Confirmation report of Bacterial Leaf Streak disease of rice caused by Xanthomonas oryzae pv. oryzicola in Senegal.

Xanthomonas oryzae pv. X. oryzicola (Xoc), the causal agent of Bacterial Leaf Streak (BLS), is considered as one of the most important emerging pathogens of rice in Africa. This disease is estimated as responsible of 20 to 30% yield loss (Sileshi et Gebeyehu 2021) and has been characterized in several west African countries including Mali and Burkina Faso since 2003 and more recently in Ivory Coast (Wonni et al. 2014, Diallo et al. 2021). Presence of BLS symptoms in Senegal were reported by Trinh in 1980 but, to our knowledge, BLS occurrence has never been validated further and no strain of Xoc have ever been isolated from Senegalese rice fields. Xoc is transmitted by seeds which contribute to its spread through the rice trade (Sileshi et Gebeyehu 2021). To confirm Trinh's observations, we surveyed rice fields between 2014 and 2016 in eight different regions where rice is produced in Senegal. Typical disease symptoms characterized by yellow-brown to black translucent leaf streaks sometimes along with exudates, were detected in fields of several regions and collected. Leaf pieces were successively sanitized, rinsed in sterile water, and symptomatic fragments were ground using the Qiagen Tissue Lyser System (QIAGEN, Courtaboeuf, France). The leaf powder was diluted in 1.5 ml of sterile water and incubated for 30 minutes at room temperature. Ten µl of the suspension was streaked on semi-selective PSA medium and incubated at 28°C for 3 to 7 days. Characteristic round, convex, mucous, straw-yellow Xoc candidate colonies were purified from six individual leaf samples from three distinct sites in the northern Senegal River Valley. To confirm their identity, isolated strains were tested for pathogenicity and molecular characterization. All isolates were subjected to the multiplex PCR developed for the identification of X. oryzae pathovars (Lang et al., 2010) and revealed the same PCR profile (two amplicons of 324 and 691 base pairs) similar to that of the Xoc reference strain BLS256. Leaves of 5-week-old plants of O. sativa cv. Kitaake were infiltrated with a needleless syringe containing a bacterial suspension set at an optical density of 0.5. Upon seven days of incubation under greenhouse conditions (27 ± 1°C with a 12-hour photoperiod), all infiltrated spots (2 spots on 3 plants per isolate) developed water-soaked lesions similar to those caused by control strain BLS256, except when leaves were infiltrated with water. Symptomatic leaf tissues were ground and plated on PSA medium, resulting in colonies with typical Xanthomonas morphology that were diagnosed as Xoc by multiplex PCR typing, thus fulfilling Koch's postulate. At last, four of the isolates were subjected to gyrB sequencing upon PCR amplification using the universal primers XgyrB1F and XgyrB1R (Young et al., 2008). Analysis of 780bp partial gyrB sequences of strains S18-3-4, S23-1-12, S52-1-4 and S52-1-10 highlighted 100% identity with the gyrB sequence of strain BLS256 (Acc. No. CP003057). To our knowledge, this is the first report of BLS in Senegal which is supported by molecular characterization methods. This study validates the presence of BLS in Senegal and will serve as a basis for future efforts of rice breeding for locally adapted resistance. More studies are needed to clarify the spatial distribution and prevalence of BLS in Senegal as rice cultivation is expanding rapidly in the country.

GWAS unveils features between early- and late-flowering pearl millets.

BACKGROUND: Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an important role in the adaptation of pearl millet to climate variability. A better understanding of the genetic makeup of these variabilities would make it possible to breed pearl millet to suit regions with different climates. The aim of this study was to characterize the genetic basis of these phenotypic differences. RESULTS: We defined a core collection that captures most of the diversity of cultivated pearl millets in Senegal and includes 60 early-flowering Souna and 31 late-flowering Sanio morphotypes. Sixteen agro-morphological traits were evaluated in the panel in the 2016 and 2017 rainy seasons. Phenological and phenotypic traits related with yield, flowering time, and biomass helped differentiate early- and late-flowering morphotypes. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) markers with more than 5% of minor allele frequencies were discovered. Sparse non-negative matrix factorization (sNMF) analysis confirmed the genetic structure in two gene pools associated with differences in flowering time. Two chromosomal regions on linkage groups (LG 3) (~ 89.7 Mb) and (LG 6) (~ 68.1 Mb) differentiated two clusters among the early-flowering Souna. A genome-wide association study (GWAS) was used to link phenotypic variation to the SNPs, and 18 genes were linked to flowering time, plant height, tillering, and biomass (P-value < 2.3E-06). CONCLUSIONS: The diversity of early- and late-flowering pearl millet morphotypes in Senegal was captured using a heuristic approach. Key phenological and phenotypic traits, SNPs, and candidate genes underlying flowering time, tillering, biomass yield and plant height of pearl millet were identified. Chromosome rearrangements in LG3 and LG6 were inferred as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes will be of paramount importance in breeding for resilience to climatic variability.

New Genetic Insights into Pearl Millet Diversity As Revealed by Characterization of Early- and Late-Flowering Landraces from Senegal.

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food and a drought-tolerant cereal well adapted to Sub-Saharan Africa agro-ecosystems. An important diversity of pearl millet landraces has been widely conserved by farmers and therefore could help copping with climate changes and contribute to future food security. Hence, characterizing its genetic diversity and population structure can contribute to better assist breeding programs for a sustainable agricultural productivity enhancement. Toward this goal, a comprehensive panel of 404 accessions were used that correspond to 12 improved varieties, 306 early flowering and 86 late-flowering cultivated landraces from Senegal. Twelve highly polymorphic SSR markers were used to study diversity and population structure. Two genes, PgMADS11 and PgPHYC, were genotyped to assess their association to flowering phenotypic difference in landraces. Results indicate a large diversity and untapped potential of Senegalese pearl millet germplasm as well as a genetic differentiation between early- and late-flowering landraces. Further, a fine-scale genetic difference of PgPHYC and PgMADS11 (SNP and indel, respectively) and co-variation of their alleles with flowering time were found among landraces. These findings highlight new genetic insights of pearl millet useful to define heterotic populations for breeding, genomic association panel, or crosses for trait-specific mapping.