Genome-wide analysis of SPL/miR156 module and their expression analysis in vegetative and reproductive organs of oil palm (Elaeis guineensis)

Abstract

Background: Oil palm (Elaeis guineensis, Jacq.) is an important oil-yielding plant, cultivated as source of oil. SPL (SQUAMOSA-promoter binding protein-like) gene family is one of the largest plant transcription factors and known to involve in the regulation of plant growth, development and stress responses. The genome-wide analysis of SPL gene members in diverse range of crops has been elucidated. However, none of the genome-wide studies on SPL gene family has been carried out in oil palm. Results In this research, a total of 24 EgSPL genes were identified via genome wide approach. Phylogenetic analysis revealed that most of the EgSPLs are closely related to the Arabidopsis and Rice SPL gene members. EgSPL genes were mapped onto the only 9 chromosomes of oil palm genome. Motif analysis revealed conservation of SBP domain and the occurrence of 1-10 motifs in EgSPLgene members. Gene duplication analysis demonstrated the tandem duplication of SPLmembers in oil palm genome. Heatmap analysis indicated the significant expression of SPL genes in shoot and flower organs of oil palm plants. Among the identified EgSPL genes, a total 14 EgSPLs were shown to be targets of miR156. Real time PCR analysis of 14 SPL genes showed that the most of the EgSPL were highly expressed in female and male inflorescences of oil palm plants than vegetative tissues. Altogether, present study revealed the significant role of EgSPL genes in inflorescence development. Conclusions A total of 24 EgSPLs were identified and analyzed 14 EgSPLs (containing miR156 sites) genes expression in vegetative and reproductive tissues of oil palm. Moreover, detailed information on SPL gene structure, their miR156 target sites, motif composition, chromosomal location and phylogenetic analysis was also reported. Furthermore, the unique expression of EgSPLs (containing miR156 sites) in oil palm inflorescences was also revealed via qPCR analysis, predicting their putative role in male and female inflorescence development of oil palm.