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.

Genetic factors underlying boron toxicity tolerance in rice: genome-wide association study and transcriptomic analysis

“…Association mapping for each trait included the determination of SNPs exceeding a significance value of −log 10 P >4.0 (an arbitrary threshold that had been previously applied by others, e.g. Ueda et al , 2015; Wissuwa et al , 2015), analyses of LD blocks surrounding each highly significant (−log 10 P >4.0) SNP, and curation of a list of candidate genes contained within these blocks (Supplementary Table S3). Out of 26 863 markers included in this analysis, we identified 18 SNP markers that satisfied the established threshold (Supplementary Table S2).…”

“…Manhattan plots were displayed, and the threshold for significantly associated markers was set to P <0.0001 (i.e. –log 10 P >4.0), as previously suggested (Zhao et al , 2011; Matthus et al , 2015; Ueda et al , 2015). …”

“…For example, Zhao et al (2011) mapped 44 100 SNPs (single nucleotide polymorphisms) across 413 diverse accessions of rice and phenotyped those for 34 traits, including straighthead susceptibility, blast resistance, flowering time in different locations, and many yield-related and quality traits. These genomic data were further used in studies targeting phosphorus utilization efficiency (Wissuwa et al , 2015), seed dormancy (Magwa et al , 2016), aluminium tolerance (Famoso et al , 2011), iron toxicity (Matthus et al , 2015), ozone tolerance (Ueda et al , 2015), nematode resistance (Dimkpa et al , 2016), and now, in the present study, tolerance to B toxicity.…”

Regulation of Phytosiderophore Release and Antioxidant Defense in Roots Driven by Shoot-Based Auxin Signaling Confers Tolerance to Excess Iron in Wheat

“…The continuation of protein level under higher Fe concentration is possibly due to the induction of stress proteins, which may comprise various antioxidant enzymes and metabolites (Lamhamdi et al, 2010). Baruah et al (2001) also reported that rice plants tolerant to higher Fe showed consistent total soluble protein in shoots. EL, a common damage in plasma membrane due to metal toxicity, was significantly changed in BR 27 plants under excess Fe.…”

Evaluation of rice wild relatives as a source of traits for adaptation to iron toxicity and enhanced grain quality

“…They consisted of 20 wild species of the Oryza genus with different countries of origin, one cross of O. glaberrima and O. barthii and two O. sativa varieties, for which crosses with wild relatives have been made (IRRI 154 and Curinga). In addition, 15 accessions of cultivated rice species (O. sativa and one O. glaberrima) that had previously been screened in Fe toxicity experiments [26,32,33] were added from the seed stocks of the Institute of Crop Science and Resource Conservation (INRES).…”