Genome-wide identification of nuclear factor -Y (NF–Y) transcription factor family in finger millet reveals structural and functional diversity

Abstract

The Nuclear Factor Y (NF–Y) is one of the widely explored transcription factors (TFs) family for its potential role in regulating molecular mechanisms related to stress response and developmental processes.Finger millet (Eleusine coracana (L.) Gaertn) is a hardy and stress-tolerant crop where partial efforts have been made to characterize a few transcription factors. However, the NF–Y TF is still poorly explored and not well documented. The present study aims to identify and characterize NF–Y genes of finger millet using a bioinformatics approach. Genome mining revealed 57 EcNF-Y (Eleusine coracana Nuclear Factor-Y) genes in finger millet, comprising 18 NF-YA, 23 NF-YB, and 16 NF-YC genes. The gene organization, conserved motif, cis-regulatory elements, miRNA target sites, and three-dimensional structures of these NF-Ys were analyzed. The nucleotide substitution rate and gene duplication analysis showed the presence of 7 EcNF-YA, 10 EcNF-YB, and 8 EcNF-YC paralogous genes and revealed the possibilities of synonymous substitution and stabilizing selection during evolution. The role of NF-Ys of finger millet in abiotic stress tolerance was evident by the presence of relevant cis-elements such as ABRE (abscisic acid-responsive elements), DRE (dehydration-responsive element), MYB (myeloblastosis) or MYC (myelocytomatosis). Twenty-three isoforms of miR169, mainly targeting a single NF–Y gene, i.e., the EcNF-YA13 gene, were observed. This interaction could be targeted for finger millet improvement against Magnaporthe oryzae (blast fungus). Therefore, by this study, the putative functions related to biotic and abiotic stress tolerance for many of the EcNF-Y genes could be explored in finger millet.

Keywords

• Abiotic stress
• Finger millet
• miRNA
• Magnaporthe oryzae
• Nuclear factor-Y
• Transcription factor