Abstract
Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn2+ leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn2+, 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2.4 to 17.4 mg g-1. The tropical japonica subpopulation was more sensitive to Mn toxicity than other subpopulations. Leaf damage symptoms were significantly correlated with Mn uptake into shoots. Association mapping was conducted for seven traits using 416741 single nucleotide polymorphism (SNP) markers using a mixed linear model, and detected six significant associations for the traits shoot manganese concentration and relative shoot length. Candidate regions contained genes coding for a heavy metal transporter, peroxidase precursor and Mn2+ ion binding proteins. The significant marker SNP-2.22465867 caused an amino acid change in a gene (LOC_Os02g37170) with unknown function. This study demonstrated significant natural variation in rice for Mn toxicity tolerance and the possibility of using GWAS to unravel genetic factors responsible for such complex traits.
Highlights
Manganese (Mn) is an essential plant micro-nutrient participating in several metabolic pathways, including photosynthesis [1], and as a cofactor of several enzymes [2]
We evaluated seven traits including growth parameters, visual leaf damage symptoms and Mn concentration in shoots of plants grown under toxic Mn conditions
For plants grown under optimal Mn supply, all the phenotypes were scored except for shoot Mn concentration
Summary
Manganese (Mn) is an essential plant micro-nutrient participating in several metabolic pathways, including photosynthesis [1], and as a cofactor of several enzymes [2]. When accumulated in higher quantity, Mn can have phytotoxic effects [3]. High concentrations of Mn in the cell apoplast have been linked to the accumulation of phenoxy radicals and oxidized Mn3+, which are strong oxidizers of macromolecules such as lipids and proteins [4]. Mn toxicity results in cell death and produces necrotic spots on leaves. Typical symptoms of Mn toxicity in rice are dark brown spots on crinkled lower leaves, chlorosis of young leaves and reduced growth [5]
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