ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Genetics, Epigenetics and Chromosome Biology
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1606220
Genome and transcriptome wide association study identify candidate genes regulating folate levels in maize
Provisionally accepted
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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Background: Maize (Zea mays L.) serves as a crucial dietary source of folate for humans. However, the genetic regulatory mechanisms underlying the natural variation of folate in maize remain poorly understood. Here, we integrated multi-omics approaches to elucidate the molecular mechanisms governing folate accumulation in maize.Methods: A total of 380 maize kernels representing 190 maize inbred lines from China, Thailand, Mexico, and Peru were collected. RNA-seq was conducted on 380 maize kernel samples, and folate content was quantified using high-performance liquid chromatography (HPLC). The samples were stratified into high and low folate groups based on median folate values. Differentially expressed genes (DEGs) were identified between the two groups identified. Candidate genes associated with folate accumulation were further located by integrating transcriptome-wide association studies (TWAS) and genome-wide association studies (GWAS) analyses. Finally, quantitative real-time PCR (qRT-PCR) was employed to validate the expression patterns of these candidate genes.Results: A total of 137 DEGs that exhibited significant differences between the high-folate and low-folate groups were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these genes were significantly enriched in pathways related to phenylpropanoid biosynthesis, oxidoreductase activity, and stress response. GWAS identified 2,153 candidate genes associated with folate traits (P ≤ 1.00E-05). Through the integration of DEGs and the intersection of genes identified by GWAS, seven candidate genes were further identified. In addition, TWAS analysis further identified 13 causal genes associated with the candidate genes, which are involved in folate biosynthesis. In addition, the expression levels of these candidate genes were validated by qRT-PCR experiments, suggesting significantly higher expressions in the high folate group compared to the low-folate group.This study identifies key regulatory genes potentially influencing folate accumulation in maize and provides critical insights for the development of biofortified maize varieties with enhanced nutritional value.
Keywords: TWAS, GWAS, Folate, Maize, candidate genes
Received: 04 Apr 2025; Accepted: 27 May 2025.
Copyright: © 2025 Zou, Yang, Huang, Mo, Zhai and Huang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Kaijian Huang, Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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