Comparative RNA-seq analysis reveals transposable element-mediated transcriptional reprogramming under phosphorus-starvation stress in rice (Oryza sativa L.)

Phosphorus (P) deficiency hinders crop productivity of 50 % of the rice grown in Asia, Africa, and South America. About 90 % of the phosphate in fertilizers applied to the crops gets fixed in the soil, reducing its availability to plants. This necessitates increased use of phosphatic fertilizers leading to higher cost of cultivation and environmental pollution. Although molecular mechanisms of P-deficiency tolerance in rice are being deciphered, the role of transposable elements (TEs) in transcriptional reprogramming under P-starvation/deficiency stress has not yet been reported. To investigate the role of Pup1 QTL in controlling TE-mediated reprogramming of gene expression, a pair of contrasting rice [Pusa-44 and its Near-Isogenic Line (NIL)-23] genotypes were grown hydroponically under control and stressed (0 ppm Pi) conditions. Comparative RNA-seq analysis of root and shoot tissues from 45-day-old plants of the rice genotypes revealed TE-mediated transcriptional reprogramming affecting biological processes and cellular components. Significantly up-regulated expression of several TEs under P-starvation stress, controlled by Pup1 QTL, particularly in shoots of NIL-23 indicates their crucial role in P homeostasis. Moreover, comparative physio-biochemical analyses confirmed the stress tolerance of NIL-23. Several biological processes including DNA replication/repair, metabolism, signaling, and phosphorylation were modulated through differential (mainly up-regulated) expression of TEs (controlled by Pup1 QTL) in shoots of NIL-23 under P-starvation. To the best of our knowledge, this is a pioneer study on the role of TEs in reprogramming biological processes/molecular functions/cellular components involved in P-use efficiency in rice under stress. The findings advance our understanding of the functions of Pup1 to improve the P-use efficiency/productivity of rice in P-deficient soils.