Analysis of regulatory elements in GA2ox, GA3ox and GA20ox gene families in Arabidopsis thaliana: an important trait

Abstract

The enzymes that are independently encoded by GA2ox, GA3ox and GA20ox genes control gibberellins (GA) biosynthesis and catabolism. This study analysed the promoter regions, transcription start site (TSS), motifs and CpG islands (CGIs) in 15 GA oxidase genes of Arabidopsis thaliana using 1-kb sequences. Excluding ATGA2ox5 and ATGA3ox4, promoter regions and TSS analysis showed that 60.00% of the genes have more than one TSS in 1000 bp. Relative to the ATG, 80.00% of TSSs with highest score were in the range of −100 bp. Sixty percent of investigated GA genes have TSS in their 5′ untranslated regions (UTRs) with highest prediction score at 0.8 cut-off values. A total of 5 motifs were discovered in 15 GA oxidase genes. More than half (53.33%) of the motifs were distributed throughout promoter regions on both strands. Positional clustering of more than half (55.31%) of motifs was found between +1 and −500 bp. MfIV was detected (100%) in all promoter regions of GA genes. Using the Plant CARE database, various similar motifs were identified in all promoter regions of GA genes. Including two gibberellin-responsive elements (GARE-motif, P-box), numerous motifs such as CAAT-box, TATA-box, ATC-motif, Gap-box and others were distinguished in the promoter regions of GA genes. CGIs were not detected in the promoter sequences of all GA oxidase genes. However, 86.66% of CGIs were discovered in the gene bodies of GA oxidase genes. Analysing the regulatory elements of GA genes is the first step to control crop height, increase yield and resistance to lodging.

Keywords

• cpg island
• motif
• ga gene
• promoter
• transcription start site