# QTL-based dissection of three key quality attributes in maize using double haploid populations

## TL;DR

This study identifies genetic regions in maize linked to starch, oil, and lysine content, aiding in breeding better quality maize varieties.

## Contribution

The study identifies 47 QTLs and five candidate genes related to key maize quality traits using double haploid populations.

## Key findings

- Genetic factors largely control variations in starch, oil, and lysine content with heritability of 63.98-80.72%.
- 47 QTLs were identified, with each explaining 2.60-17.24% of phenotypic variation.
- Five candidate genes involved in starch, oil, and lysine metabolism were proposed based on QTL analysis.

## Abstract

Maize is a crucial source of nutrition, and the quality traits such as starch content, oil content, and lysine content are essential for meeting the demands of modern agricultural development. Understanding the genetic basis of these quality traits significantly contributes to improving maize yield and optimizing end-use quality. While previous studies have explored the genetic basis of these traits, further investigation into the quantitative trait loci (QTL) responsible for variations in starch content, oil content, and lysine content still requires additional attention.

Double haploid (DH) populations were developed via a nested association mapping (NAM) design. Phenotypic data for starch, oil, and lysine content were collected using near-infrared spectroscopy and analyzed via ANOVA. Genotyping employed a 3K SNP panel, and genetic maps were constructed using QTL IciMapping. QTL analysis integrated single linkage mapping (SLM) and NAM approaches, with candidate genes identified via maizeGDB annotation and transcriptome data.

The broad-sense heritability of the populations with a range of 63.98-80.72% indicated the majority of starch content, oil content and lysine content variations were largely controlled by genetic factors. The genetic maps were constructed and a total of 47 QTLs were identified. The phenotypic variation explained (PVE) of the three traits is in a range of 2.60-17.24% which suggested that the genetic component of starch content, oil content and lysine content was controlled by many small effect QTLs. Five genes encoding key enzymes in regulation of starch, oil and lysine synthesis and metabolism located within QTLs were proposed as candidate genes in this study.

The information presented herein will establish a foundation for the investigation of candidate genes that regulate quality traits in maize kernels. These QTLs will prove beneficial for marker-assisted selection and gene pyramiding in breeding programs aimed at developing high-quality maize varieties.