Natural allelic variation in rice reveals root-centric transcriptome and haplotype networks underpinning arsenic tolerance for food safety

Arsenic contamination in paddy soils compromises rice yield, grain safety, and human health. Flooded conditions mobilize arsenic, which enters roots via silicon and phosphate transporters, causing spikelet sterility and straighthead disease. In this study, the emphasis is placed on differentiating tolerant and sensitive genotypes, where inclusion type genotypes are expected to display arsenic toxicity symptoms. We evaluated 266 diverse rice accessions under reproductive stage arsenite stress, revealing that indica and aus maintain higher yield than japonica accessions and reduced straighthead incidence, reflecting adaptive alleles. Genome wide association studies identified 263 arsenic stress specific loci, including eight SNPs linked to filled grain weight, highlighting regulatory networks that coordinate metabolic, structural, and developmental pathways rather than classical transporters. Transcriptome analyses revealed regulation of genes related to arsenite influx, thiol-based detoxification via glutathione and phytochelatins, redox homeostasis via Ferredoxin-NADP reductase, protein stabilization via molecular chaperones, and structural reinforcement by wall-associated kinases and glucosyltransferases. Small RNA mediated pathways (MEL1) protected reproductive tissues. Tolerant genotypes repressed non-essential growth while activating efficient stress networks. Integrating genetics, haplotypes, and transcriptomics identified allelic variants underpinning arsenic tolerance, detoxification, structural resilience, and reproductive protection. The results from our study provide SNPs for rapid screening and selection of arsenic tolerant genotypes, contributing to improved crop resilience and supporting food safety related breeding efforts.