Genome-wide analysis and identification of nuclear factor Y gene family in switchgrass (Panicum virgatum L.)

NF-Y is a class of heterotrimeric transcription factor composed of three subunits; NF-YA, NF-YB, and NF-YC. This complex binds to the CCAAT box found in eukaryotic promoters and is involved in the plant development and proliferation at various stages. Although many studies were conducted on NF-Y gene family in various species, but no study has been reported yet in switchgrass (Panicum virgatum L.). In this study, 47 PvNF-Y genes (17 PvNF-YA, 18 PvNF-YB, and 12 PvNF-YC) have been identified and named according to their subfamily. Chromosome location analysis revealed that all 47 PvNF-Y genes are randomly distributed across nine chromosomes. Moreover, multiple sequence alignment showed the DNA-binding domain and NF-YA/NFYB interacting domains flanking with non-conserved domains. In addition, prediction of functional similarities among PvNF-Ys genes phylogenetic tree was constructed corresponding to Arabidopsis. The gene structure, conserved domains and motifs analysis of PvNF-Ys genes demonstrated their specificity and functional conservation. Cis-regulatory elements analysis identified numerous key CREs that are significantly associated with light, hormone, stress and plant development responses. Expression profiling indicated higher expression levels of many PvNF-YA genes during drought and heat stress. Additionally, qRT-PCR analysis showed that some PvNF-Ys genes have high expression level in root. In conclusion, the findings of this study could provide a foundation for further cloning and functional analysis of NF-Y genes in switchgrass.