Genetic characterization and population structure of maize populations using SSR markers

Abstract

Maize is a major staple food in sub-Saharan Africa. However, due to the threats posed by biotic and abiotic constraints to its production, it is a prerequisite to conserve germplasm with diverse genetic background and to seek for favourable genotypes with such background for improvement of superior genotypes. This study assessed the diversity of 70 white maize populations developed at CSIR-Savanna Agricultural Research Institute with resistance/tolerance to drought and low soil nitrogen (Low-N) using 31 SSR markers. A total of 288 alleles were detected among the germplasm used with a range of 4 to 17 alleles per locus and an average allele number of 9.60 alleles per locus. Polymorphic Information Content values for the SSR markers ranged from 0.32 to 0.85 with a mean value of 0.68. The average heterozygosity obtained from the markers was 0.54 and gene diversity ranged from 0.35 to 0.87 with a mean gene diversity value of 0.71 indicating a high level of polymorphism among the populations. Clustering based on Jaccard's similarity coefficient and an Unweighted Pair Group Method with Arithmetic Mean (UPGMA) revealed 5 clusters for the 70 populations. Evanno method for population structure clustering further revealed two sub-populations. Sub-population 1 was more genetically diverse with an Fst value of 0.18 than sub-population 2 which recorded an Fst value of 0.013. These results indicated that the SSR used were very polymorphic for diversity studies. Also, the studied maize populations are diverse and heterozygous, making them ideal source populations for extraction of drought and low-N tolerant inbred lines.