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Article

Comprehensive Characterization of the FATs Gene Family in Maize: Phylogeny, Expression Patterns, and Regulatory Networks

by
Yunlong Li
†,
Shuai Hou
†,
Yan Sun
,
Shujun Li
,
Minghao Sun
,
Baitao Guo
,
Luyao Wang
,
Quan Cai
,
Xin Li
,
Sinan Li
and
Jianguo Zhang
*
Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2025, 16(9), 1035; https://doi.org/10.3390/genes16091035 (registering DOI)
Submission received: 15 July 2025 / Revised: 22 August 2025 / Accepted: 29 August 2025 / Published: 30 August 2025
(This article belongs to the Section Plant Genetics and Genomics)
Browse Figures
Versions Notes

Abstract

Background: Fatty acyl–ACP thioesterase (FAT) genes regulate fatty acid composition and content, yet the FAT family in maize has not been systematically characterized. Methods: Ten ZmFAT genes were identified from the maize genome and analyzed for gene structure, protein properties, phylogeny, collinearity, cis-acting elements, and predicted interactions. Transcriptome and qRT–PCR data were used to assess expression patterns during seed development. Results: The ten ZmFAT genes were grouped into two subfamilies (three ZmFATA and seven ZmFATB genes). Two pairs of collinear genes were detected within maize and one pair between maize and rice. Promoter analysis revealed light- and development-responsive elements. Two genes were functionally annotated in fatty acid biosynthesis, while five proteins exhibited interactions and 14 miRNAs were predicted to regulate ZmFAT genes. Expression analysis showed that ZmFATA1/2 and ZmFATB4/6/7 maintained high expression in both upper and lower seed parts, and qRT–PCR confirmed their gradual upregulation during seed development. Conclusion: This study provides the first comprehensive characterization of the maize ZmFAT family, offering insights into fatty acid metabolism and valuable genetic resources for improving maize oil composition.

1. Introduction

Fatty acid biosynthesis (FAS) is an indispensable fundamental metabolic pathway extensively involved in phospholipid synthesis, cell membrane assembly, cellular signal transduction, energy storage, and gene expression regulation [1,2]. In higher plants, fatty acid biosynthesis occurs in plastids [3]. Acetyl–CoA serves as the precursor for this pathway and is converted into malonyl–CoA by acetyl–CoA carboxylase, which provides the elongation substrate for fatty acid biosynthesis [4,5]. Subsequently, type II fatty acid synthase catalyzes successive condensation reactions between malonyl–CoA and acyl–ACP derivatives, elongating acyl chains by two carbons per cycle to produce 16– to 18–carbon saturated fatty acids [6]. Fatty acyl–ACP thioesterase (FAT) terminates fatty acid synthesis by hydrolyzing the thioester bond between the acyl group and ACP, thereby releasing free fatty acids and ACP [7]. The fatty acids are transported to the cytoplasm for further esterification to form acyl–CoA, which then undergoes fatty acid chain elongation and desaturation on the endoplasmic reticulum, incorporation into membrane lipids as phospholipids, and metabolism and storage through triacylglycerol synthesis [8,9,10]. FAT plays a crucial role in regulating lipid metabolism and storage.
FATs are plastid-targeted soluble enzymes encoded by nuclear genes [11]. Based on their amino acid sequences and substrate specificities, FATs are classified into two subfamilies: FATA and FATB [12]. The substrate specificity of FATs largely determines the chain length and degree of unsaturation of plant fatty acids. FATA preferentially acts on unsaturated acyl–ACP, exhibiting the highest activity toward 18:1–ACP. In contrast, FATB shows limited activity toward 18:1–ACP but exhibits high activity toward saturated acyl–ACPs [13,14]. The FAT genes family has been identified and characterized in the genomes of various plants including Glycine max [15], Arachis hypogaea [16], Elaeis guineensis [17], and others. Moreover, FAT genes have been cloned and functionally analyzed in plants such as Brassica napus [18], Cinnamomum longepaniculatum [19], Helianthus annuus [20], and cotton [21].
The substrate specificity of FAT determines fatty acid composition and content [21]. Disruption of the AtFATB gene resulted in a 40–50% reduction in total saturated fatty acid content in different tissues compared with wild-type Arabidopsis, with palmitic acid content significantly decreased [22]. In soybean, GmFATs determine the ratio and composition of saturated and unsaturated fatty acids. Mutations in GmFATA1A and GmFATB resulted in increased oleic acid content, while GmFATB mutation reduced palmitic acid content [15]. Fatty acid profiling of tobacco leaves transiently expressing GhA-FatB3 or GhD-FatB4 demonstrated that they have high substrate preference for 16:0-ACP and resulted in palmitic acid enrichment [21].
Maize (Zea mays L.) is widely cultivated worldwide [23]. Maize germ can be processed through a series of refining procedures to produce high-quality vegetable oil rich in linoleic acid, oleic acid, and palmitic acid [24]. Studies have shown that long-term consumption of corn oil reduces cholesterol absorption and synthesis to some extent [25], thereby slowing the development of atherosclerosis [26]. This study, ZmFATs were identified and characterized from maize, providing a foundation for the genetic improvement of maize oil composition and content.

