Multiplex-ready PCR assay of SSR marker diversity among quality protein maize inbred parental lines

Abstract

Phenotypic markers have long been used for classification of maize (Zea mays) cultivars. However, because of shortcomings in detecting differences among closely related genotypes, coupled with sensitivity to environmental conditions, molecular marker techniques have been employed in the determination of relationships among parental genotypes at the DNA level. In this study, simple sequence repeat (SSR) multiplex-ready PCR was used to determine the diversity among 24 quality protein maize (QPM) inbred lines. Analysis of SSR loci of the 24 QPM lines yielded 101 scorable alleles with an average of 5.05 alleles per locus. The highest polymorphic information content (0.77) was observed in di-repeat motifs (Bng 11714) and the least (0.15) in tetra-nucleotide repeat motifs (Phi 053). The expected and observed mean heterozygosities were 0.62 and 0.11, respectively. These values showed deviation from the Hardy–Weinberg equilibrium, an affirmation of genetic diversity among the maize accessions. UPGMA cluster analysis resolved four major clusters with grouping patterns consistent with ancestry information. The results indicate that the multiplex-ready PCR technique could avail breeders in developing countries, especially Africa where research funding is limited, the opportunity of making use of marker techniques in breeding programmes because it is highly economical and time efficient.