AfricaRice and CIRAD elucidate the fungal species complex

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. This study contributes to highlighting the importance of the varied species coexisting in one area and how their interactions potentially threaten rice production in Sub-Saharan Africa (SSA). This will help in developing disease management plans and regulations, as each species may necessitate distinct diagnostic and control procedures.

Brown spot is widespread in rice-growing areas throughout the world. A severe outbreak of brown spot in Côte d’Ivoire is currently causing critical concern to rice farmers and the rice industry in the entire West African region. The disease is spread through seed and wind within and between rice fields. Brown spot infection reduces yield and seed quality, as seeds from infected plants may exhibit discoloration. 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 in lowland irrigated areas is a cause for concern. Moreover, the range of species linked to brown spot remains mostly unidentified, primarily due to the current lack of clarity in identifying this pathogen. Therefore, identifying the specific species responsible for occurrences would allow for the classification of lineages now present in SSA and specify the risk to rice production, thus aiding in improving disease management and phytosanitary regulation.

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

For 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 results of this study highlight the high occurrence of brown spot in rice in the six most important rice production areas in 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. 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.

This study revealed that the severe brown spot disease symptoms observed in Côte d'Ivoire farmer fields were caused by Bipolaris oryzae. Bipolaris oryzae was the sole species found in Bondoukou, San Pedro, and Agboville. In contrast, other surveyed locations had a mixture of more than one species, indicating a varied presence and species composition of brown spot pathogens among the main rice production zones in Côte d’Ivoire. Additional species identified include Curvularia sp., Exserohilum rostratum, C. geniculata, C. lunata, C. papendorfi, B. bicolor and B. maydis (Figure 2). The study highlights not only the high incidence of B. oryzae in rice production fields in Côte d'Ivoire, but also the differential occurrence and composition of other species for the first time, including at the field level. 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.