2. Materials and Methods

2.1. Identification of FATs Family Members in Maize

The maize genome and its annotation files were downloaded from the Ensembl Plants database (Zm-B73-REFERENCE-NAM-5.0). A genome-wide search was performed using the HMM model of the acyl-ACP thioesterase N-terminal domain (PF01643) with a threshold set at E < 1 × 10−5. Sequences were manually submitted to the CDD (http://blast.ncbi.nlm.nih.gov, accessed on 20 December 2024), pfam (https://www.ebi.ac.uk/interpro/, accessed on 20 December 2024) and SMART (http://smart.embl-heidelberg.de/, accessed on 20 December 2024) databases to exclude genes with incomplete structures and lacking conserved domains [27,28]. Corresponding protein sequences were retrieved based on the identified genes. Sequences were submitted to the ExPASy database (http://web.expasy.org/compute_pi/, accessed on 20 December 2024) to calculate the physicochemical properties of the proteins [29].

2.2. Phylogenetic Analysis of ZmFATs Family Members

To classify FATs family members from maize, Arabidopsis, and soybean, their protein sequences were aligned using the ClustalW algorithm in MEGA (v7) software [30]. After sequence alignment, a phylogenetic tree was constructed using the neighbor-joining (NJ) method with 1000 bootstrap replicates to build a robust evolutionary tree. FATs from Arabidopsis and soybean served as references for the systematic classification of maize ZmFATs. We used EvolView-v3 (https://www.evolgenius.info/evolview-v3/, accessed on 21 December 2024) to optimize the visualization of the phylogenetic tree.

2.3. Gene Structure and Motif Analysis of ZmFATs Family

The online tool MEME Suite v1.1 (http://meme-suite.org/tools/meme, accessed on 22 December 2024) was used to analyze gene structure and conserved motifs [31]. The maximum number of motifs was set to 15. TBtools (v2.301) was used to visualize motifs, introns, and exons of genes [32].

2.4. Chromosomal Localization and Collinearity Analysis of Maize ZmFAT Genes

The MCScanX tool was used to analyze homologous relationships among FAT genes from maize, rice, and Arabidopsis [33]. TBTools was used to visualize gene positions on chromosomes [32]. Genes with collinear relationships were connected by lines.

2.5. Cis-Elements Analysis

The upstream 2000 bp sequence of each ZmFAT was extracted as its promoter sequence and submitted to the PlantCARE database (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 25 December 2024) to predict cis-acting elements (CREs) in the promoter region [34]. The R ggplot2 package was used for visualization.

2.6. Functional Annotation Analysis

Gene Ontology (GO) functional annotation was performed using EggNOG database and clusterProfiler (v4.17.0) software package with pvalueCutoff = 0.05 and qvalueCutoff = 0.05. Functional annotation results were visualized using the R package ggplot2 (v3.5.2).

2.7. Protein Interaction Prediction

ZmFAT protein sequences were submitted to the STRING database (https://string-db.org/, accessed on 26 December 2024) to search and predict protein interaction relationships [35], and the protein interaction network was visualized using the R package ggplot2.

2.8. miRNA Interaction Analysis with Maize ZmFATs

To construct the miRNA–gene interaction network, ZmFATs CDS sequences were submitted to the psRNATarget website (https://www.zhaolab.org/psRNATarget/, accessed on 27 December 2024). Using the website’s default parameters, putative miRNAs targeting ZmFAT genes were predicted, and the results were visualized using Cytoscape (v3.10.3) [36].

2.9. Transcriptome Analysis

Transcriptome data from different developmental stages of maize seed upper (U) and lower (B) parts after pollination were downloaded from the NCBI website (https://www.ncbi.nlm.nih.gov/, accessed on 28 December 2024) (BioProject IDs: PRJNA1027494 and PRJNA1027500) to analyze the expression patterns of the ZmFAT family at different developmental stages of maize seeds (4, 5, 6, 8, 10, 12, 16, 20, 24, 28, 32 d). Salmon V1.10.3 software was used to quantify the expression of ZmFATs from the transcriptome data.

