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As a major plant-specific transcription factor family,  SPL  genes play a crucial role in plant growth, development, and stress tolerance. The SPL transcription factor family has been widely studied in various plant species; however, systematic studies on  SPL  genes in the genus  Ipomoea  are lacking. Here, we identified a total of 29, 27, 26, and 23  SPLs  in  Ipomoea batatas ,  Ipomoea trifida ,  Ipomoea triloba , and  Ipomoea nil , respectively. Based on the phylogenetic analysis of SPL proteins from model plants, the  Ipomoea  SPLs were classified into eight clades, which included conserved gene structures, domain organizations and motif compositions. Moreover, segmental duplication, which is derived from the  Ipomoea  lineage-specific whole-genome triplication event, was speculated to have a predominant role in  Ipomoea SPL  expansion. Particularly, tandem duplication was primarily responsible for the expansion of SPL subclades IV-b and IV-c. Furthermore, 25 interspecific orthologous groups were identified in  Ipomoea , rice,  Arabidopsis , and tomato. These findings support the expansion of  SPLs  in  Ipomoea  genus, with most of the  SPLs  being evolutionarily conserved. Of the 105  Ipomoea SPLs , 69 were predicted to be the targets of miR156, with seven  IbSPLs  being further verified as targets using degradome-seq data. Using transcriptomic data from aboveground and underground sweet potato tissues,  IbSPLs  showed diverse expression patterns, including seven highly expressed  IbSPLs  in the underground tissues. Furthermore, the expression of 11  IbSPLs  was validated using qRT-PCR, and two ( IbSPL17/IbSPL28 ) showed significantly increased expression during root development. Additionally, the qRT-PCR analysis revealed that six  IbSPLs  were strongly induced in the roots under phytohormone treatments, particularly zeatin and abscisic acid. Finally, the transcriptomic data of storage roots from 88 sweet potato accessions were used for weighted gene co-expression network analysis, which revealed four  IbSPLs  ( IbSPL16/IbSPL17/IbSPL21/IbSPL28 ) clusters with genes involved in “regulation of root morphogenesis,” “cell division,” “cytoskeleton organization,” and “plant-type cell wall organization or biogenesis,” indicating their potential role in storage root development. This study not only provides novel insights into the evolutionary and functional divergence of the  SPLs  in the genus  Ipomoea  but also lays a foundation for further elucidation of the potential functional roles of  IbSPLs  on storage root development.

frontiers in plant science

Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato (Ipomoea batatas)