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

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.

Comparative analysis of the SPL gene family in five Rosaceae species: Fragaria vesca, Malus domestica, Prunus persica, Rubus occidentalis, and Pyrus pyrifolia

“…In addition, conserved motifs could also play a part in the function of SPLs [ 4 , 29 ], although the significance of these motifs needs to be further investigated. Twenty motifs were identified ( Figure 5 and Table S3).…”

Hierarchical Action of Mulberry miR156 in the Vegetative Phase Transition

“…In A. thaliana , AtSPLs were downstream factors of miR156-regulated vegetative stage development [ 3 , 27 , 28 ]. The SPL family gene function as promoters of vegetative phase transition and are distributed across angiosperms [ 29 , 30 , 31 , 32 ]. In total, there are 16 AtSPL genes in A. thaliana and 10 members ( AtSPL2 , AtSPL3 , AtSPL4 , AtSPL5 , AtSPL6 , AtSPL9 , AtSPL10 , AtSPL11 , AtSPL13 , and AtSPL15 ) were the miR156 target genes [ 3 ].…”

Comprehensive genomic survey, structural classification and expression analysis of C2H2-type zinc finger factor in wheat (Triticum aestivum L.)

“…Synonymous (Ks) and non-synonymous (Ka) substitution rates were calculated for each duplicated C 2 H 2 -ZF genes using a maximum likelihood model averaging in Ka/Ks Calculator [ 68 ]. For each gene pair, the divergence time of collinear gene pairs was calculated using the mean Ks values from T = Ks/(2λ × 10 –6 ) Mya (λ = 6.5 × 10 –9 ) [ 69 ].…”