Background: As waxy maize is considered a key economic crop in Korea, an understanding of its genetic variation and differentiation is fundamental for the selective plant breeding. The maize genome is primarily composed of transposable elements, for which large and stable insertions generate variations that reflect selection during evolution.
Objectives: This study was to elucidate the genetic diversity based on the contribution of TEs and to investigate the effect of Mu transposition on the genetic divergence of waxy and common maize. We also performed an association analysis on these inbred lines to determine the Mu insertions associated with agronomic traits.
Methods: In this study, we utilized a Mutator-based transposon display method to study the genetic diversity and population structure of 40 waxy and 40 common inbred lines of maize in the Gangwon Agricultural Research and Extension Services collection at the Maize Research Institute.
Results: We detected polymorphisms in 86.33% of 278 Mutator (Mu) anchored loci, reflecting the activity of the Mu element and its contribution to genetic variation. Common maize showed a substantial amount of genetic diversity, which was greater than that observed in waxy maize. Principal-coordinate and neighbor-joining cluster analyzes consistently supported the presence of two genetically distinct groups. However, the distribution of genetic variation within the populations was much higher than the genetic differentiation among the populations. To explore the contribution of the Mu element to phenotypic variation, we analyzed the associations with ten important agronomical traits. On the basis of the combined results from two models (QGLM and Q + KLM), we found significant associations between seven Mu loci and four different traits.
Conclusions: These results will assist waxy maize breeders in choosing parental lines and be useful for marker-assisted selection.
Keywords: Mutator insertion polymorphism; association analysis; genetic diversity; inbred lines; maize.