title: Loci, genes, and mechanisms associated with tolerance to ferrous iron toxicity in rice (Oryza sativa L.).
abstract: A genome-wide association study in rice yielded loci and candidate genes associated with tolerance to iron toxicity, and revealed biochemical mechanisms associated with tolerance in contrasting haplotypes. Iron toxicity is a major nutrient disorder affecting rice. Therefore, understanding the genetic and physiological mechanisms associated with iron toxicity tolerance is crucial in adaptive breeding and biofortification. We conducted a genome-wide association study (GWAS) by exposing a population of 329 accessions representing all subgroups of rice to ferrous iron stress (1000 ppm, 5 days). Expression patterns and sequence polymorphisms of candidate genes were investigated, and physiological hypotheses related to candidate loci were tested using a subset of contrasting haplotypes. Both iron including and excluding tolerant genotypes were observed, and shoot iron concentrations explained around 15.5 % of the variation in foliar symptom formation. GWAS for seven traits yielded 20 SNP markers exceeding a significance threshold of -log10 P > 4.0, which represented 18 distinct loci. One locus mapped for foliar symptom formation on chromosome 1 contained two putative glutathione-S-transferases, which were strongly expressed under iron stress and showed sequence polymorphisms in complete linkage disequilibrium with the most significant SNP. Contrasting haplotypes for this locus showed significant differences in dehydroascorbate reductase activity, which affected the plants' redox status under iron stress. We conclude that maintaining foliar redox homeostasis under iron stress represented an important tolerance mechanism associated with a locus identified through GWAS.
authors.affiliation: Institute of Crop Science and Resource Conservation (INRES) - Plant Nutrition, University of Bonn, Karlrobert-Kreiten Straße 13, Bonn, 53115, Germany.
authors.forename: Elsa
authors.initials: E
authors.lastname: Matthus
authors.affiliation: Institute of Crop Science and Resource Conservation (INRES) - Plant Nutrition, University of Bonn, Karlrobert-Kreiten Straße 13, Bonn, 53115, Germany.
authors.forename: Lin-Bo
authors.initials: LB
authors.lastname: Wu
authors.affiliation: Institute of Crop Science and Resource Conservation (INRES) - Plant Nutrition, University of Bonn, Karlrobert-Kreiten Straße 13, Bonn, 53115, Germany.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Ueda
authors.affiliation: Institute of Crop Science and Resource Conservation (INRES) - Plant Nutrition, University of Bonn, Karlrobert-Kreiten Straße 13, Bonn, 53115, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Höller
authors.affiliation: Institute of Crop Science and Resource Conservation (INRES) - Plant Nutrition, University of Bonn, Karlrobert-Kreiten Straße 13, Bonn, 53115, Germany.
authors.forename: Mathias
authors.initials: M
authors.lastname: Becker
authors.affiliation: Institute of Crop Science and Resource Conservation (INRES) - Plant Nutrition, University of Bonn, Karlrobert-Kreiten Straße 13, Bonn, 53115, Germany. mfrei@uni-bonn.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Frei
mesh_terms: D002874:Chromosome Mapping; D056726:Genetic Association Studies; D005838:Genotype; D005982:Glutathione Transferase / Q000235:genetics; D006239:Haplotypes; D007501:Iron / Q000633:toxicity*; D015810:Linkage Disequilibrium; D012275:Oryza / Q000201:enzymology / Q000235:genetics*; D010088:Oxidoreductases / Q000235:genetics; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
chemical_list: D007501:Iron; D010088:Oxidoreductases; C020666:glutathione dehydrogenase (ascorbate); D005982:Glutathione Transferase