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Loci, genes, and mechanisms associated with tolerance to ferrous iron toxicity in rice (Oryza sativa L.)

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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.

Abstract

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.

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Acknowledgments

This study was financially supported by the fiat panis Foundation and Deutsche Forschungsgemeinschaft (DFG, Project ID FR2952-1/1). The authors also wish to thank IRRI for providing seeds and the members of the GRiSP Global Rice Phenotyping Network for sharing experiences in phenotyping and association mapping. We highly appreciate the contributions of many volunteers during the plant phenotyping.

Conflict of interest

The authors declare that they have no conflict of interest.

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    Authors and Affiliations

    1. Institute of Crop Science and Resource Conservation (INRES) - Plant Nutrition, University of Bonn, Karlrobert-Kreiten Straße 13, Bonn, 53115, Germany

      Elsa Matthus, Lin-Bo Wu, Yoshiaki Ueda, Stefanie Höller, Mathias Becker & Michael Frei

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    1. Elsa Matthus
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    2. Lin-Bo Wu
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    3. Yoshiaki Ueda
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    4. Stefanie Höller
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    6. Michael Frei
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    Correspondence to Michael Frei.

    Additional information

    Communicated by M. Wissuwa.

    E. Matthus and L.B. Wu contributed equally to the work.

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    Matthus, E., Wu, LB., Ueda, Y. et al. Loci, genes, and mechanisms associated with tolerance to ferrous iron toxicity in rice (Oryza sativa L.). Theor Appl Genet 128, 2085–2098 (2015). https://doi.org/10.1007/s00122-015-2569-y

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