Differential Expression of Iron Deficiency Responsive Rice Genes under Low Phosphorus and Iron Toxicity Conditions and Association of OsIRO3 with Yield in Acidic Soils

With the hypothesis that iron (Fe) deficiency responsive genes may play a role in Fe toxicity conditions, we studied five such genes OsNAS1, OsNAS3, OsIRO2, OsIRO3 and OsYSL16 across six contrasting rice genotypes for expression under high Fe and low phosphorus (P) conditions, and sequence polymorphism. Genotypes Sahbhagi Dhan, Chakhao Poirieton and Shasharang were high yielders with no bronzing symptom visible under Fe toxic field conditions, and BAM350 and BAM811 were low yielders but did not show bronzing symptoms. Hydroponic screening revealed that the number of crown roots and root length can be traits for consideration for identifying Fe toxicity tolerance in rice genotypes. Fe contents in rice roots and shoots of a high-yielding genotype KMR3 showing leaf bronzing were significantly high. In response to 24 h high Fe stress, the expression levels of OsNAS3 were up-regulated in all genotypes except KMR3. In response to 48 h high Fe stress, the expression levels of OsNAS1 were 3-fold higher in tolerant Shasharang, whereas in KMR3, it was significantly down-regulated. Even in response to 7 d excess Fe stress, the transcript abundances of OsIRO2 and OsNAS3 were contrasting in genotypes Shasharang and KMR3. This suggested that the reported Fe deficiency genes had a role in Fe toxicity and that in genotype KMR3 under excess Fe stress, there was disruption of metal homeostasis. Under the 48 h low P conditions, OsIRO2 and OsYSL16 were significantly up-regulated in Fe tolerant genotype Shasharang and in low P tolerant genotype Chakhao Poirieton, respectively. In silico sequence analysis across 3 024 rice genotypes revealed polymorphism for 4 genes. Sequencing across OsIRO3 and OsNAS3 revealed nucleotide polymorphism between tolerant and susceptible genotypes for Fe toxicity. Non-synonymous single nucleotide polymorphisms and insertion/deletions (InDels) differing in tolerant and susceptible genotypes were identified. A marker targeting 25-bp InDel in OsIRO3, when run on a diverse panel of 43 rice genotypes and a biparental population, was associated with superior performance for yield under acidic lowland field conditions. This study highlights the potential of one of the vital genes involved in Fe homeostasis as a genic target for improving rice yield in acidic soils.