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Abstract Understanding the genetic relationships between the key founder inbred lines and derived inbred lines could provide insight into the breeding history and the structure of genetic diversity of the available elite inbred lines with desirable target traits. The maize improvement program at the International Institute of Tropical Agriculture (IITA) analyzed the pedigree information of 623 sub-tropical maize inbred lines generated at the IITA maize breeding program to identify the key founder inbred lines. We also used 5032 SNP markers to assess the genetic similarities of the founder inbred lines with their progenies subsequently developed for specific target traits. The results of pedigree analysis and SNP markers-based similarity scores identified 20 key founder inbred lines with significant contributions to the development of drought tolerant, early maturing, productive, Striga resistant, provitamin A enriched, and quality protein maize inbred lines. In our breeding program, line TZMi501 belonging to a flint heterotic group (HGA), and TZMi407-S and TZMi214, representing the dent heterotic group (HGB), were identified as the most useful founder inbred lines. The 623 inbred lines were consistently separated into four clusters based on Ward’s hierarchical clustering, structure, and principal component analyses, with the 20 founder inbred lines spread into all clusters. The founder inbred lines were more genetically related to the productive inbred lines but showed genetic divergence from the provitamin A enriched inbred lines. These results provide a better understanding of the breeding history of the sub-tropical maize inbred lines to facilitate parental selection aligned to existing heterotic groups for use in breeding programs targeting the improvement of essential traits in maize.

Abstract African yam bean, AYB (Sphenostylis stenocarpa), is an underutilized legume of tropical Africa. AYB can boost food and nutritional security in sub-Saharan Africa through its nutrient-rich seeds and tubers. However, inadequate information on germplasm with desirable agro-morphological traits, including insufficient data at the genomic level, has prevented the full exploitation of its food and breeding potentials. Notably, assessing the genetic diversity and population structure in a species is a prerequisite for improvement and eventual successful exploitation. The present study evaluated the population structure and genetic diversity of 169 accessions from the International Institute of Tropical Agriculture (IITA) collection using 26 phenotypic characters and 1789 single nucleotide polymorphism (SNP) markers. The phenotypic traits and SNP markers revealed their usefulness in uniquely distinguishing each AYB accession. The hierarchical cluster of phenotypes grouped accessions into three sub-populations; SNPs analysis also clustered the accessions into three sub-populations. The genetic differentiation (F ST ) among the three sub-populations was sufficiently high (0.14–0.39) and significant at P = 0.001. The combined analysis revealed three sub-populations; accessions in sub-population 1 were high yielding, members in sub-population 2 showed high polymorphic loci and heterozygosity. This study provides essential information for the breeding and genetic improvement of AYB.