Comparative root transcriptome analysis suggests down-regulation of nitrogen assimilation in DJ123, a highly phosphorus-efficient rice genotype

Many cultivable lands across the globe are characteristically low for plant-available phosphorus (P). This necessitates application of P fertilisers, but this increases farming costs beyond the affordability of marginal farmers. Thus, developing cultivars with high P-use efficiency (PUE) is necessary in high-yielding modern rice varieties, which are typically inefficient in P usage. However, the molecular and physiological bases to increase PUE in crops remain elusive. Here, we studied root transcriptomes of two breeding parents contrasting in PUE via RNA-seq to elucidate key physiological and molecular mechanisms that underlies efficient use of P in rice. Examination of transcriptome data obtained from plants grown under P-sufficient and P-deficient hydroponic conditions in DJ123 (an upland rice genotype adapted to low P soils) and IR64 (a modern rice variety less efficient in P use) revealed that the genes encoding nitrogen assimilation-related enzymes such as glutamine synthetase [EC. 6.3.1.2], glutamate synthase [EC. 1.4.1.13], and asparagine synthetase [EC. 6.3.5.4] were down-regulated only in DJ123 roots while it was not significantly affected in IR64 under low P conditions. In addition, DJ123 roots had a lower total nitrogen (N) concentration than IR64 irrespective of P conditions. Taken together, we surmise that the low level of N concentration together with down-regulation of the N assimilation-related genes allow DJ123 to operate at a low level of N, thus leading to formation of root tissues with lower metabolic investment and a greater PUE.