Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional, and multinational efforts to develop germplasm and policy initiatives to boost production for a more food-secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under suboptimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae, represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multiple crop production constraints through integrated research and outreach programs. More specifically, we highlight recent progress in establishing international networks for rice blast disease surveillance, farmer engagement, monitoring pathogen virulence spectra, and the establishment of regionally based blast resistance breeding programs. To develop blast-resistant, high yielding rice varieties for Africa, we have established a breeding pipeline that utilizes real-time data of pathogen diversity and virulence spectra, to identify major and minor blast resistance genes for introgression into locally adapted rice cultivars. In addition, the project has developed a package to support sustainable rice production through regular stakeholder engagement, training of agricultural extension officers, and establishment of plant clinics.

Salinity may strongly influence the interaction between plant roots and surrounding soil, but this has been poorly studied for sodium sulfate (Na₂SO₄). The aim of this study was to investigate the effect of sodium chloride (NaCl) and Na₂SO₄ salinities on the soil chemical properties as well as rice physiological- and yield-related parameters of two contrasted cultivars (V14 (salt-sensitive) and Pokkali (salt-resistant)). Pot experiments were conducted using soil and electrolyte solutions, namely NaCl and Na₂SO₄, inducing two electrical conductivity levels (EC: 5 or 10 dS m⁻¹) of the soil solutions. The control treatment was water with salt-free tap water. Our results showed that soil pH increased under Na₂SO₄ salinity, while soil EC increased as the level of saline stress increased. Salinity induced an increase in Na⁺ concentrations on solid soil complex and in soil solution. NaCl reduced the stomatal density in salt-sensitive cultivar. The total protein contents in rice grain were higher in V14 than in Pokkali cultivar. Saline stress significantly affected all yield-related parameters and NaCl was more toxic than Na₂SO₄ for most of the studied parameters. Pokkali exhibited a higher tolerance to saline stress than V14, whatever the considered type of salt. It is concluded that different types of salts differently influence soil properties and plant responses and that those differences partly depend on the salt-resistance level of the considered cultivar.

Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a devastating disease of rice crops which can lead to yield losses ranging from 20 to 30% and as high as 50% (Mew 1987). BLB was first reported in Japan in 1884 and is now prevalent in most of the rice-producing countries in Asia. In Africa, Xoo was first reported in Mali and Cameroon (Buddenhagen et al., 1979) and later in many West African countries. Recently, BLB also appears to be spreading in East Africa with reports in Tanzania (Schepler-Luu et al., 2023) and in Madagascar (Raveloson et al., 2023). In June 2023, typical symptoms of BLB such as water-soaked areas and yellowish lesions along the leaf margins and tips were observed on rice plants in the coastal region of Kenya. Five rice fields of the Taita Taveta County with an incidence of 5-10% were surveyed, and 10-15 symptomatic leaf samples were collected in each field following a W pattern. Rice varieties were either Saro 5 or Arize 6444, two high productivity rice. 4-5cm long leaf fragments of 45 samples were next processed for bacterial isolation and surface disinfected, rinsed with sterile water, and ground individually in tubes with steel beads using a TissueLyser (Qiagen). Thirty-four round, pale yellow pigmented, and mucoid Xanthomonas-like colonies were obtained upon plating of 30 µl of the leaf powder resuspended in 1mL of sterile water on a semi-selective medium (peptone, 10 g/L; sucrose, 10 g/L; purified bacteriological agar, 16 g/L; glutamic acid, 1g/L; cycloheximide, 25 mg/L; cephalexin, 20 mg/L and kasugamycin, 10 mg/L) 72h after incubation at 28°C. To confirm that the isolates were Xoo, multiplex PCR established for the identification of X. oryzae pathovars was used (Lang et al. 2010). Thirty-two strains resulted in the amplification of two bands characteristic of the Xoo pattern. In addition, 6 of these strains (namely CIX5498, CIX5504, CIX5513, CIX5514, CIX5516 and CIX5539) were subjected to gyrB sequencing using the universal primers XgyrB1F and XgyrB1R (Young et al., 2008). The resulting partial 800 bp gyrB sequences of these 6 strains showed 100% identity (767/767 nt) with that of the PX099A Asian reference Xoo strain (accession CP000967.2). The pathogenicity of these 6 strains and the reference strain PX099A used as positive control was tested on 1-month-old Oryza sativa cv. Komboka plants (n=8 per treatment, 1 repetition). Rice leaves were inoculated by leaf clipping using sterile scissors dipped in the bacterial suspension at an optical density of 0.2. Three weeks after inoculation, plants exhibited typical BLB lesions for each of the six tested strains similarly to that of the positive control, whereas Mock-inoculated plants remained symptomless. Bacteria re-isolated from these diseased leaves yielded colonies that were confirmed as Xoo by multiplex PCR, fulfilling Koch's postulate. All strains isolated in this study are referenced in the CIX collection of the French National Research Institute for Sustainable Development in Montpellier. To our knowledge, this study represents the first molecular confirmation of the presence of BLB in Kenya and complement our knowledge of this important disease in East Africa. This work will serve as a basis for future rice breeding for BLB resistance efforts in Kenya. Further surveys are needed to clarify the spatial distribution and prevalence of BLB in other regions of Kenya and further analysis will be needed to understand the origin of the outbreak and to identify strategies to control BLB in Kenya.

Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of bacterial leaf streak (BLS) is one of the most prevalent rice pathogens in lowland ecologies of Asia and Africa. In Africa, BLS has been reported in several countries, including Nigeria, Senegal, Burkina Faso, Mali, and more recently in Burundi, Uganda and Madagascar (Poulin et al. 2015). BLS can survive in crop debris from season to season or on infected seed, and may be transmitted through irrigation water or on seed (Xie and Mew 1998). In September 2016, we conducted a reconnaissance survey in Ahero rice growing area, Kisumu, Kenya. We observed water-soaked translucent lesions and yellow-brown streak symptoms on three popular rice varieties grown in Kisumu: Pishori, BW96 and Komboka, at the vegetative stage when the plants were about 20 cm tall. The field exhibited 30 to 50% incidence, and severity on infected plants ranged from 20 to 60%, based on IRRI standard evaluation system 2013 (IRRI 2013). We collected six rice leaf samples infected with BLS, and bacteria were isolated, from surfaced sterilized (with 70% ethanol) symptomatic leaf discs, by streak-plating bacterial cells released in sterile water on nutrient agar (NA). Yellow-pigmented Xanthomonas-like positive colonies, following colony PCR, were multiplied by re-streaking on Peptone sucrose agar (PSA) medium (sucrose 10 g, peptone 10 g, bacto agar 16 g, distilled water 1,000 ml), supplemented with three antibiotics, actidione 50 mg liter–1, cephalexin 40 mg liter–1, and kasugamycin 20 mg liter–1. PCR was used to amplify 691 bp DNA fragment used for identification of Xoc (Lang et al. 2010). Xoc strain BLS256 from the Philippines was used as a positive control. The expected DNA fragment corresponding to DNA gyrase subunit B (gyrB) gene was obtained from all isolates upon PCR amplification using the primers XgyrB1-F and XgyrB1-R (Poulin et al., 2014). Negative controls (distilled water as the template) did not show any band. Isolated DNA fragments were submitted to Bioneer (www.bioneer.com) for sequencing. Sequence analysis by BLAST search in the GenBank revealed 99% identity to the sequences of gyrB gene of strains CFBP2286, RS105, L8, BXOR1, BLS279 and B8-12 among others. Two isolates were subjected to pathogenicity test on 4-week-old rice cultivars, IR24 and Pishori. Bacterial cultures grown overnight on PSA medium were centrifuged at 4000 rpm for 5 min, washed and resuspended in sterile water at a concentration of A600 = 0.5, and used for pathogenicity tests in the greenhouse using the 5-week-old rice plants. Rice leaves syringe-infiltrated with bacterial cells showed water-soaked lesions with prominent yellow exudates, typical of BLS symptoms. Control plants infiltrated with sterile water remained symptomless. On re-isolation, typical colonies with Xoc morphology were observed, thus fulfilling Koch's postulates. Partial nucleotide sequences (~670 bp) corresponding to gyrB gene from the two strains used for pathogenicity test (named KN_1 and KN_2) were submitted to GenBank (MF284713 and MF284714). The two isolates have also been deposited to Plant Pathology and Plant-Microbe Biology Section, Cornell University, USA. To our knowledge, this is the first report of Xoc in Kenya. Further work on pathogen collection is required to understand the genotypic and geographic distribution of BLS in Kenya.