DNA Profiling of Indonesian Maize Hybrids and their Parental Lines Using SSR Markers

Abstract

Abstract DNA fingerprinting is an effective genomic tool for hybrid/elite genotype identification. The objective of the research was to conduct DNA fingerprint characterisation of national maize hybrids and their parental lines using SSR markers. This research was conducted from April to July 2020. Moreover, 57 SSR markers were used for genotyping 10 maize genotypes of 4 national maize hybrids, three male and three female parents. SSR analysis in maize fingerprinting evaluates allele number, frequency, polymorphism, heterozygosity, PIC value, genetic similarity, distance, and relationships among samples. A dendrogram was constructed using the Unweighted Pair Group Method with Arithmetic Mean and Sequential Agglomerative Hierarchical Non-overlapping (SAHN) clustering. The results indicated that 230 SSR alleles were generated with molecular weights of 75.60 – 553.00bp. The polymorphism information content values varied between 0.10 – 0.85 (average = 0.59). A coefficient similarity of 42% classified the maize genotypes into 4 clusters, A, B, C, and D. JH 27 and two-parent lines (CY7 and MR14) made up Cluster A while B11209 was in Cluster B with 35% resemblance to Cluster A. Two pure lines and two hybrids comprised cluster C, C1, and C2 formed out of cluster C. The hybrid (JH 37) and its parental line (MAL03) had the most similarity (70%) in the C2 subcluster. A hybrid (NASA 29) and a single parental line (G1026-12) comprise cluster D.

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