2.10. qRT–PCR Analysis

Maize inbred line B73 was planted in Harbin. Seeds from different developmental stages in the upper (U) and lower (B) parts were collected for qPCR analysis, with three independent biological replicates for each sample. RNA was extracted from maize seeds using the RNAqueous™ Micro Total RNA Isolation Kit (ThermoFisher, Waltham, MA, USA). Then, cDNA was synthesized from total RNA using the RevertAid™ First Strand cDNA Synthesis Kit (ThermoFisher, Waltham, MA, USA). Real-time qPCR analysis was performed on a Bio–Rad CFX96 Real-Time PCR Detection System (Bio–Rad, Hercules, CA, USA) with ChamQ Universal SYBR qPCR Master Mix (Vazyme, Nanjing, China). ZmActin1 was used as the reference gene, and the primer sequences are listed in Table S1. The following qPCR protocol was used: denaturation at 95 °C for 3 min, followed by 40 cycles of 15 s at 95 °C and 20 s at 65 °C for amplification. Target genes were quantified using the 2−ΔΔCt method [37].

2.11. Statistical Analysis

Experimental data are presented as means ± standard error from at least three independent biological replicates. p-values were calculated by one-way ANOVA method using SPSS ver. 25.0 (SPSS Inc., Chicago, IL, USA), with p < 0.05 representing significant differences. Data were visualized using GraphPad Prism 9.

3. Results

3.1. Identification and Characterization of Maize FAT Family Members

To identify the maize FAT gene family, we searched the maize genome using HMM search and BLASTP. All candidate sequences were subsequently verified by manual domain analysis with Pfam, SMART, and NCBI–CDD databases. Ten FATs were identified. Based on their chromosomal positions and phylogenetic relationships, they were designated as ZmFATA1–3 and ZmFATB1–7 (Table 1 and Figure 1). The physicochemical properties of proteins encoded by ZmFAT genes were calculated (Table 1). ZmFATAs comprised 157–426 amino acids (aa) with molecular weights ranging from 16.96–47.67 kDa. Among ZmFATBs, ZmFATB5 had the fewest amino acids and lowest molecular weight (83 aa, 9.74 kDa). ZmFATB6 contain the most amino acids (434 aa) and had the highest molecular weight (47.76 kDa). Furthermore, the isoelectric point (pI) reflects the acidity and alkalinity of proteins. Only ZmFATB1 had a pI below 6 (5.4), indicating acidity. ZmFATA1–3 and ZmFATB2–7 all had pI values greater than 6 (6.37–10.29), indicating alkalinity. The grand average of hydropathicity (GRAVY) values were all < 0 (−0.75 to −0.08), suggesting that ZmFATs generally possess hydrophilic and soluble characteristics.

3.2. Phylogenetic Classification of the Maize FATs Family

Twelve GmFATs, 3 AtFATs, and the identified 10 ZmFATs were used to construct the phylogenetic tree. The phylogenetic tree was divided into 3 major clades. Three ZmFATAs, 2 AtFATAs, and 4 GmFATAs clustered in a common clade (FATA). FATBs comprised two clades. ZmFATB3 clustered with 4 GmFATBs in the same clade. The other clade contained 1 AtFATB, 4 GmFATBs, and 6 ZmFATBs.

3.3. Analysis of Conserved Motifs and Gene Structure

Gene structure potentially reflects gene function and evolutionary relationships [38]. Members of ZmFAT family were divided into 3 subgroups in the phylogenetic tree (Figure 2). ZmFATs contained 3–10 motifs. ZmFATB6/7 contained the most motifs (10), followed by ZmFATA3 (8), while ZmFATA1 and ZmFATB1/5 had the fewest motifs (3). Motif2 was present in all ZmFATs and represented the most conserved motif. Motif8/9 were most conserved in ZmFATAs. The gene structures of ZmFATs exhibited considerable variation. ZmFATB2 contained the fewest introns (3), while ZmFATB1/6/7 contained the most introns (6).

3.4. Chromosomal Localization and Collinearity Analysis

ZmFATs were distributed on 6 chromosomes (chromosomes 1/2/6/7/9/10). Chromosomes 1, 2, 7, and 9 each harbored 2 genes, while chromosomes 6 and 10 each contained 1 gene. Among the collinearity relationships of 4 members of the ZmFAT family, 2 pairs of duplicated genes were identified (Figure 3). These included ZmFATA1 and ZmFATA2, and ZmFATB4 and ZmFATB7. No collinear gene pairs were found between ZmFATs and AtFATs, but 1 pair was identified between maize and rice (Figure 4). This result suggests that the differentiation of ZmFATs occurred after the divergence of monocotyledons and dicotyledons.

