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

Abstract

SQUAMOSA promoter-binding protein-like (SPL) transcription factors are very important for the plant growth and development. Here 15 RoSPLs were identified in Rubus occidentalis. The conserved domains and motifs, phylogenetic relationships, posttranscriptional regulation, and physiological function of the 92 SPL family genes in Fragaria vesca, Malus domestica, Prunus persica, R. occidentalis, and Pyrus pyrifolia were analyzed. Sequence alignment and phylogenetic analysis showed the SPL proteins had sequence conservation, some FvSPLs could be lost or developed, and there was a closer relationship between M. domestica and P. pyrifolia, F. vesca and R. occidentalis, respectively. Genes with similar motifs clustering together in the same group had their functional redundancy. Based on the function of SPLs in Arabidopsis thaliana, these SPLs could be involved in vegetative transition from juvenile to adult, morphological change in the reproductive phase, anthocyanin biosynthesis, and defense stress. Forty-eight SPLs had complementary sequences of miR156, of which nine PrpSPLs in P. persica and eight RoSPLs in R. occidentalis as the potential targets of miR156 were reported for the first time, suggesting the conservative regulatory effects of miR156 and indicating the roles of miR156-SPL modules in plant growth, development, and defense response. It provides a basic understanding of SPLs in Rosaceae plants.

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)

“…The results showed that the SPL members had the SBP domain, which comprised two non-interleaved zinc finger-like structures (Zn-1/2) and one NLS motif (Supplementary Figures 1c, 2). Based on the alignments of the Ipomoea SPLs, the Zn-2 motif showed higher conservation than the Zn-1 and NLS motifs, which was consistent with the results in Rosaceae (Jiang et al, 2021) and Oryza species (Zhong et al, 2019; Supplementary Figure 2). The Zn-2 motif in all Ipomoea SPLs was a Cys-Cys-His-Cys (C2HC) type (except IbSPL23) whereas the Zn-1 motif showed varied types: Cys-Cys-Cys-Cys (C4) type in clade I and Cys-Cys-Cys-His (C3H) type in the remaining clades.…”

Comparative analysis of the SPL genes among four Ipomoea species and the evidence for a role of some IbSPLs in storage root development in sweet potato (Ipomoea batatas)

“…The results showed that all of the SPL members had the SBP domain, which was composed of two non-interleaved zinc nger-like structures (Zn-1/2) and one nuclear localization signal (NLS) motif (Figure 3b, Supplementary Figure S1). Based on the alignments, the Zn-2 motif is more conserved than the Zn-1 and NLS motif in all Ipomoea SPLs analyzed, which was also observed in Rosaceae [30] and Oryza species [31] (Supplementary Figure S1). For example, the Zn-2 motif in all Ipomoea SPLs was a Cys-Cys-His-Cys (C2HC) type (except IbSPL23); and the Zn-1 motif showed different signatures, which was Cys-Cys-Cys-Cys (C4) type in clade I and Cys-Cys-Cys-His (C3H) type in the remaining clades.…”

Mapping quantitative trait loci and predicting candidate genes for Striga resistance in maize using resistance donor line derived from Zea diploperennis

“…The QTL qSC 8 associated with Striga emergence count was found to be linked with the gene model, GRMZM2G371033, SBP-transcription factor. The SBP-transcription factors are very important for plant growth, development, and defense response as they regulate the specific downstream gene expression, such as the phase transition from vegetative to reproductive stage, leaf development, plant hormone signaling, toxin resistance, copper deficiency response, temperature, and drought stress tolerance ( Jiang et al, 2021 ). The gene model GRMZM2G075715, ARF-transcription factor was associated with the QTL qSC 7 identified for Striga emergence count.…”