The genetic diversity of cultivated rice in farmers’ fields remains understudied in West Africa despite the importance of rice for food security in this region. In this study, we genotyped rice samples from Burkina Faso using the C6AIR SNP (Single Nucleotide Polymorphism) array (IRRI), including 27 registered cultivars and 50 rice samples collected in rice fields from three geographical zones in western Burkina Faso. Most of the registered cultivars clustered with the indica genetic group, except seven assigned to japonica and one admix. All but one of the rice samples from farmers’ fields belonged to the indica group. The other field sample, which unexpectedly clustered with the Aus genetic group, originated from a rainfed lowland site known to differ in terms of agronomic practices, and which revealed to be highly differentiated from the five other sites. Apart from this peculiar site, the rice grown in irrigated areas did not differ from rice sampled in rainfed lowlands. Finally, obtained genetic data confirmed the high frequency of one cultivar, in congruence with farmers’ interviews. We argue on the importance to document and preserve the high agro-biodiversity observed in rice from Burkina Faso as a prerequisite to face the current challenges of growing rice demand and global change.

Bacterial Leaf Blight of rice (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat for food security in many rice growing countries including Burkina Faso, where the disease was first reported in the 1980’s. In line with the intensification of rice cultivation in West-Africa, BLB incidence has been rising for the last 15 years. West-African strains of Xoo differ from their Asian counterparts as they (i) are genetically distant, (ii) belong to new races and, (iii) contain reduced repertoires of Transcription Activator Like (TAL) effector genes. In order to investigate the evolutionary dynamics of Xoo populations in Burkina Faso, 177 strains were collected from 2003 to 2018 in three regions where BLB is occurring. Multilocus VNTR Analysis (MLVA-14) targeting 10 polymorphic loci discriminated 24 haplotypes and showed that Xoo populations were structured according to their geographical localization and year of collection. Considering their major role in Xoo pathogenicity, we assessed the TAL effector repertoires of the 177 strains upon RFLP-based profiling. Surprisingly, an important diversity was revealed with up to eight different RFLP patterns. Finally, comparing neutral vs. tal effector gene diversity allowed to suggest scenarios underlying the evolutionary dynamics of Xoo populations in Burkina Faso, which is key to rationally guide the deployment of durably resistant rice varieties against BLB in the country.

Cassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv . manihotis ( Xpm), is one of the most important diseases threatening cassava and has recently been reported in Burkina Faso. Better management of CBB calls for the combined use of genetically resistant varieties and appropriate cultural practices. The objectives of this study were to evaluate the potential role of weed plants present in cassava fields as inoculum reservoirs for CBB. An inventory of weeds growing in eight cassava fields at four locations in Burkina Faso, and the cultivation of soil samples from the same eight fields, indicated the existence of 27 different species, reaching 28.32 plants per square meter. Field characterization led to the identification of seven species of weeds displaying symptoms reminiscent of Xpm infection, but no Xpm could be isolated from or detected in those plants. Artificial inoculations with Xpm resulted in 21 species producing symptoms of necrosis around the inoculation points. The presence of Xpm in the leaves of all these weed species was confirmed by re-isolation of the pathogen 2 weeks after inoculation. Thus, weeds that can harbor Xpm were prevalent in the cassava fields we studied, but their role as potential sources of Xpm inoculum for CBB epidemics remains to be demonstrated. [ ] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .