Bioinformatic analysis of promoter, motifs and CpG islands of genes encoding potassium transporters in crop plants

Abstract

ABSTRACT Potassium transporter genes are essential for plant salt stress tolerance. Identification of gene regulatory elements is vital for the recognition of gene expression patterns. Thus, understanding gene regulatory systems of potassium transporter genes is useful to improve the salt tolerance of crop plants. The present study was aimed at in silico analysis of promoter and regulatory elements of potassium transporter genes in coffee, peanut, soybean, maize, sorghum and potato crops. A total of 19 potassium transporter genes were identified, and the transcription start site (TSS), conserved motif, CpG islands were analysed using various computational tools. The highest promoter prediction score (1) was obtained in one gene sequence (LOC113728271) for Coffea arabica transcription start site, whereas the lowest score (0.8) was recorded in one gene sequence (LOC8065633) for Sorghum bicolor transcription start site. The analysis also showed that 66% of the genes contained more than one transcription start site whereas 63.16% had only one transcription start site. Five motifs were identified. Motif 1 was found as the common promoter motif residing on 78.95% of potassium transporter promoter sequences with an E-value of 3.4e − 002.C2H2 zinc finger transcription factors are predicted to bind to these conserved motifs with high statistical probability (2.28e − 03). Very few CpG islands were observed both in the promoter and body region of the gene sequences using two algorithms. The present study could contribute for better understanding of gene expression and the improvement of crops’ tolerance to environmental stresses through molecular assisted breeding or genetic engineering techniques.