Genome-Wide Association Mapping of Rice Ionome Suggests a Role for NAS3 in Endosperm Zn Accumulation.

Zinc (Zn) is an essential micronutrient which plays a role in human growth and development, immune responses, enzyme function and other physiological processes. It is estimated that approximately 30% of the global human population suffer dietary Zn deficiency, many of whom rely on rice or other staple foods to meet their daily calorific requirements. Biofortification of these crops represents an effective approach to increasing their nutritional content and subsequently improving human health outcomes. It is likely that rice encompasses sufficient natural genetic variability to increase Zn and achieve these benefits through traditional plant breeding.

The PRAY Indica diversity panel, consisting of 300 genotypes, was developed at IRRI for the GRiSP Global Rice Phenotyping Network (http://ricephenonetwork.irri.org) and grown for four seasons across two years in the Philippines. Grain was harvested at maturity and ionomic analysis performed by ICP-MS, quantifying 18 elements. A large proportion (229 individuals) of the panel was genotyped on the High Density Rice Array (HDRA) at up to 700,000 positions.

Association mapping identified several QTLs for grain Zn, the most significant (p<1x10^-6) and stable of which is located on chromosome 7. Candidate gene analysis revealed the presence of the NAS3 gene within this QTL, whose product synthesises the metal chelator, nicotianamine (NA). Previous studies have isolated NA-Zn complexes in the rice phloem, implicating NA in long distance micronutrient transport. This suggests a model for the effect of NAS3 on rice grain Zn phenotype.