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The occurrence of phenotypic and genotypic diversity is the key factor in crop improvement including abiotic stress tolerance. The focal objectives of this study were to evaluate and characterize 74 tropical indica rice breeding lines for phenotypic and genotypic diversity, screening for the most devastating abiotic stresses in rice; drought and salinity at the seedling stage at morpho-physiological and molecular levels. To fulfill these objectives, five studies were conducted in pots; first two experiments aimed at assessing phenotypic and yield variability at seedling and maturity stages respectively; based on several (more than 20) root and shoot traits which exploited a wide range of variability among genotypes for measured traits. Germplasm was then screened for drought stress at two moister regimes, 50%, and 100% moisture levels, under mini-hoop structures. Nine percent of the genotypes exhibited a high tolerance to drought stress, and genotypes IR86638 and IR49830 were identified as the most and least drought tolerant respectively. Germplasm was also screened for salinity tolerance in pure sand pot-culture (a simple, efficient and alternate screening method) at three levels; high salt stress (EC 12 dSm-1), moderate salt stress (EC 6 dSm-1), and control imposed one week after emergence. Thirteen genotypes (17.57%) were identified as highly salt tolerant; genotypes FED 473 and IR85427 were highly salt tolerant and salt sensitive, respectively. Root traits were found more crucial and best descriptors in identifying both salinity and drought tolerant genotypes. Genotypes were further used in Genome-wide Association Study (GWAS) to uncover important SNPs, QTLs or genes related to salinity tolerance. A higher number of significant SNPs were discovered for root traits, indicting the importance of root traits in identifying abiotic stress tolerance in rice. The knowledge gained from this investigation could be useful in breeding for better crop establishment, yield improvement, screening for any abiotic stress tolerance.