Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Feb 10;12(1):2241.
doi: 10.1038/s41598-022-06009-w.

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

Suresh Kumar  1 , Karishma Seem  2 , Santosh Kumar  3 , Trilochan Mohapatra  4
Affiliations

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

Suresh Kumar et al. Sci Rep. .

Erratum in

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.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
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
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
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
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
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
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
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
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
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.
See this image and copyright information in PMC

References

    1. Seck PA, Diagne A, Mohanty S, Wopereis MC. Crops that feed the world. Rice Food Security. 2012;4:7–24.
    1. Rao AN, Johnson DE, Sivaprasad B, Ladha JK, Mortimer AM. Weed management in direct-seeded rice. Adv. Agron. 2007;93:155–255.
    1. Bouman BAM. How much water does rice use. Rice Today. 2009;69:115–133.
    1. Tuong TP, Bouman BAM, Mortimer M. More rice, less water-integrated approaches for increasing water productivity in irrigated rice-based systems in Asia. Plant Prod. Sci. 2005;8:231–241.
    1. Sun L, et al. Implications of low sowing rate for hybrid rice varieties under dry direct-seeded rice system in Central China. Field Crop Res. 2015;175:87–95.

Publication types

Substances