Phosphorus which is a key element for plant growth is found to be very limited in soil and also most of the commercial modern cultivars have low phosphorus use efficiency. So phosphorus use efficient crops have to be developed. This can be better accomplished by the utilization of molecular tools in addition to field breeding programmes. A quantitative trait locus Pup1 (phosphorus uptake 1) for phosphorus deficiency tolerance was identified in an aus-type traditional variety Kasalath about a decade ago. By subsequent sequencing of the region, a protein kinase gene PSTOL1 (Phosphorus starvation tolerant 1) responsible for the trait P use efficiency was identified. This gene is absent in rice reference genome and phosphorus use inefficient modern cultivars. We planned to introgress PSTOL1 gene in commercial varieties of South India through backcross breeding. For that we evaluated both the donors and the recipients for the presence of PSTOL1 gene. Kasalath was used as positive control. When genotyping was done with gene specific molecular marker, the NILs introgressed with Kasalath alleles which we planned to use as donors, were clearly differentiated from the modern varieties for P use efficiency due to presence of the PSTOL1 gene. Also the modern varieties which were improved for blast and bacterial blight diseases resistance were checked for the presence of the resistance genes through the use of concerned gene specific markers. By combining the P use efficiency of the NILs with the high yield efficiency and multiple disease resistance of the modern varieties, it is possible to increase the grain yield of modern commercial varieties even under P deficient conditions.