M. Krishna Kumar+, D.P. Syamaladevi*+£, S.M. Balachandran and D. Subrahmanyan
ICAR-Indian Institute of Rice Research, Hyderabad, India. PIN 500 030
£ Currently at: ICAR-Indian Institute of Spices Research, Kozhikode
Email: dpsdevi@gmail.com
Received-01.05.2023, Revised-12.05.2023, Accepted-23.05.2023
Abstract: The abundance of transcription factor binding sites (TFBSs) on promoter sequences differs from gene to gene. Understanding how this difference affects gene expression would enable us to develop superior lines through allele mining based genomic selection or genome editing. To understand the relationship between the TFBSs abundance and transcription in carbohydrate metabolism-related genes that are central to growth and grain yield in rice. For this, we first analysed the expression pattern of four carbohydrate metabolism-related enzymes – Sucrose Phosphate Synthase (SPS), PME (Pectin Methyl Esterase), Galacturonosyl transferase (GalAT) and Phosphoglucomutase (PGM). Then, we obtained a reliable set of TFBSs on the core and distal promoters of these genes following Support Vector Machine (SVM) method and stringent cut off of 90% TFBS motif similarity. Fold change in gene expression during phenology change from vegetative to flowering showed a linear relationship with the TFBS abundance in the case of an SBP family transcription factor, SPL12. Further, identification of CpG islands in the promoters explained the deviations in this linear relationship between gene expression and TFBS abundance. Using two DNA parameters – the TFBS abundance and the CpG islands – we provide predictive insights to the gene expression of carbohydrate metabolism-related genes in rice.
Keywords: Transcription factor binding sites, Gene expression, Carbohydrate metabolism, Phosphoglucomutase, Rice
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