Abstract
Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.
Highlights
Plants require at least 14 essential mineral nutrients and several beneficial elements for growth, development, and resistance to biotic and abiotic stresses (Marschner and Marschner, 2012)
By performing genome-wide association studies (GWAS) on the concentrations of 17 elements in different tissues of 295 indica and 156 japonica rice accessions grown under different locations, years, and field conditions, we identified 72 locus-element associations with high reproducibility across plant tissues, growth stages, and field conditions (Supplemental Data Sets 3 to 6)
GWAS of the rice ionome requires a number of limiting factors to be overcome, including the relatively small variation in plant elemental concentrations due to the homeostasis of essential mineral nutrients and the usually large environmental variation
Summary
Plants require at least 14 essential mineral nutrients and several beneficial elements for growth, development, and resistance to biotic and abiotic stresses (Marschner and Marschner, 2012). Increasing the use efficiencies of macronutrient fertilizers is critical for environmental quality and agricultural sustainability. Cultivated rice (Oryza sativa) is one of the most important crops, as it feeds about half of the world’s human population. For people who consume rice as a staple food, rice is a major dietary source of both essential micronutrients (e.g., iron [Fe] and zinc [Zn]) and toxic elements (e.g., cadmium [Cd] and arsenic [As]) (White and Broadley, 2009; Zhao et al, 2010; Clemens and Ma, 2016). Enhancing the accumulation of essential micronutrients and reducing the concentrations of potentially toxic elements in rice grain are of fundamental importance for food quality and human health
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