Genetic Analysis of Agronomic Traits and Grain Iron and Zinc Concentrations in a Doubled Haploid Population of Rice (Oryza sativa L.)

Abstract

The development of micronutrient dense rice varieties with good agronomic traits is one of the sustainable and cost-effective approaches for reducing malnutrition. Identification of QTLs for high grain Fe and Zn, yield and yield components helps in precise and faster development of high Fe and Zn rice. We carried out a three-season evaluation using IR05F102 x IR69428 derived doubled-haploid population at IRRI. Inclusive composite interval mapping was carried out using SNP markers and Best Linear Unbiased Estimates of the phenotypic traits. A total of 23 QTLs were identified for eight agronomic traits and grain Fe and Zn concentration that explained 7.2 to 22.0% PV. A QTL by environment interaction analysis confirmed the stability of nine QTLs, including two QTLs for Zn on chromosomes 5 and 12. One epistatic interaction for plant height was significant with 28.4% PVE. Moreover, five QTLs were identified for Fe and Zn that harbor several candidate genes, e.g. OsZIP6 on QTL qZn_5.1. A number of QTLs were associated with a combination of greater yield and increased grain Zn levels. These results are useful for development of new rice varieties with good agronomic traits and high grain Zn using MAS, and identification of genetic resources with the novel QTLs for grain Zn.

Figure 1

Correlations among agronomic traits and grain Fe and Zn concentrations in DH population. *Indicates significance at p ≤ 0.05. **Indicates significance at p ≤ 0.01. ***Indicates significance at p ≤ 0.001. †DF: days to flowering (days); PH: plant height (cm); NT: number of tillers; NP: number of panicles; YLD: yield (kgha⁻¹); TGW: thousand grain weight (g); GL: grain length (mm); GW: grain width (mm); Fe: Iron (ppm); and Zn: Zinc (ppm).

Figure 2

Principal component analysis in DH population using the two PC with highest proportion of variance. Numbers inside the box correspond to DH lines.

Figure 3

QTLs identified for agronomic traits and grain micronutrient concentrations in DH population. †Blue font: QTLs for agronomic traits; red font: QTLs for grain element concentrations.

Figure 4

QTL by Environment Mapping: Chromosome locations of QTLs identified in the DH population.

Figure 5

The haplotypes of the major effect QTLs for grain Zn, qZn_5.1 (A) and qZn_12.1 (B), and their effect on Zn phenotype in different environments. Blue and orange color indicates different haplotypes within the QTLs, n indicates the number of DH lines with different haplotypes.