Genome-wide identification, phylogenetic and expression analysis of SBP-box gene family in barley (Hordeum vulgare L.)

Abstract

The SQUAMOSA PROMOTER BINDING PROTEIN box (SBP-box) gene family is a unique family of transcription factors in plants, which is found widely in green plants. This family functions involve many aspects of crop genetic improvement, such as yield, floral period, and stress resistances; therefore, it has an important practical application value. In this study, 14 non-redundant SBP-box genes were identified and isolated in barley (Hordeum vulgare L.) using Hordeum vulgare.IBSC_v2 in combination with bioinformatics analysis. The results revealed that 13 of these genes were unevenly distributed on five chromosomes, and another gene has not been anchored yet. Sequence alignments demonstrated that each SBP protein has highly conserved functional elements (zinc finger structure and nuclear localization signal sequence). Gene structure analysis indicated their diversified exon-introns structure. Phylogenetic analysis was used to classify the barley SBP-box genes into five subfamilies (D–H). Each subfamily was found to contain similar protein motifs and gene structures. Expression profiles based on the barley RNA-seq database found that the barley SBP-box gene family expresses the highest amount in the inflorescence and showed different expression patterns in different tissues and different stages. Overall, the results indicated that the barley SBP-box gene family is relatively conserved in evolution and function, and plays a crucial role in many stages of barley plant growth development. Our results provide a theoretical reference for subsequent studies of molecular regulation and genetic breeding of SBP-box family genes in barley growth and development.