spot. All fungal spores found in the brown spot lesions were cultured and DNA was obtained from the mycelia for genotyping using Genotyping By Sequencing (GBS). GBS data were mapped on reference genomes of varied species of Bipolaris, Exserohilum and Curvularia. The scientists found varied species composition in the brown spot lesions observed in the six most important rice production areas in Côte d’Ivoire.

Figure 1: Sources of several species identified in brown spot infected leaves collected from Côte d'Ivoire.

Bipolaris oryzae was the predominant species in most regions, and was the sole species found in Bondoukou, San Pedro, and Agboville (Figure 2). In contrast, other surveyed locations had a mixture of more than one species, indicating a varied presence and species composition of the brown spot causing pathogens in the main rice production zones of Côte d’Ivoire. The varying incidence and species composition of the six species indicate the necessity for tailored management techniques potentially due to the unique requirements of each species. With these findings, scientists have been able to hypothesize one key element: the interaction among these species could potentially account for the increase in the intensity of brown spot observed in farmer’s fields, which warrants additional studies. “Special focus is needed on areas where multiple species are prevalent in the country,” explained Arsene Boka, scientist at Côte d’Ivoire National Agricultural Research Centre (CNRA).

Figure 2: The maximum likelihood tree illustrating the link among different brown spot producing species in Côte d’Ivoire. ND – not defined.