Unraveling the genetics underlying micronutrient signatures of diversity panel present in brown rice through genome-ionome linkages
E. A. Pasion 1,a,b   , G. Misra 1,c  , A. Kohli 1 , N. Sreenivasulu 1

Rice ( Oryza sativa ) is an important staple crop to address the Hidden Hunger problem. The brown rice is known to be nutritious due to elevated mineral composition. The genetics underlying brown rice ionome remains largely unexplored. Hence, we conducted a comprehensive study to dissect the genetic architecture of the brown rice ionome. We used genome-wide association studies (GWAS), gene set analysis, and targeted association analysis for 12 micronutrients in the brown rice grains. A diverse panel of 300 resequenced indica accessions, with more than 1.02 million single nucleotide polymorphisms, was used. We identified 109 candidate genes with 5-20% phenotypic variation  explained (PVE) for the 12 micronutrients with epistatic interactions for multiple micronutrients. Pooling all candidate genes per micronutrient exhibited PVE values ranging from 11% to almost 40%. The key donor lines with larger concentrations for most of the micronutrients possessed superior alleles, which were absent in the breeding lines. Through gene regulatory networks we identified enriched functional pathways for central regulators that were detected as key candidate genes through GWAS. This study provided important insights on the ionome variations in rice, on the genetic basis of the genome-ionome relationships, and on the molecular mechanisms underlying micronutrient signatures.

1   International Rice Research Institute, Los Baños, Laguna, 4030, Philippines; a   University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany;  b   Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; Present address:  c  King Abdullah University of Science and Technology, Thuwal, 23955 Thuwal, Makkah province, Saudi Arabia