Open Access

ARTICLE

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

Pengcheng Li^1,2,#, Tianze Zhu^1,#, Yunyun Wang^1,2, Shuangyi Yin¹, Xinjie Zhu¹, Minggang Ji¹, Wenye Rui¹, Houmiao Wang¹, Zefeng Yang^1,2,*, Chenwu Xu^1,2,*

1 Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
2 Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China

* Corresponding Authors: Zefeng Yang. Email: ; Chenwu Xu. Email:

Phyton-International Journal of Experimental Botany 2024, 93(7), 1441-1453. https://doi.org/10.32604/phyton.2024.052219

Received 26 March 2024; Accepted 24 June 2024; Issue published 30 July 2024

Abstract

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 filling 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 post-pollination. All the traits exhibited considerable phenotypic variation. During the grain-filling stage, the levels of protein and starch content generally increased, whereas oil content decreased, with significant 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 profiling, and comparative genomics, we identified 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 significant insights into the genetic architecture of maize kernel nutritional quality and identifies promising QTLs and candidate genes, which are crucial for the genetic enhancement of these traits in maize breeding programs.

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Supplementary Material

Supplementary Material File

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