Abstract
Mali, rice production is affected by diseases caused by phytopathogenic bacteria Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) responsible respectively for bacterial leaf blight (BLB) and bacterial leaf streak (BLS). Varietal resistance is one of the most effective ways to control these diseases under the different agro-ecological conditions of rice cultivation. Characterization of the diversity of X. oryzae strains as well as the identification of broad-spectrum resistance sources (BSRs) are prerequisites for this approach. During the study, a collection of strains of X. oryzae obtained from different rice growing areas in Mali was characterized in order to examine the response of a panel of rice varieties to BLB and BLS. Thus, the identification of sources of resistance, QTLs (quantitative trait loci) and BSR genes associated with resistance were revealed. The screening of 12 isogenic rice lines (NILS, IRBBs) and their recurrent parent IR24 revealed the presence of 7 races, noted from A3 to A9 among the X. oryzae pv. oryzae strains. Most of the known resistance (R) genes were proved ineffective against several Xoo races found in Mali. The Xa3 resistance gene is the most effective of the 13 lines and recurrent parent tested in controlling BLB disease in Mali. However, its resistance is circumvented by Xoo strains belonging to race A9. The absence of a resistance gene to control the race A9 represents a significant challenge for rice growing in Mali. We tested the response of a panel of 29 varieties of rice for resistance to X. oryzae strains. The data showed that varieties Gigante and SK20-28 are resistant to all races and strains of Xoo and Xoc from Mali. Further, eight pathotypes within strains of Xoo (P1 to P8) and eleven within strains of Xoc (P1 to P11) were characterized. We observed a weak association between Xoo races and pathotypes, suggesting that the determinism underlying Gigante's resistance and SK20-28 to Xoo is different from the known R genes. Two genome-wide association studies (GWAS) were conducted. The first one exploited a MAGIC indica (Multiparent Advanced Generation Intercross) population to map the major QTLs conferring broad-spectrum resistance to Xoo and Xoc. A combination of GWAS analysis and interval mapping revealed at least three interesting QTLs (qXO-2-1, qXO-4-1 and qXO-11-2) conferring effective resistance against both pathovars. The second study focused on a panel of 258 indica rice lines sequenced from the "3000 genomes" (or 3K) project and selected according to their origins (89 countries).These lines were tested with Xoo and Xoc strains. The data revealed a dozen of QTLs including a QTL with a broad spectrum of resistance on chromosome 4. In total, 5 candidate genes associated with SNP, indel and resistance phenotype markers were identified in the region of chromosome 4 including Xa1 gene. Taken together, the results shed new light on the genetic determinism of bacterial resistance and should contribute significantly to a better control of Xanthomonas in Mali.Key words: Rice, bacterial leaf blight, bacterial leaf streak, Xanthomonas oryzae pv. oryzae, Xanthomonas oryzae pv. oryzicola, resistance.