Assessment of Molecular Diversity and Heterozygosity in Corn (Zea mays L.) Inbred Lines Using Simple Sequence Repeat (SSR) Markers

Abstract

In this study, polymerase chain reaction (PCR) was used to genotype 30 corn inbred lines using 32 simple sequence repeat (SSR) markers. The goal was to establish the level and pattern of genetic diversity as well as to define probable heterotic groups of corn inbred lines. The 32 SSR primers detected a total of 238 alleles in a total of 150 individuals analyzed. The mean different number of alleles, effective number of alleles, Shannon’s information index, plus observed (Ho) and expected (He) heterozygosity were estimated (Na = 1.33, Ne = 1.29, I = 0.21, Ho = 0.28, He = 0.15) – exhibiting the highest values for phi079 (Na = 2.00, Ne = 1.96, I = 0.68, Ho = 0.89, He = 0.49) and the lowest for phi050 (Na = 1.00, Ne = 1.00, I = 0.00, Ho = 0.00, He = 0.00). The mean values of Ho > He indicates that the population has a mating system avoiding inbreeding. The high level of overall observed heterozygosity in corn inbred lines (mean Ho = 0.28 > mean He = 0.15) may indicate greater allelic polymorphism present in these populations and the possible mixing of previously isolated materials in the germplasm collection. Polymorphism information content ranged from 0.79 (umc1109) to 0.25 (umc1143), with an overall average value of 0.37, indicating that the loci were moderately low to highly informative and could thus detect and quantify genetic diversity in the population studied. In our maize gene pool, total genetic differentiation is somewhat high (0.57), with an excess of homozygotes. Seventeen (17) SSR loci had negative fixation indices (F), indicating a significant heterozygosity level. The population genetic diversity indices were also computed based on the 30 populations analyzed. The Na, Ne, Shannon’s information index, Ho, and He varied from population S8L17 to S8L27 with mean values of 1.327, 1.293, 0.214, 0.284, and 0.151, respectively. Populations showed negative F values, indicating significantly higher heterozygosity, whereas polymorphic loci had a mean value of 32.71%. The estimated molecular variance among the corn population was 2.29 and 3.06 for the variance within populations with a total of 5.35. The results of AMOVA also revealed that genetic variation within individuals accounts for 57% of overall genetic diversity, whereas among populations variability accounts for 43%. The cluster analysis, population structure analysis, and principal coordinate analysis revealed the presence of two distinct subpopulations. As a result, the findings of this study provide a foundation for identifying heterotic groups and parental selection, providing a source of unique alleles for future maize breeding efforts.