Multi-locus genome-wide association study reveals the genetic architecture of kernel fat content in maize.
5 affiliations
- 1State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
- 2State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China. [email protected].
- 3State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China. [email protected].
- 4The Shennong Laboratory, Zhengzhou, 450046, P.R. China. [email protected].
- 5State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China. [email protected].
Abstract
Background
Kernel fat content (KFC) is a key determinant of oil quality and nutritional value in maize, yet the genetic architecture underlying its natural variation remains incompletely understood. Here, we performed a genome-wide association study (GWAS) using 239 maize inbred lines genotyped with 1.25 million single nucleotide polymorphisms (SNPs), applying six complementary statistical models: MLM, MLMM, FarmCPU, BLINK, SUPER, and 3VmrMLM.Results
KFC exhibited substantial phenotypic variation across the three environments, ranging from 5.48% to 8.72%, with a broad-sense heritability (H²) of 0.81. In total, 200 significant quantitative trait nucleotides (QTNs) were detected, each explaining 0.53%-23.49% of the phenotypic variance. Twenty QTNs were consistently identified across multiple models and/or environments and were consolidated into 18 non-redundant QTL intervals. Within these intervals, 58 candidate genes were annotated. Gene Ontology and KEGG enrichment analyses revealed significant enrichment in catalytic activities and metabolic pathways, notably α-linolenic acid metabolism-a core pathway in fatty acid biosynthesis. Based on multi-model co-localization and pathway evidence, Zm00001d025166, encoding a plastid-localized putative quinone-oxidoreductase, was prioritized as the primary candidate gene. Haplotype analysis identified two major haplotypes, with Hap1 conferring significantly higher KFC than Hap2 (7.09% vs. 6.46%, p = 0.003), although the difference was modest. Selective sweep analysis detected moderate selection pressure on this gene in U.S. breeding germplasm compared with Chinese and CIMMYT accessions, while weak differentiation between tropical and temperate ecotypes suggested a conserved role in fatty acid metabolism.Conclusions
These findings provide a foundation for marker-assisted selection in high-oil maize breeding and demonstrate the value of multi-model GWAS strategies for dissecting complex quantitative traits.
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BibTeX
@article{zong2026multilocus,
title = {{Multi-locus genome-wide association study reveals the genetic architecture of kernel fat content in maize.}},
author = {Jun Zong and Xiaolong Ju and Yaliang Li and Na Liu and Dong Ding and Jihua Tang and Xuehai Zhang},
journal = {BMC plant biology},
year = {2026},
month = oct,
doi = {10.1186/s12870-026-10081-z},
url = {https://europepmc.org/article/MED/42963586},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Multi-locus genome-wide association study reveals the genetic architecture of kernel fat content in maize.
AU - Jun Zong
AU - Xiaolong Ju
AU - Yaliang Li
AU - Na Liu
AU - Dong Ding
AU - Jihua Tang
AU - Xuehai Zhang
PY - 2026
DA - 2026/10/09
JO - BMC plant biology
DO - 10.1186/s12870-026-10081-z
UR - https://europepmc.org/article/MED/42963586
AB - Background Kernel fat content (KFC) is a key determinant of oil quality and nutritional value in maize, yet the genetic architecture underlying its natural variation remains incompletely understood. Here, we performed a genome-wide association study (GWAS) using 239 maize inbred lines genotyped with 1.25 million single nucleotide polymorphisms (SNPs), applying six complementary statistical models: MLM, MLMM, FarmCPU, BLINK, SUPER, and 3VmrMLM.Results KFC exhibited substantial phenotypic variation across the three environments, ranging from 5.48% to 8.72%, with a broad-sense heritability (H²) of 0.81. In total, 200 significant quantitative trait nucleotides (QTNs) were detected, each explaining 0.53%-23.49% of the phenotypic variance. Twenty QTNs were consistently identified across multiple models and/or environments and were consolidated into 18 non-redundant QTL intervals. Within these intervals, 58 candidate genes were annotated. Gene Ontology and KEGG enrichment analyses revealed significant enrichment in catalytic activities and metabolic pathways, notably α-linolenic acid metabolism-a core pathway in fatty acid biosynthesis. Based on multi-model co-localization and pathway evidence, Zm00001d025166, encoding a plastid-localized putative quinone-oxidoreductase, was prioritized as the primary candidate gene. Haplotype analysis identified two major haplotypes, with Hap1 conferring significantly higher KFC than Hap2 (7.09% vs. 6.46%, p = 0.003), although the difference was modest. Selective sweep analysis detected moderate selection pressure on this gene in U.S. breeding germplasm compared with Chinese and CIMMYT accessions, while weak differentiation between tropical and temperate ecotypes suggested a conserved role in fatty acid metabolism.Conclusions These findings provide a foundation for marker-assisted selection in high-oil maize breeding and demonstrate the value of multi-model GWAS strategies for dissecting complex quantitative traits.
SN - 1471-2229
ER -