Article (Scientific journals)
Integrating GWAS, QTL Mapping, and RNA-seq to Identify Candidate Genes for Kernel Weight and Oil Traits in Maize (Zea mays ssp. mays).
Zhang, Lijun; Song, Yuhan; Chen, Meiyan et al.
2026 • In Journal of Agricultural and Food Chemistry, 74 (13), p. 11285 - 11295
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Keywords :
GWAS analysis; Maize; Oil content; QTL mapping; RNA-seq; Plant Proteins; Plant Oils; Corn Oil; Genome-Wide Association Study; Chromosome Mapping; RNA-Seq; Polymorphism, Single Nucleotide; Phenotype; Zea mays/genetics; Zea mays/metabolism; Zea mays/chemistry; Zea mays/growth & development; Quantitative Trait Loci; Seeds/genetics; Seeds/chemistry; Seeds/metabolism; Seeds/growth & development; Plant Proteins/genetics; Plant Proteins/metabolism; Plant Oils/metabolism; Plant Oils/analysis; Corn Oil/metabolism; Candidate genes; Genome-wide association studies; Genome-wide association study analyze; K- models; Kernel weight; Oil contents; Quantitative trait loci mappings; Quantitative trait locus; Fatty Acids; Seeds; Zea mays; Chemistry (all); Agricultural and Biological Sciences (all)
Abstract :
[en] The evaluation of the kernel oil content and fatty acid composition in maize is crucial for understanding maize nutrition. This study utilized an association population of 278 inbred lines and a F2 population of 229 individuals to identify candidate genes for 8 kernel weight and oil traits. By employing two genome-wide association study (GWAS) models, the K model and Q+K model, key SNP loci and candidate genes were identified. A total of 10 pleiotropic quantitative trait loci (QTLs) were discovered that collectively encompassed 82 candidate genes. Notably, the SAD gene catalyzed the conversion of stearoyl-acyl carrier protein (ACP) to oleoyl-ACP, playing a crucial role in regulating the content of unsaturated fatty acids in plants. Three candidate genes were identified through three methods (GWAS, QTL mapping, and RNA-seq), with the FALDH gene playing a role in regulating the grain oil content. Through the integration of GWAS analysis and QTL mapping, one stable QTL related to the oil content (qOC5) and one stable QTL related to arachidic acid (qAA9) were identified. Among them, the FAE2 gene was located in qAA9, which plays a crucial role in regulating the fatty acid content in plants. Additionally, the gene TT12, identified through a combination of GWAS and RNA-seq analyses, has been found to play a pivotal role in seed development. Overall, these findings provide a foundation for deeper insights into the genetic mechanisms underlying maize oil traits and offer valuable insights for molecular marker-assisted breeding.
Disciplines :
Genetics & genetic processes
Author, co-author :
Zhang, Lijun ✱;  Guangxi Sugarcane Bio-breeding Laboratory, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
Song, Yuhan   ✱;  Université de Liège - ULiège > TERRA Research Centre > Plant Sciences ; National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
Chen, Meiyan;  Guangxi Sugarcane Bio-breeding Laboratory, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
Hu, Chunyu;  Guangxi Sugarcane Bio-breeding Laboratory, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
Wang, Wanru;  Guangxi Sugarcane Bio-breeding Laboratory, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
Zhou, Xunbo ;  College of Agriculture, Guangxi University, Nanning 530005, China
Hao, Xiaoqin;  College of Agriculture, Guangxi University, Nanning 530005, China
Zhang, Xingtan ;  National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
Yang, Xiping ;  Guangxi Sugarcane Bio-breeding Laboratory, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China ; College of Agriculture, Guangxi University, Nanning 530005, China
✱ These authors have contributed equally to this work.
Language :
English
Title :
Integrating GWAS, QTL Mapping, and RNA-seq to Identify Candidate Genes for Kernel Weight and Oil Traits in Maize (Zea mays ssp. mays).
Publication date :
08 April 2026
Journal title :
Journal of Agricultural and Food Chemistry
ISSN :
0021-8561
eISSN :
1520-5118
Publisher :
American Chemical Society, United States
Volume :
74
Issue :
13
Pages :
11285 - 11295
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
NSCF - National Natural Science Foundation of China
Funding text :
This work was supported by the Science and Technology Major Project of Guangxi (GK AD25069107), the National Natural Science Foundation of China (31960429), and the \u201COne Hundred Person\u201D Project of Guangxi Province.
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since 28 August 2026

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