Assessment of molecular diversity among maize inbred lines using SSR markers

Abstract

This study aimed to assess the genetic diversity among 112 maize inbred lines using Simple Sequence Repeat (SSR) markers to support targeted breeding programs and heterotic group classification. Understanding the molecular genetic diversity among and within inbred lines is important for maize improvement in different breeding programs. Only seven primer pairs out of 22 SSR primers used in the study showed clear polymorphism yielding 2-4 alleles per locus with an average of 3.28 alleles per marker. Among the 7 polymorphic markers, bnlg 238, umc 1029, umc 2077 and bnlg 1335 recorded the higher PIC values, the most effective alleles and the higher Shannon’s information index and Nei’s genetic diversity index confirming their utility for diversity studies. The polymorphism information content (PIC) of the SSR loci ranged from 0.46 to 0.71. PIC was highest for the SSR primer Bnlg 238 (0.71) followed by Umc 1029 and Umc 2077 (0.67) and lowest for the primer Bnlg 1666 (0.46). By using UPGMA cluster analysis, the 112 inbred lines were grouped into three major clusters. Cluster II was the largest with 46 inbred lines followed by cluster I with 39 inbred lines and cluster III with 27 inbred lines. Sub-clusters further diverged at higher similarity coefficients, reflecting fine-scale genetic differences. The SSR markers effectively captured high polymorphism among maize inbred lines, enabling precise genotype identification.The heterotic potential of clusters (e.g., divergent groups I vs. III) can be exploited for hybrid breeding..