Comparative methylome analysis in contrasting rice genotypes (O. sativa L. ssp. Indica) during Pi-starvation

Phosphorus (P) is a critical element required for plant growth and development due to its major role in diverse cellular processes varying from photosynthesis, carbohydrate metabolism, energy production, signaling and redox homeostasis. Phosphate (Pi) deficit affects the growth and development of crop plants grown in semi-arid regions and marginal areas. To cope with Pi-deficiency, plants have evolved several adaptive strategies in genotype specific manner. To better understand the intricate mechanisms regulating Pi homeostasis in contrasting rice genotypes (O. sativa L. ssp. Indica) having different sensitivity towards phosphate starvation, we used two rice genotypes [viz Pusa-44 (sensitive) and its near isogenic lines (NIL-23; tolerant) harbouring a QTL from Kasalath genotype] grown in the medium (containing 0 or 15 ppm Pi) to get a comprehensive understanding of the molecular processes involved. Methylome analysis carried out in roots and shoots from 6 wk old rice seedlings grown hydroponically in Pi-sufficient (15 ppm Pi) or deficient (0 ppm Pi). A total of 8 libraries(in replicate) were prepared from the shoots and roots tissues and subjected to deep sequencing to find out the differentially methylated genes under Pi-starvation in NIL-23 and Pusa-44 genotypes. Further analysis suggested that the main variations between two rice genotypes [viz Pusa-44 (sensitive) and its near isogenic lines (NIL-23; tolerant) in promoter region. Moreover, the preference of methylation status alterations also fell in CHH sequence context. Further analysis of the correlation between DMRs and DEGs indicated in both genotypes, the DMRs in promoter were significantly negatively correlated with DEGs.