Identification of qAs1—A Minor-Effect QTL Controlling Grain Arsenic Accumulation in Rice Using Near-Isogenic Lines Under High-Arsenic and Flooded Conditions

Arsenic (As) contamination in rice poses a serious risk to food safety and human health. Genetic dissection of As-related quantitative trait loci (QTLs) provides a sustainable strategy for breeding low-As cultivars. In this study, we aimed to improve the detection of minor-effect QTLs for total As accumulation by optimizing both environmental and genetic factors. A recombinant inbred line (RIL) population derived from the cross between Yuzhenxiang (YZX, indica) and YBK (Javanica) was used for initial QTL mapping, and a single locus, qAs1, was identified on chromosome1. To enhance As uptake and phenotypic differentiation, we conducted QTL validation and fine mapping under high-As and continuously flooded conditions using near-isogenic lines (NILs) to minimize background genetic interference. The effect of qAs1 was consistently validated across generations, and the locus was refined to a 159.5 kb genomic interval. Transcriptome analysis revealed three differentially expressed genes (LOC_Os01g52110, LOC_Os01g52214, and LOC_Os01g52260) involved in redox regulation and detoxification. These findings demonstrate the effectiveness of NIL-based fine mapping under optimized environmental conditions and provide promising targets for the genetic improvement of low-As rice cultivars.