Molecular markers are more useful in identifying parental inbred lines crosses of which create genetic variation among progenies in the advanced generation more realistically than selection based on phenotypic data. In this study, 37 maize inbred lines including 14 of Ethiopian and 23 of CIMMYT origin were studied using 28 microsatellite markers. Among the 23 CIMMYT inbred lines, 13 were soil acidity tolerant lines and were recently introduced. The main objective was to identify distantly related Ethiopian maize inbred lines and soil acidity tolerant inbred lines of CIMMYT origin that could be used in broadening the genetic basis of maize for tolerance to soil acidity. Analysis of molecular variance indicated higher genetic variability (77%) among the inbred lines indicating ability of the SSR markers in discriminating the inbred lines. One-hundred and seven alleles were identified in the inbred lines with average of 3.71 alleles per locus. Expected hetrozygosity (He) and major allele frequency ranged from 0.09 to 0.61 and from 0.34 to 0.95, respectively, indicating higher genetic variability among the inbred lines, which could be exploited in breeding program. Polymorphic information content (PIC) generated by each marker ranged from 0.10 (Bnlg 1063) to 0.74 (Umc 2205) with a mean of 0.50 indicating their power in discriminating the inbred lines. Nei’s genetic distance among pairs of the 37 maize inbred lines varied from 0.16 to 0.98. Pairs of inbred lines of Ethiopian origin had genetic distance that ranged from 0.26 to 0.98 and the highest genetic distance was in this population. Pairs of inbred lines of Ethiopian and CIMMYT inbred lines developed for tolerance to soil acidity had genetic distance that varied from 0.42 to 0.95 and 41.6 % of the pairs had genetic distance of more than 0.8 indicating their potential in broadening the genetic basis of maize for developing varieties tolerant to soil acidity. Specifically, 124-b(109) was distantly related with five inbred lines, viz., CML359, CML360, CML361, CML436 and CML438, and F-7215 was also distantly related with CML361 with Nei’s genetic distance of more than 0.9. These pairs of inbred lines could be exploited in pedigree breeding through which segregating populations can be selected for desirable traits in combination with tolerance to soil acidity. However, the soil acidity tolerant inbred lines have to be evaluated for adaptation to Ethiopian environment before embarking on exploiting their potential in breeding for tolerance to soil acidity.
