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.

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Acknowledgements

This study was financially supported by the National Natural Science Foundation of China (31401316) and Hangzhou Scientific, Technological Program (20140432B03) and State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control (No. 2010DS700124-KF1913). The authors are grateful to the reviewers and editors for their helpful comments on this paper. We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript.

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DX conceived and designed the project; TT, YF, ZZ, JZ. XL and XZ performed the experiments and analyzed the data; TT, YF and DX wrote and revised the paper. All authors reviewed and approved the final manuscript.

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Correspondence to Dawei Xue.

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Tong, T., Fang, Y., Zhang, Z. et al. Genome-wide identification, phylogenetic and expression analysis of SBP-box gene family in barley (Hordeum vulgare L.). Plant Growth Regul 90, 137–149 (2020). https://doi.org/10.1007/s10725-019-00559-2

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Keywords

  • Barley
  • SBP-box gene family
  • Evolutionary analysis
  • Gene structure
  • Expression analysis