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Background  Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity and greatly affect rice yield and quality. To improve rice production, understanding the genetic and molecular resistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is an effective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the genetic relationship between them in a genetically diverse population.    Results  A total of 29 and 31 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW), shoot water content (SWC) and shoot ion concentrations (SFe or SZn) were identified at seedling stage in Fe and Zn experiments, respectively. Five toxicity tolerance QTL ( qSdw3a ,  qSdw3b ,  qSdw12  and  qSFe5  /  qSZn5 ) were detected in the same genomic regions under the two stress conditions and 22 candidate genes for 10 important QTL regions were also determined by haplotype analyses.    Conclusion  Rice plants share partial genetic overlaps of Fe and Zn toxicity tolerance at seedling stage. Candidate genes putatively affecting Fe and Zn toxicity tolerance identified in this study provide valuable information for future functional characterization and improvement of rice tolerance to Fe and Zn toxicity by marker-assisted selection or designed QTL pyramiding.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4221-5) contains supplementary material, which is available to authorized users.

QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study