QTL for the iron and zinc contents of the milled grains of a doubled-haploid rice (Oryza sativa L.) population grown over two seasons

Identifying iron- and zinc-related quantitative trait loci (QTL) with consistent effects across environments and genetic backgrounds is necessary to develop rice varieties with high grain iron content (GIC) and grain zinc content (GZC). In this work, a doubled haploid population was developed through a cross between the Korean japonica cultivars Goami 2 and Hwaseonchal and phenotyped during the 2018 wet season (POP2018) and 2019 wet season (POP2019). The milled rice grains of POP2018 and POP2019 were used to identify GIC- and GZC-related QTL that was consistent between years. Digenic interactions and genes that affected GIC and GZC were also identified. Paired sample t test revealed that the GIC of POP2018 was not significantly different from that of POP2019 (t = 0.24, p =0.81), whereas the GZC of POP2018 was significantly different from that of POP2019 (t = − 4.35, p =0.00). Three moderate-effect (phenotypic variance [PVE] < 10.00%) GIC- and GZC-related QTL that were consistent between POP2018 and POP2019 were identified through inclusive composite interval mapping: qFe9, qFe11, and qZn7. All three QTL originated from the inferior parent Hwaseonchal. Epistasis analysis revealed that the GIC and GZC of POP2018 and POP2019 were affected by 79 significant digenic interactions with moderate and minor effects. By contrast, GZC was unaffected by digenic interactions. An interaction between loci on chromosomes 1 and 5 provided the highest contribution to the PVE (13.72%) for GIC. Candidate gene analysis revealed that 12 genes related to iron and zinc homeostasis or that require iron or zinc as ligands colocated with qFe9, qFe11, and qZn7. The QTL and epistatic regions identified here may be useful for developing rice varieties with high GIC and GZC in their milled grains.