A comparison study of root architecture and morpho-physiological traits were taken up using nine tolerant and three check germplasm lines. The experimental work was done under rain protected condition using an innovative approach. A significant differences was observed in the root and shoot length of Pup1 positive genotypes than Pup1 negative germplasm lines under both phosphorous supplemented and deficient soil conditions. A higher uptake of phosphorus was noticed in Pup1 positive plants of leaf phosphorus analysis under water stressed condition as compared to normal. The higher p-uptake genotypes showed higher tiller number and high plant dry weight. The Pup 1 negative genotypes showed low root width and low root density than the positive plants. The Pup1 positive plants showed higher root dry weight, root length and root density under both phosphorus and water stress condition.