Distribution, Pathogen Characterisation and Management of Brachiaria Grass Diseases in Rwanda

Abstract

The genus Brachiaria (syn. Urochroa) is ranked among the high-quality nutritious forages that originate from Africa. It remains a favourite forage for Sub-Saharan Africa due to different traits including high quantity and quality of its biomass. However, diseases were reported as one of the major constraints of Brachiaria production worldwide. The general objective of the study was to increase livestock productivity and improve income of farmers through sustainable management of diseases affecting Brachiaria grass in Rwanda. The study analysed the effect of growing seasons on distribution, disease incidence and severity of Brachiaria grass diseases in prevailing climatic conditions of Rwanda. Disease surveys were conducted in five districts during the dry season and the wet season in 2018 and 2019. Surveys showed that leaf spot, leaf rust and leaf blight diseases were largely distributed across the country. Incidence and severity of these diseases differed significantly (p ≤ 0.05) by districts, seasons, and district × season interactions, however, exception was non-significant effect of season and district × season interactions on leaf rust incidence in 2018. Furthermore, isolation and confirmation of causative relationship between Bipolaris secalis/ Phakopsora apoda and leaf spot/leaf rust were evaluated. Brachiaria leaf samples with disease symptoms were taken from farmers’ fields during the wet season of the year 2018. Fungi associated with major diseases were isolated and identified based on morphological, molecular characteristics and pathogenicity tests. Molecular identification confirmed the results of morphological identification and revealed Phakopsora apoda as the only fungus associated with leaf rust, and predominant association of fungi Epicoccum spp. and Nigrospora spp. with leaf blight while Bipolaris secalis and Fusarium spp. were associated with leaf spot symptoms. Morphological, molecular identification and symptoms reproduced on inoculated Brachiaria seedlings confirmed Bipolaris secalis and Phakopsora apoda as causal agents of leaf spot and leaf rust, respectively. Moreover, whole genome sequencing and genomic characterisation of Bipolaris secalis isolates from Brachiaria grass (Humidicola and Basilisk.) grown in Bugesera, Nyagatare, Rwamagana and Huye districts were performed. Illumina platform to give 151 bp reads in paired – end sequencing was used. The phylogenomic relationships of 12 isolates was also constructed and de novo assembly of one isolate (BS7) was performed. Eleven isolates were re-sequenced based on BS7 and they were mapped to the reference (BS7). Illumina sequencing results of BS7 produced the estimated genome size of 34,813,291 bp with an average GC content of 50.01%, organised into 108 contigs with the longest contig of 2,265,317 bp, the N50 of 1,032,497 bp and the L50 of 12. xviii The self-mapping of BS7 was 97.69%. The results obtained when mapping dataset of 11 isolates to BS7 indicated that the final mapping ratio was in the range of 80 – 95%, consisting of 28,950,637 – 15,611,348 total mapped reads. Finally, field experiments were established to evaluate management options against foliar diseases affecting Brachiaria grass in Rwanda. One study evaluated the reaction of nine improved Brachiaria cultivars (Marandu, MG 4, Piata, Xaraes, Basilisk, Humidicola, Cayman, Cobra and Mulato II) against leaf rust, leaf spot and leaf blight diseases and agronomic performances in two agro-ecological zones of Rwanda. Experiments were established under natural disease pressure for three distinct consecutive harvests in 2019 and 2020. Analysis of variance (ANOVA) was performed for data on disease and agronomic parameters of Brachiaria grass and Pearson correlation analysis was used to determine the relationships between agronomic traits and the extent of the diseases expressed as Area Under Disease Progress Curve (AUDPC). Basilisk, Marandu, MG4 and Xaraes exhibited moderately resistant to resistant response to all three diseases but Cayman and Cobra were the most susceptible to leaf rust. Cultivars differed for biomass production (p ≤ 0.05), as well as percentage of dry matter content. The highest biomass producers were Marandu, Mulato II and Xaraes but a high percentage of dry matter content was registered for Cayman and Cobra. The interaction of between site, cultivar and harvest was evident (p ≤ 0.05) for disease development and agronomic performances. Moreover, an experiment was established to evaluate different management options including mineral fertiliser application, fungicide application, manual weeding, no fungicide application, no weeding, and no fertiliser application for leaf rust using the susceptible cultivar (Brachiaria hybrid cv. Cayman) for four consecutive harvests. The results showed a significant reduction in the incidence and severity of leaf rust as a result of mancozeb and mineral fertiliser treatments, leading to simultaneous increases in plant growth, number of tillers and biomass production. The findings of the study provide baseline information on diseases affecting Brachiaria grass in Rwanda. Farmers can use resistant cultivars identified in this study and they can be explored for further use in breeding programmes. The information generated in the study is therefore, useful for sustainable management of diseases affecting Brachiaria grass and other crops in Rwanda and in the Sub-Saharan Africa region. Likewise, this is the first study to provide a whole genome sequence of Bipolaris secalis hence, the generated genome data under this study will contribute to the database improvement of Bipolaris secalis for future investigation and it will contribute to identification of novel sources of genetic resistance for improving disease management in Brachiaria grass and other new strategies for the control of this pathogen.