Genome-wide investigation of SQUAMOSA promoter binding protein-like transcription factor family in pearl millet (Pennisetum glaucum (L) R. Br.)

Abstract

Abiotic stress negatively affects the yield of many crops. The SQUAMOSA promoter binding protein-like proteins (SBPs) represent a family of plant-specific transcription factors which play essential roles in plant growth, development, and stress responsiveness. In this study, 18 putative SBPs (PgSBPs) were identified in the genome of pearl millet on the basis of the SBP domain. One or two zinc finger-like structure(s) and a nuclear localization signal (NLS) were found in the SBP domains of all the PgSBPs. Fourteen PgSBPs were distributed on 7 chromosomes unevenly, while the other 4 were located on the scaffolds (i.e., non-chromosomal genomic sequences). Moreover, all the PgSBPs were clustered into seven groups (I-VII) based on the phylogenetic analysis. The intron/exon structures and the motif composition were similar between PgSBPs within the same groups. PgSBPs in groups V and VII were predicted as the targets of two microRNAs, PgmiR156q and PgmiR529b. Some PgSBPs have abscisic acid (ABA)-responsive elements and stress-responsive elements in their promoters. Expression levels of these PgSBPs were upregulated by abiotic stresses and downregulated by ABA. Together, this study shows a comprehensive overview of PgSBPs and provides vital information for elucidating the biological functions of PgSBPs.