Quantitative trait loci for grain mineral element accumulation in Vietnamese rice landraces

by Hien Linh Tran, Giang Thi Hoang, Nhung Thi Phuong Phung, Ham Huy Le, Alexandre Grondin, Pascal Gantet

Rice (Oryza sativa L.) is a staple food for half of the world’s population, and its biofortification is a key factor in fighting micronutrient malnutrition. However, harmful heavy metals tend to accumulate in rice grains due to soil and water contamination. Therefore, it is important to improve beneficial micronutrient contents and reduce the accumulation of undesirable metals in rice grain. To better characterize the genetic control of mineral accumulation in rice, we conducted association genetics on the ion contents of white and brown grains using a collection of 184 Vietnamese rice landraces. In total, 27 significant associations were identified and delimited into quantitative trait loci associated with macronutrients such as phosphorus, potassium or calcium; micronutrients such as iron or zinc; or toxic heavy metals such as arsenic and cadmium. Several genes related to ion homeostasis or ion transport were identified in the different quantitative trait loci. LOC_Os10g30610, present in qRAs10-1 associated with arsenic content in brown rice, encodes an ABC transporter (OsABCG25), which is involved in the silicon-induced formation of the Casparian strip in the rice exodermis and could act as a barrier restricting As diffusion within the root cortex. LOC_Os05g04330, present in qRP5-1 and associated with phosphorus content in brown rice, encodes a CHH methylation maintenance protein, and its expression is downregulated in roots in the presence of the phosphorus uptake 1 (Pup1), suggesting a role for epigenetics in the regulation of phosphorus uptake and accumulation in grain. These findings reveal novel quantitative trait loci associated with grain ion content and candidate genes that are potentially valuable for breeding programs aimed at rice grain biofortification and reducing toxic metal accumulation.