Genome-wide identification and expression profiling of the SPL family genes in wheat

The SQUAMOSA promoter-binding protein-like (SPL) proteins constitute a family of plant-specific transcription factors that play a vital role in plant development. Wheat (Triticum aestivum, AABBDD) is universally well-known as a cash crop; however, the SPLs of this important crop have not been systematically investigated as yet. In the current study, we conducted a genome-wide survey in wheat and found 56 SPL genes belonging to 19 homologous groups. SPLs were divided into 7 classes by phylogenetic tree analyses. We mapped these genes on to the wheat chromosomes and examined their structures and conserved motifs. Moreover, we performed a synteny analysis on wheat, and summarized the SPL family as well as the evolutionary relationships between SPLs. Thereafter, we compared the expression patterns of wheat SPLs under different conditions, thereby confirming that SPLs play an important role in spike development. To conclude, the SPLs in triplets have analogous structures and similar expression patterns. The three-pair triplet response to jasmonic acid (JA) and abscisic acid (ABA) was determined by quantitative real-time polymerase chain reaction (RT-qPCR). This work provides a comprehensive understanding of the SPL gene family in wheat. Our investigation of the wheat SPL gene family provides a starting point for additional functional studies of these significant transcription factors in wheat.

SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer

SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identification, evolutionary analysis, structure analysis, and expression characteristics analysis of SPL gene family in Panax ginseng by bioinformatics. We annotated the PgSPL gene family and found that they might involve in multiple functions including encoding structural proteins, but the main function were still focused on the binding function. The result showed that 106 PgSPL transcripts were classified into two clades - A and B, both of which respectively consisted of three groups. Besides, we profiled PgSPL transcripts’ genotypic, temporal, and spatial expression characteristics. Furthermore, we calculated the correlation of PgSPL transcripts in the 14 tissues of a 4 years old ginseng and 42 farmers’ cultivars farmers’ cultivars of 4 years old ginsengs’ roots with both results showing that SPL transcripts formed a single network, which indicated that PgSPLs inter-coordinated when performing their functions. What’s more, we found that most PgSPL transcripts tended to express in older ginseng instead of younger ginseng, which was not only reflected in the expression of more types of SPL transcripts in older ginseng, but also in the higher expression of SPL transcripts in older ginseng. Additionally, we found that four PgSPL transcripts were only massively expressed in roots. According to PgSPL transcripts’ expression characteristics, we found that PgSPL23-35 and PgSPL24-09 were most proper two transcripts to further study as ginseng age’s molecular marker. These results provide the basis for further elucidation of the PgSPL transcripts’ biological function in ginseng and ginseng genetics improvement and gene breeding in the future.