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. 2025 Jun 23:16:1587217.
doi: 10.3389/fpls.2025.1587217. eCollection 2025.

Mining candidate genes for maize plant height based on a GWAS, Meta-QTL, and WGCNA

Fu Qian  1 , Zhanqin Zhang  2 , Shubin Chen  2 , Zhiqin Sang  2 , Weihua Li  1
Affiliations

Mining candidate genes for maize plant height based on a GWAS, Meta-QTL, and WGCNA

Fu Qian et al. Front Plant Sci. .

Abstract

Introduction: In maize, plant height (PH) is one of the most important agronomic traits that directly influences planting density and yield. Therefore, identifying candidate genes related to PH will help manipulate maize yield indirectly.

Methods: The present research carried out a genome-wide association study (GWAS) of PH using a natural population of 580 maize inbred lines. Further, after collecting the published transcriptome data of maize B73, tissue-specific gene co-expression modules related to PH were generated using weighted gene co-expression network analysis (WGCNA). Furthermore, a meta-analysis of the already reported PH-related quantitative trait loci (QTLs).

Results: The integrated analysis of the results based on the different approaches screened three candidate genes: Zm00001d031796, encoding AP2-EREBP transcription factor 172; Zm00001d009918, encoding Phytochrome A-associated F-box protein; and Zm00001d042454, encoding plastid specific ribosomal protein 4.

Keywords: GWAS; Meta-QTL; WGCNA; candidate gene; maize; plant height.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Manhattan plot and QQ plot of PH.
Figure 2
Figure 2
Analysis of the allelic effects of colocalized SNPs for PH. *** indicates a significant difference at the 0.001 probability level.
Figure 3
Figure 3
Construction of the co-expression network by weighted gene co-expression network analysis. (A) The clustering dendrogram of samples and tissue correspondence; (B) the determination of soft threshold; (C) gene clustering and module construction; (D) correlation between traits and modules. The red color represents a positive correlation between the module and the trait. The green color represents a negative relationship between the module and the trait.
Figure 4
Figure 4
Projection and distribution of QTLs and MQTLs (Meta-QTLs) identified for PH on chromosome 7. The bars on the left side of the chromosome correspond to QTLs related to the plant height trait, the black bars within the chromosomes represent marker density, the colored segments within the chromosome represent MQTLs, and on the right side of the chromosome are molecular markers and genetic distances (cM).
Figure 5
Figure 5
Circos plot showing the Meta-QTLs, significant SNPs, and genes on a physical map. The colored bars show the 10 maize chromosomes, and the red and blue areas represent the positions of MQTL and SNPs on the chromosome. * indicates candidate genes jointly identified by Meta-QTL analysis and WGCNA.
Figure 6
Figure 6
Local regulation network of gene co-expression of key modules. The red nodes are reported plant height trait genes, the green nodes are plant height trait candidate genes. * candidate genes jointly identified by WGCNA and Meta QTL or GWAS.
See this image and copyright information in PMC

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