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Background  Arsenic (As) is an unwanted toxic mineral that threatens the major rice-growing regions in the world, especially in South Asia. Rice production in Bangladesh and India depends on As-contaminated groundwater sources for irrigating paddy fields, resulting in elevated amounts of As in the topsoil. Arsenic accumulating in rice plants has a significant negative effect on human and animal health. Here, we present a quantitative trait locus (QTL) mapping study to identify candidate genes conferring As toxicity tolerance and accumulation in rice ( Oryza sativa  L . ) seedlings. An early backcross breeding population consisting of 194 lines derived from a cross between WTR1 ( indica)  and Hao-an-nong  (japonica ) was grown in hydroponics for 25 days, from the seventh day exposed to an environmentally relevant concentration of 10 ppm As.    Results  Arsenic toxicity leads to significantly negative plant responses, including reduced biomass, stunted plant growth, reduced leaf chlorophyll content, and increased shoot As concentration ranging from 9 to 20 mg kg − 1 . Marker-trait association was determined for seven As-related traits using 704 single nucleotide polymorphism (SNP) markers generated from a 6 K SNP-array. One QTL was mapped on chromosome 1 for relative chlorophyll content, two QTLs for As content in roots were mapped on chromosome 8, and six QTLs for As content in shoots were mapped on chromosomes 2, 5, 6, and 9. Using the whole-genome sequence of the parents, we narrowed down the number of candidate genes associated with the QTL intervals based on the existence of a non-synonymous mutation in genes between the parental lines. Also, by using publicly available gene expression profiles for As stress, we further narrowed down the number of candidate genes in the QTL intervals by comparing the expression profiles of genes under As stress and control conditions. Twenty-five genes showing transcription regulation were considered as candidate gene nominees for As toxicity-related traits.    Conclusions  Our study provides insight into the genetic basis of As tolerance and uptake in the early seedling stage of rice. Comparing our findings with the previously reported QTLs for As toxicity stress in rice, we identified some novel and co-localized QTLs associated with As stress. Also, the mapped QTLs harbor gene models of known function associated with stress responses, metal homeostasis, and transporter activity in rice. Overall, our findings will assist breeders with initial marker information to develop suitable varieties for As-contaminated ecosystems.    Electronic supplementary material  The online version of this article (10.1186/s12284-019-0321-y) contains supplementary material, which is available to authorized users.

Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.)