Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

Ting Zhu,Qin Ding,Liting Ma,Lingjian Ma,Xiaoying Wang,Dazhong Zhang,Yucui Han,Yue Liu

doi:10.1186/s12870-020-02576-0

Abstract

BackgroundMembers of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat.ResultsIn this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR).ConclusionsThe wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

Highlights

Members of the plant-specific SPL gene family contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites
TaChr7A and TaChr7D contain a large number of SPL genes, but no Wheat SPL (TaSPL) genes are located on chromosomes 4B and 4D
We found 22 paralogous gene pairs in the neighbor joining (NJ)-tree, among them, 4 gene pairs are from A. thaliana and 18 genes from wheat, indicating that the TaSPL genes expanded in a species-specific manner

Summary

Introduction

Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. Guo [8] reported that 120 SPL genes from nine species divided into 3 groups, all SPL genes from land plants have been classed into two distinct groups and 7 subgroups. Little research has been conducted to show the classification of the SPL gene family in wheat

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Discussion

Conclusion