Rice feeds more than half the world's population. But as farmers increasingly shift to direct-seeded rice farming (a method that saves water and labour) a problem is becoming harder to ignore: iron deficiency.
Iron is essential for plants. It helps them make chlorophyll, carry out photosynthesis, and generate energy. Yet in the oxygen-rich soils typical of direct-seeded rice systems, iron becomes chemically unavailable to plants. Young rice seedlings often respond by turning yellow, growing poorly, and producing lower yields.
A recent collaborative effort between NCBS and ICAR-NISST set out to understand why some rice varieties cope with iron deficiency better than others. By comparing the activity of thousands of genes in two contrasting rice varieties, the team uncovered a distinct survival strategy, and identified previously uncharacterised genes that may help rice thrive in iron-poor soils.
“We began by screening 116 rice varieties under iron-deficient conditions. Among them, two varieties stood out,” says Dr Ananya, the lead author of the study. “A variety called RA23 remained relatively healthy despite the lack of iron, while LalatMas showed severe symptoms of stress. These two varieties became the focus of the study,” she added.
Under iron deficiency, LalatMas developed pronounced yellowing of leaves, shorter shoots, weaker roots, and lower biomass. RA23, on the other hand, maintained greener leaves, stronger roots, and continued growing despite the nutrient shortage.
Using RNA sequencing, the team measured the activity of thousands of genes in the leaves of both varieties. Plants respond to environmental challenges by switching genes on and off, and these changes can reveal how they cope with stress.
Both varieties activated a common set of iron-deficiency genes. These included well-known genes involved in iron uptake, transport, and distribution throughout the plant. This means that both varieties recognised that they were starving for iron and attempted to solve the problem. Yet their responses differed in an important way.
LalatMas reacted dramatically. Hundreds of genes were switched on at high levels, particularly genes involved in iron acquisition. At first glance, this might seem like a sign of resilience. But the researchers suggest it reflects a plant struggling to compensate for severe stress.
RA23 followed a different strategy. Instead of launching an intense emergency response, it maintained a more stable pattern of gene activity. The variety appeared to manage its iron resources more efficiently, avoiding the need for an extensive stress response at molecular level
“Among the many genes responding to iron deficiency was a little-studied gene called OsFE97. Until now, virtually nothing was known about its role in rice. Computational analyses suggested that the gene belongs to an ancient family of proteins found across the plant kingdom and is predicted to function in chloroplasts, the structures responsible for photosynthesis,” says Dr Ananya.
Further analyses revealed that OsFE97 sits close to major iron-regulation genes within cellular interaction networks. The gene was consistently activated during iron deficiency, and follow-up experiments confirmed that this response was genuine. The findings suggest that OsFE97 could represent a previously uncharacterised component of the cellular response to iron deficiency.
“In general, RNA sequencing techniques provide quantitative estimates of spatio-termporal regulation of transcripts and comparative analysis of the same plant in different conditions or different tissues or, as in this case, two different varieties. These comparative analyses undoubtedly provide a translational edge, since it is possible to over-express such transcripts in the susceptible variety to provide better resistance against stress,” says Prof R Sowdhamini, the Principal Investigator of the study.
"The initial screening of 116 rice genotypes at CRRI, Cuttack, laid the foundation for this study by identifying the contrasting varieties RA23 and LalatMas. It is gratifying to see these valuable genetic resources now being explored at the molecular level to better understand iron deficiency tolerance in rice," says Dr Anandan Annamalai, the co-Principal Investigator of the study.
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