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 concomitantly improve beneficial micronutrients content and reduce accumulation of non-desirable metals in rice grain.
In this project, we aimed at identifying new QTLs governing rice grain ion content. For this, we measured ion content in brown and white grains produced by 184 sequenced genotypes from a Vietnamese rice collection grown in the field in Vietnam, and performed association genetics (GWAS).
Ion content was measured at the ionomic platform of the University of Nottingham using Inductively Coupled Plasma Mass Spectrometers (ICP-MS) following a similar procedure to Danku et al (2013). ICP-MS analyses detected the presence of Mg, P, S, K, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Rb, Sr, Mo and Cd while Li, B, Na, Ti, Cr, Se and Pb fell below the quantification limit. These latest elements were consequently excluded for further analysis. On the 16 remaining elements, BLUEs per genotypes for each ion in BR and WR were calculated using StatgenSTA package considering a resolvable incomplete block design for the analysis.
BLUEs were further used for association genetics on ion content in white and brown grains using a previously described genotypic dataset composed of 21,623 SNP markers (Phung et al, 2014).
In total, 27 significant associations were identified and delimited into QTL regions associated with macronutrients such as phosphate, potassium or calcium, micronutrients such as iron or zinc, or toxic heavy metals such as arsenic and cadmium.
The findings offer novel QTLs associated with grain ion content and candidate genes that are potentially valuable for breeding programs aiming at rice grain biofortification and reduction in toxic metal accumulation.
