Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice

Narendra Sharma; Bhumika Madan; M Suhail Khan; Kuljeet S Sandhu; Nandula Raghuram

doi:10.3389/fpls.2023.1135675

Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice

Front Plant Sci. 2023 Jun 7:14:1135675. doi: 10.3389/fpls.2023.1135675. eCollection 2023.

Authors

Narendra Sharma¹, Bhumika Madan¹, M Suhail Khan¹, Kuljeet S Sandhu², Nandula Raghuram¹

Affiliations

¹ Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India.
² Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) - Mohali, Nagar, Punjab, India.

Abstract

Rice is an important target to improve crop nitrogen (N) use efficiency (NUE), and the identification and shortlisting of the candidate genes are still in progress. We analyzed data from 16 published N-responsive transcriptomes/microarrays to identify, eight datasets that contained the maximum number of 3020 common genes, referred to as N-responsive genes. These include different classes of transcription factors, transporters, miRNA targets, kinases and events of post-translational modifications. A Weighted gene co-expression network analysis (WGCNA) with all the 3020 N-responsive genes revealed 15 co-expression modules and their annotated biological roles. Protein-protein interaction network analysis of the main module revealed the hub genes and their functional annotation revealed their involvement in the ubiquitin process. Further, the occurrences of G-quadruplex sequences were examined, which are known to play important roles in epigenetic regulation but are hitherto unknown in N-response/NUE. Out of the 3020 N-responsive genes studied, 2298 contained G-quadruplex sequences. We compared these N-responsive genes containing G-quadruplex sequences with the 3601 genes we previously identified as NUE-related (for being both N-responsive and yield-associated). This analysis revealed 389 (17%) NUE-related genes containing G-quadruplex sequences. These genes may be involved in the epigenetic regulation of NUE, while the rest of the 83% (1811) genes may regulate NUE through genetic mechanisms and/or other epigenetic means besides G-quadruplexes. A few potentially important genes/processes identified as associated with NUE were experimentally validated in a pair of rice genotypes contrasting for NUE. The results from the WGCNA and G4 sequence analysis of N-responsive genes helped identify and shortlist six genes as candidates to improve NUE. Further, the hitherto unavailable segregation of genetic and epigenetic gene targets could aid in informed interventions through genetic and epigenetic means of crop improvement.

Keywords: G-quadruplexes (G4); N-responsive genes; NUE (nitrogen use efficiency); WGCNA (weighted gene co-expression network analyses); epigenetic regulation; hub genes; nitrogen; rice.

Grants and funding

We are thankful for research grants from UKRI-GCRF South Asian Nitrogen Hub (SANH) (NE/S009019/1), including a fellowship to NS; GGSIPU FRGS (GGSIPU/DRC/FRGS/2022/1223/14) and CSIR Fellowship to BM {09/806(0038)/2019-EMR-I}. KS acknowledges financial support from the Department of Biotechnology (BT/PR40149/BTIS/137/36/2022).