Expression profiling of iron deficiency responsive microRNAs and gene targets in rice seedlings of Madhukar x Swarna recombinant inbred lines with contrasting levels of iron in seeds

To test if microRNAs are involved in iron (Fe) homeostasis in Oryza sativa. Recombinant inbred lines (RILs) of rice with contrasting levels of iron in seeds (high iron line HL, low iron line LL) and parent Swarna were grown in Fe sufficient (+Fe) and deficient (-Fe) environment. miRNAs whose target genes underlie the QTLs mapped for iron concentration (mapped in our previous study) were identified using bioinformatics. The expression analysis of these miRNAs and their targets along with few other miRNAs involved in nutrient homeostasis was done in root and shoot tissue. Real time PCR was used to study the relative expression of miRNAs and their target genes. Out of nine miRNAs used in this study, 7 miRNAs-miR156, 168, 172, 162, 167, 171, and 398 showed down-regulation under Fe deficiency in root and shoot of high iron line when compared with Fe sufficient condition. Further, most of the miRNAs showed down-regulation while their target genes showed up-regulation under Fe deficiency in roots of all three genotypes (HL, LL and Swarna) suggesting roots are more responsive to Fe deficiency. Important role of miRNAs in iron homeostasis was analyzed by comparing the expression of these miRNAs in HL, LL and Swarna under + Fe and -Fe. MicroRNAs showed differential expression in + Fe and -Fe environment. Further, their expression is more effectively regulated in root under Fe deficiency. This indicates that miRNAs might be playing regulatory roles in iron homeostasis in rice. This study suggests that Fe deficiency responsive miRNAs are involved in cross talk between other nutrients stress.