Combining QTL Mapping and Multi-Omics Identify Candidate Genes for Nutritional Quality Traits during Grain Filling Stage in Maize

The nutritional composition and overall quality of maize kernels are largely determined by the key chemical components: protein, oil, and starch. Nevertheless, the genetic basis underlying these nutritional quality traits during grain fi lling remains poorly understood. In this study, the concentrations of protein, oil, and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages postpollination. All the traits exhibited considerable phenotypic variation. During the grain- fi lling stage, the levels of protein and starch content generally increased, whereas oil content decreased, with signi fi cant changes observed between 30 and 40 days after pollination. Quantitative trait locus (QTL) mapping was conducted and a total of 32 QTLs, comprising 14, 12, and 6 QTLs for grain protein, oil, and starch content were detected, respectively. Few QTLs were consistently detectable across different time points. By integrating QTL analysis, global gene expression pro fi ling, and comparative genomics, we identi fi ed 157, 86, and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein, oil, and starch content, respectively. Subsequent gene function annotation prioritized 15 candidate genes potentially involved in regulating grain quality traits, including those encoding transcription factors (NAC, MADS-box, bZIP, and MYB), cell wall invertase, cellulose-synthase-like protein, cell division cycle protein, trehalase, auxin-responsive factor, and phloem protein 2-A13. Our study offers signi fi cant insights into the genetic architecture of maize kernel nutritional quality and identi fi es promising QTLs and candidate genes, which are crucial for the genetic enhancement of these traits in maize breeding programs.