# Genetic Mapping Identifies Stable QTL and Candidate Genes Regulating Internode Proportion for Maize Plant Architecture Improvement

## TL;DR

This study identifies genetic regions and genes that influence the structure of maize plants, which could help breeders improve crop yield.

## Contribution

The study discovers stable QTL and candidate genes related to maize internode proportion using genome-wide association analysis.

## Key findings

- 821 significant SNPs and 417 QTL were identified for traits related to maize internode proportion.
- Four stable QTL (qU1–qU4) were identified through colocalization analysis.
- Two candidate genes were supported by haplotype analysis and showed significant differences in internode-related traits.

## Abstract

Background: Ideal plant architecture is central to high-yield maize breeding. The proportional length of internodes above the ear plays a crucial role in determining plant architecture. Methods: In this study, we used an association panel comprising 288 maize inbred lines and performed genome-wide association studies (GWASs) with 1.25 M high-density single nucleotide polymorphism (SNP) markers under a Q + K mixed linear model. Results: A total of 821 significant SNPs associated with plant height (PH), height above ear (HAE), and internode-related traits were detected, which were further classified into 417 quantitative trait loci (QTL). Among these, 128 significant SNPs and 44 QTL were identified for the U1/HAE trait, and 37 significant SNPs and 27 QTL for the U1/PH trait. Four stable QTL (qU1–qU4) were identified through colocalization analysis. Two candidate genes, Zm00001d013222 (involved in gibberellin signaling) and Zm00001d021304 (involved in cell wall metabolism), were further supported by haplotype analysis. For the former gene, U1/PH values in Hap1 and Hap3 were significantly lower than those in Hap2 (p < 0.01). For the latter gene, Hap2 exhibited a significantly higher U1/HAE value compared to Hap1 (p < 0.001). Conclusions: These findings provide new genetic insights into the regulation of maize internode proportion and plant architecture, offering potential targets for molecular breeding.