Genomic regions associated with arsenic accumulation and responses in rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a crucial staple grain, predominantly produced and consumed in Asia, playing a vital role in the food chain's mineral nutrient entry. However, its growth in major rice-growing regions is threatened by the toxic heavy metal arsenic (As). Arsenic accumulation in rice adversely affects plant, human, and livestock health, though its interaction and accumulation in rice are poorly understood. To mitigate this, we did a number of studies to determine rice germplasm that was As-tolerant and excluded based on several features at various development stages. Initially, fifty-three genotypes from the core Green Super Rice (GSR) breeding panel were evaluated for As tolerance and accumulation. A germination screening assessed germplasm's ability to germinate under varying As concentrations, while seedling-stage screening identified tolerant and excluder genotypes under hydroponics. A field experiment identified genotypes with lower As accumulation in grain. Genotypes differed in germination, tolerance, and As accumulation. Excluding As from the shot system increased tolerance in WTR1-BRRI dhan69, NPT-IR6855255-3-2, OM997, and GSR IR1-5-Y4-S1-Y1. Grain arsenic varied from 0.12 mg kg-1 in HuangHua-Zhan from China to 0.48 mg kg-1 in IRAT 109 from Brazil. Additionally, an early backcross breeding population consisting of 194 lines derived from a cross between WTR1 and Hao-an-nong was grown in hydroponics for 25 days, from the seventh day on, exposed to an environmentally relevant concentration of 10 ppm As. 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 6K 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. Twenty-five genes were considered as candidate gene nominees for As toxicity-related traits. These studies provide a valuable basis for future functional gene characterization and improvement of rice varieties for As-contaminated ecosystems. Overall, our findings will assist breeders with initial screening strategies and marker information to develop suitable varieties for As-contaminated ecosystems.