Inoussa Drabo, Roger Gomgoudougou Zangre, Eric Yirenkyi Danquah, Kwadwo Ofori, John Witcombe and Charl Tom Hash Pearl millet, genome wide association study, simple sequence repeat marker, B-line population, association analysis 1-10 3 (1) 2019 January,2019 Downy mildew (DM) caused by S. graminicola is the most important disease of pearl millet. It constitutes a serious threat to single cross F1 hybrid. Marker-Traits Association analysis is a powerful method of detecting quantitative trait loci (QTL) underlying a trait. In this study, genetic variation for DM reaction was explored in 195 S2 progenies of two pearl millet cytoplasmic male sterile (CMS) maintainer populations. Progenies were genotyped with 30 known SSR markers and phenotyped in greenhouse by screening with three different isolates of S. graminicola from Burkina Faso. Large variation (0-100% disease incidence) was observed for downy mildew reaction within the population. Heritability ranged from 93 to 96% for the three screening. The population was structured in three subpopulations based on genotypic data. Different statistical models were tested to account for population structure and control false positive. With general linear model (GLM), eight markers-trait associations were detected. Using GLM plus Q-matrix six significant marker-trait associations were found. And when mixed linear model (MLM) + Q-matrix + kinship was applied, four significant marker-trait associations were detected among which, three were validation of QTLs and one was a newly found QTLs. The associated markers reported in this study provide resources for marker-assisted selection for downy mildew resistance in Burkina Faso.