A set of hundred homozygous maize inbred lines were analyzed for drought toleranceby studying twenty-four traits related to maturity, morphological, physiological, yield, quality and few root traits. Evaluation confirmed a wide range of variability revealing significant response of main effects (lines, irrigations and years and their respective digenic and trigenic interactions). These lines were subjected to different stress regimes over years leading to identification of fifteen elite lines which performed well under droughtstress showing inbuilt drought tolerance. A set of 32 SSR markers, having genome-wide coverage, were chosen for genotyping the inbred lines. These markers generated a total of 239 polymorphic alleles with an average of 7.47 alleles per locus. The minimum and maximum PIC value was 0.886 and 0.608 with a mean of 0.782. The coefficient of genetic dissimilarity ranged from 0.215 to 0.148. DARwin derived cluster analysis grouped 15 elite maize lines in three major clusters with five lines each in cluster-III and II and four lines in cluster-I with KDM-361A as root. Molecular diversity however, confirmed diverse genetic nature of six lines (KDM-372, KDM-343A, KDM-331, KDM-961, KDM-1051 and KDM-1156) showing drought tolerance. Exploitation of identified elite lines in a crossing program involving all possible combinations would help to develop hybrids with inbuilt mechanism to drought tolerance. Markers viz., umc -1766, umc-1478 and phi-061 recorded PIC >8 and alleles per locus more than 9 and therefore, discriminated the set of lines more efficiently. Genotyping data complemented by morpho- hysiological parameters were used to identify a number of pair-wise combinations for the development of mapping population segregating for drought tolerance and potential heterotic pairs for the development of drought tolerant hybrids.
