RNA-seq analysis reveals the genes/pathways responsible for genetic plasticity of rice to varying environmental conditions on direct-sowing and transplanting

Abstract

Rice cultivation by transplanting requires plenty of water. It might become a challenging task in future to grow rice by transplanting due to the climatic change, water and labor scarcities. Direct-sown rice (DSR) is emerging as a resource-conserving and climate-smart alternative to transplanted rice (TPR). However, no specific variety has been bred for dry/direct-sown conditions. The present study was undertaken to decipher the molecular basis of genetic plasticity of rice under different planting methods. Comparative RNA-seq analysis revealed a number (6133) of genes exclusively up-regulated in Nagina-22 (N-22) leaf under DSR conditions, compared to that (3538) in IR64 leaf. Several genes up-regulated in N-22 were down-regulated in IR64. Genes for growth-regulation and nutrient-reservoir activities, transcription factors, translational machinery, carbohydrate metabolism, cell cycle/division, and chromatin organization/epigenetic modifications were considerably up-regulated in the leaf of N-22 under DSR conditions. Complementary effects of these factors in rendering genetic plasticity were confirmed by the agronomic/physiological performance of rice cultivar. Thus, growth-regulation/nutrient-reservoir activities, transcription factors, and translational machinery are important molecular factors responsible for the observed genetic plasticity/adaptability of Nagina-22 to different planting methods. This might help to develop molecular markers for DSR breeding, replacing TPR with DSR for better water-productivity, and minimizing greenhouse-gas emission necessary for negative emission agriculture.

Figure 1

Performance of rice under transplanted and direct-sown conditions. (A) The number of tillers produced by each plant of Nagina-22 and IR64 under transplanted and direct-sown conditions, (B) the number of panicles produced by each plant of Nagina-22 and IR64 under transplanted and direct-sown conditions.

Figure 2

Differentially expressed genes (DEGs) in rice cultivars on direct-sowing over transplanting (control). Leaf and root tissues were collected at the panicle initiation stage of the plant for transcriptome analysis.

Figure 3

Tissue-specific differential expression of genes on direct-sowing. (A) Leaf, and (B) Root. Change in expression (Up = up-regulation, or Dn = down-regulation) was calculated based on the expression level of the genes on direct sowing (treatment) over transplanting (control).

Figure 4

Gene ontology (GO) analysis of enriched biological processes under direct-sown [over transplanted (control)] conditions in the leaf of rice cultivars. (A) Over-represented GO terms in the leaves of Nagina 22, and (B) over-represented GO terms in the leaves of IR64 rice cultivar.

Figure 5

Gene ontology (GO) analysis of enriched molecular functions under direct-sown [over transplanted (control)] conditions in the leaf of rice cultivars. (A) Over-represented GO terms in the leaves of Nagina 22, and (B) over-represented GO terms in the leaves of IR 64 rice cultivar.

Figure 6

Heat map showing differential expression of some of the differentially expressed genes associated with nutrient reservoir activities under direct-sown conditions in the leaves and roots of rice cultivars.

Figure 7

Heat map showing differential expression of some of the differentially expressed genes for transcription factors under direct-sown conditions in the leaves and roots of rice cultivars.

Figure 8

RT-qPCR validation of five randomly selected differentially expressed genes. cDNA was prepared from the total RNA isolated from leaf and root tissues of Nagina 22 (N-22) and IR64 collected at the reproductive stage of plants grown by transplanting (control) or direct-sowing (treatment). Data represent the mean ± SD (n = 6).

Figure 9

Differentially enriched GO terms and the number of respective genes up-regulated in the leaves of (A) Nagina-22 (N-22) and (B) IR64 rice cultivars grown by the different methods of planting (transplanting, control; direct-sowing, treatment). For comparative evaluation of N-22 and IR64, some of the important/similar GO terms have been numbered (I–VIII) and/or encircled.