Adaptability of rice to different planting methods: A proof of cumulative transcriptional memory

Abstract

Plenty of water is required for cultivation of rice by transplanting that is challenging its cultivation, particularly on erratic rainfall or under drought. Direct-sown rice (DSR) is emerging as an alternative to transplanted rice (TPR) to save water. Performance of rice under DSR conditions varies greatly. While the molecular basis of adaptive plasticity of rice is subtle, tolerance to environmental stresses in crops is important for sustainable food production/security. The present study explores the molecular basis of adaptive/genetic plasticity in rice grown by different methods of planting, emphasising the concept of cumulative transcriptional memory. Our findings of comparative RNA-seq analysis highlighted differential gene expression with ∼6130 genes exclusively upregulated in the leaf of Nagina22 (N22) in contrast to only ∼3540 genes upregulated exclusively in the leaf of IR64 grown by dry/direct-sowing. In addition, our findings revealed that numerous genes showing upregulation in N22 were detected downregulated in IR64 that highlight distinct molecular strategies adopted by the rice cultivars. By activating diverse sets of genes coding for transcription factors, growth-regulating factors, translational machinery, nutrient-reservoirs, chromatin organization/epigenetic modifications, cell cycle/division, carbohydrate metabolism, etc., N22 adapts more effectively/efficiently to direct-sown conditions. Complementarity between these factors emerged to play important roles in adaptability of N22 to fluctuating environmental conditions. This helps adjust physio-biochemical responses of N22 to multiple abiotic/biotic stresses experienced under DSR conditions. Thus, our findings make a foundation for the development of molecular markers to facilitate varietal development of DSR for improved water productivity and sustainable agriculture.