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Background  Sorghum ( Sorghum bicolor  L. Moench) productivity is severely impeded by low phosphorus (P) and aluminum (Al) toxic soils in sub-Saharan Africa and especially West Africa (WA). Improving productivity of this staple crop under these harsh conditions is crucial to improve food security and farmer’s incomes in WA.    Results  This is the first study to examine the genetics underlying sorghum adaptation to phosphorus limitation in a wide range of WA growing conditions. A set of 187 diverse sorghum genotypes were grown in 29 –P and + P field experiments from 2006-2012 in three WA countries. Sorghum grain yield performance under –P and + P conditions was highly correlated (r = 0.85***). Significant genotype-by-phosphorus interaction was detected but with small magnitude compared to the genotype variance component. We observed high genetic diversity within our panel, with rapid linkage disequilibrium decay, confirming recent sequence based studies in sorghum. Using genome wide association mapping based on 220 934 SNPs we identified one genomic region on chromosome 3 that was highly associated to grain yield production. A major Al-tolerance gene in sorghum,  SbMATE , was collocated in this region and  SbMATE  specific SNPs showed very high associations to grain yield production, especially under –P conditions, explaining up to 16% of the genotypic variance.    Conclusion  The results suggest that  SbMATE  has a possible pleiotropic role in providing tolerance to two of the most serious abiotic stresses for sorghum in WA, Al toxicity and P deficiency. The identified SNPs can help accelerate breeding for increased sorghum productivity under unfavorable soil conditions and contribute to assuring food security in WA.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-014-0206-6) contains supplementary material, which is available to authorized users.

Two in one sweep: aluminum tolerance and grain yield in P-limited soils are associated to the same genomic region in West African Sorghum