Genome-wide analysis of NF-Y genes and assessing their potential as miRNA targets in rice.

Abstract

Abiotic stress significantly impacts plant productivity, leading to complex responses that involve various physiological, biochemical, and transcriptional mechanisms. Nuclear transcription factor Y emerges as a crucial candidate gene in managing these stress responses. Although several NF-Y genes have been identified in Arabidopsis thaliana, Oryza sativa, Cicer arietinum and Sorghum bicolor, comprehensive investigations remain limited. Therefore, genome-wide exploration of NF-Y gene members across four genera led to identification of thirty-six AtNF-Ys, thirty-four OsNF-Ys, forty CaNF-Ys and forty-two SbNF-Ys. Protein structure analysis of NF-YA subunits revealed the conserved CCAAT-binding factor domain across four genera, responsible for binding to the CCAAT-box within eukaryotic promoters. Additionally, the NF-YB and NF-YC sub-families exhibited conserved histone fold domains, serving as a structural scaffold facilitating NF-Ys trimerization. Cis-Acting Regulatory Elements identified in OsNF-Ys were found to be associated with either stress or hormone responsiveness. Meta-analysis revealed that NF-Y genes responded variably in different environmental stress consistent with the qRT-PCR experiments that were meticulously performed at seedling and tillering developmental stages, revealing significant upregulation of OsNF-YA1, A4, A7, C1 and C4 in response to drought and salinity across different time points in shoot and root tissues. Eventually, we investigated potential miRNAs targeting NF-Y genes to elucidate the plausible mechanism in O. sativa. Osa-miR169a was found to target 3' UTR of OsNF-YA1, OsNF-YA4 and OsNF-YA10 while Osa-miR2919 was found to target 3' UTR of OsNF-YC1 and Osa-miR5075 was found to target 3' UTR of OsNF-YC4. Exploring these interactions offered valuable insights into the molecular mechanisms of NF-Ys governing stress responses in plants.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-026-01743-1.