Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat
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RESEARCH ARTICLE
Open Access
Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat Ting Zhu1, Yue Liu2, Liting Ma1, Xiaoying Wang1, Dazhong Zhang1, Yucui Han1, Qin Ding3 and Lingjian Ma1*
Abstract Background: 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. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results: In 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). Conclusions: The 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. Keywords: SPL gene family, Phylogenetic analysis, Expression patterns analysis, Wheat
Background Gene families, consisting of multiple genes that share similar structures and functions, act in important roles for a given organism. Now, all kinds of gene families have been found in eukaryotes, such as bHLH [1], TCP [2], and Prx [3]. Among all gene families, SPL (squamosa promoter * Correspondence: [email protected] 1 College of Agronomy, Northwest A&F University, Yangling 712100, China Full list of author information is available at the end of the article
binding protein, SBP) is a plant-specific family that is widely distributed in green plants. The plant SPL proteins, bind to the SQUAMOSA promoter of MADS-Box genes, were first identified in a cDNA library of the Antirrhinum majus inflorescence [4]. These proteins contain a specific SB
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