Comparative transciptomics of Indica Rice Grown by Different Planting Methods

Rice is a staple food crop for more than half of the global population . Cultivation of rice requires plenty of water for its continuous irrigation, particularly when grown by transplanting. There is lack of report on RNAseq analysis to elucidate the pathways involved in adaptation to DSR conditions. Therefore, an attempt was made to decipher the mechanisms associated with a better performance under DSR conditions using a pair of contorting rice cultivars grown by transplanting and direct-sowing. Nagina 22, a tall, deep rooted, drought and heat tolerant aus rice cultivar, is one of the suitable cultivars for DSR in the rainfed areas where intermittent water-deficit stress is common. In contrast, IR 64 is a dwarf, shallow rooted, high-yielding rice cultivar developed primarily for transplanted conditions. It is sensitive to abiotic stresses, and shows a considerable reduction in yield under water-deficit stress particularly on reproductive stage drought.Mature seeds of two rice cultivars Nagina 22 and IR 64 were used for raising plants. Before initiating the present study, both the rice cultivars were grown by direct-sowing and transplanting continuously for four subsequent generations. Finally, plants of both the rice cultivars were grown from the mature seeds by DSR and TPR for the present study. For TPR, seedlings were raised in nursery, followed by uprooting, and transplanting of 28 days old seedlings in pots filled with puddled soil. Whereas, for DSR mature seeds were directly sown in the pots filled with dry soil. The plants were grown in a net-house under natural conditions during Kharif season at the experimental farm of ICAR Indian Agricultural Research Institute, New Delhi, India. While TPR pots were frequently irrigated with tap water, DSR pots were provided with life-saving irrigation in absence of the seasonal rainfall. Leaf and root tissue samples were collected at flowering stage of plant in six replications using liquid nitrogen for molecular analyses. 16 cDNA libraries were prepared following mRNA enrichment, RNA fragmentation, first and second-strand cDNA synthesis, purification, sequencing adaptor ligation, and PCR amplification as per Tru Seq RNA Sample Preparation kit, Illumina. The libraries were sequenced by PE150 at Illumina platform.