Comprehensive in silico analysis of upstream sequences of TaNRT2 gene family of bread wheat: Unveiling effects of hormonal cross-talk on differential homeolog expressions of TaNRT2.1-6 under low nitrogen conditions

Abstract

Nitrate is one of the major nitrogen forms available in soil that are crucial for plant growth and development. This study employed multiple bioinformatics tools for a comprehensive In silico analysis of approximately 3 kb upstream regions of all TaNRT2 family genes, which encode members of high-affinity nitrate transporters (HATS) in wheat, retrieved from the Chinese Spring reference genome sequence. The analysis concentrated on identifying Cis-Regulatory Elements (CREs), Transcription Factor Binding Sites (TFBS), evolutionary relationships, tandem repeats, and CpG/CpNpG islands. Furthermore, transcript expression patterns were studied based on CREs of three homeologs of TaNRT2.1-6 in root and shoot tissues at the seedling stage under low nitrate conditions along with Gibberellic acid (GA₃) and Salicylic acid (SA). The sequence analysis of 3 kb upstream sequence revealed varied types and occurrences of Cis-Regulatory Elements and Transcription Factor Binding Sites, predicting variations in nitrate-dependent gene expression. Key TFBS (LBD, GATA, NIN-like, Dof, MYB, NAC, MIKC_MADS, and bZIP), involved in growth regulation under low nitrogen conditions, were identified in all TaNRT2 promoters. The present study provides a detailed analysis of the TaNRT2 gene promoters in wheat, offering insights for designing future studies to understand regulatory mechanisms underlying wheat’s N-responsive growth responses.