# Genomic-assisted refinement of heterotic groups in short-duration maturing tropical yellow and orange maize inbred lines

## TL;DR

This study uses genomic data to refine heterotic groups in tropical maize inbreds, improving hybrid breeding strategies for better yield.

## Contribution

The study introduces a genomic-assisted approach to refine heterotic groups in tropical maize inbreds based on maturity and genetic diversity.

## Key findings

- Genomic analysis identified three genetic clusters, with maturity being the main driver of sub-group formation.
- Hybrid performance was significantly higher when crossing lines from different maturity-based heterotic subgroups.
- Two major heterotic groups were defined for breeding applications, enhancing hybrid yield potential.

## Abstract

Understanding the genetic diversity and population structure of maize inbred lines is fundamental for effective hybrid development and strategic heterosis exploitation. The objective of this study was to refine and validate heterotic groups within a diverse collection of extra-early and early maturing tropical yellow and orange maize inbred lines. A total of 1,437 elite tropical yellow and orange maize inbred lines spanning early and extra-early maturing groups were genotyped using a panel of 3,305 DArTag SNP markers. In addition, the study evaluated 280 hybrids comprising 276 hybrids (from 214 inbred lines crossed with four standard testers) and four commercial checks. The yield performance trials used a 14 × 20 alpha-lattice design with two replicates over two years.

Marker-based diversity analysis revealed average marker polymorphism of 0.328, minor allele frequency of 0.265, and expected heterozygosity of 0.315. Principal component analysis (PCA), discriminant analysis of principal components (DAPC), and ancestral admixture analysis revealed three genetic clusters, while phylogenetic analysis supported the existence of two major clusters with groups one and three from DAPC and admixture methods combined into a single phylogenetic group. Several sub-groups were identified within the main genetic pools and maturity rather than kernel color was the major driver of these sub-groups. For operational ease in breeding applications, the lines were assigned to two major heterotic groups. The average performance of the hybrid for grain yield and heterosis estimates from between maturity-based heterotic subgroups were consistently and significantly (p < 0.001) higher than those from within maturity-based heterotic subgroups.

These results provide a robust framework for parental line selection, heterotic grouping, and hybrid breeding strategies, facilitating the development of extra-early and early superior yellow/orange maize hybrids adapted to tropical environments.

The online version contains supplementary material available at 10.1186/s44399-026-00032-2.