Parental inbred lines used in the present study.

Understanding the genetic diversity of inbred lines is vital for development of superior F1 varieties. The present study aimed to analyze Japanese maize parental inbred lines and determine their genetic diversity for future breeding. Genetic analyses were conducted using multiple methods. Principal component analysis (PCA), phylogenetic trees, and Bayesian clustering reflected borders between heterotic groups according to the derivation of each inbred line. A self-pollinated line derived from a classic F1 variety and another line from an open-pollinated population from the same derivation were classified as separate components by PCA and Bayesian clustering. The result suggests that open pollination could be essential in modern breeding. Of those classified as dent or flint based on their derivation, some had a combination of all components or clusters. Therefore, the classification of inbred lines should be based on their derivation and DNA markers. The findings will be valuable for breeding and genetic studies in Japan. Additionally, these techniques may be used to obtain a more significant number of SNPs and related phenotypic data.