3.5. Cis-Acting Element Analysis

Cis-acting element analysis was performed on 2000 bp upstream of ZmFATs obtained from genomic sequences to characterize their potential biological functions (Figure 5). ZmFATs harbored abundant cis-acting elements related to light response and plant growth and development. CAAT box and TATA box are the core cis-acting elements of ZmFATs. ZmFATB7 had the fewest CAAT boxes (19) and TATA boxes (8), while ZmFATB3/5 had 44 CAAT boxes. Furthermore, ZmFATB3 contained the most TATA boxes (92) and AT–TATA boxes (37). In addition, all ZmFAT promoters contain 24 light-responsive cis-acting elements G box. ZmFATs contain abundant plant hormone-related elements. Except for ZmFATB3, other ZmFATs collectively contain 20 ABRE elements. Except for ZmFATA1/2, other ZmFATs collectively contain 15 CGTCA motifs and 15 TGACG motifs. Numerous cis-acting elements of ZmFATs are related to stress response. ZmFATs contain 85 MYB, 40 MYC, and 26 STRE elements. Except for ZmFATA2, other ZmFATs contain 33 MBS elements. Except for ZmFATA1 and ZmFATB3, other ZmFATs have 21 ARE elements. Except for ZmFATB5, other ZmFATs have 17 WRE3 elements. Except for ZmFATA1/2, other ZmFATs have 15 as–1 elements. ZmFATB3 contained the most MYB (24) and MBS (18) elements. ZmFATB5 had 9 MYB and 12 MYC elements.

3.6. Functional Annotation Analysis of ZmFAT Genes

To further investigate the functions of FAT genes, GO functional annotation was performed (Table S2). Five ZmFATs were annotated with biological processes and molecular functions (Figure 6). In biological processes, the gene proportions for purine nucleobase metabolic process, purine nucleobase biosynthetic process, purine-containing compound salvage, purine-containing compound metabolic process, purine-containing compound biosynthetic process, pigment metabolic process, pigment biosynthetic process, nucleobase metabolic process, nucleobase biosynthetic process, nucleobase-containing small molecule metabolic process, and cellular metabolic compound salvage were all 3/5. In molecular functions, the proportions for phosphoribosyltransferase activity, pentosyltransferase activity, glycosyltransferase activity, and phosphoribosyltransferase activity were 3/5, indicating their involvement in the formation and conversion of ribose in nucleotides. This suggests that these genes are extensively involved in the synthesis and metabolism of nuclear nucleic acids and their units. Additionally, the proportions for monocarboxylic acid biosynthetic process, fatty acid metabolic process, and fatty acid biosynthetic process were 2/5. The proportions for thiolester hydrolase activity, purine fatty acid synthase activity, adenine transferring groups other than amino–acyl groups, and acyltransferase activity were 2/5. This indicates that ZmFATs participate in fatty acid accumulation by affecting enzyme synthesis.

3.7. Interaction Analysis Among ZmFATs and miRNA Regulation Analysis

Protein–protein interaction analysis revealed that six ZmFAT proteins are predicted to interact with each other (Figure 7). Among them, ZmFATA1 and ZmFATA2, as well as ZmFATB6 and ZmFATB7, exhibited the strongest direct interactions, while additional indirect associations were observed between ZmFATA1/2 and ZmFATB3/4/6/7. These results suggest that ZmFATA1 and ZmFATA2 may act as central nodes within the interaction network.
Furthermore, gene–miRNA interaction analysis identified 14 miRNAs potentially regulating five ZmFATs (Figure 8). Notably, ZmFATB6 was targeted by the largest number of miRNAs, while five miRNAs regulated ZmFATA3. In addition, ZmFATB2, ZmFATB3, and ZmFATB7 were regulated by zma–miR159e–5p, zma–miR164g–3p, and zma–miR395c–5p, respectively.

3.8. Analysis of ZmFATs Expression Levels in Maize Seeds at Different Developmental Stages

Transcriptomic analysis revealed differential expression patterns of ZmFAT genes in maize seeds across developmental stages. Compared with other genes, ZmFATA1/2 and ZmFATB4/6/7 consistently exhibited high expression levels during seed development (Figure 9 and Figure 10). During seed development, the expression levels of ZmFATA1/2 and ZmFATB1/4/6 in the upper part of maize seeds gradually increased (Figure 9). At later developmental stages, ZmFAT2 exhibited the highest expression level. ZmFATB7 showed high expression levels at early developmental stage (especially at 5 d and 8 d), but declined at the later stage. In the lower part of maize seeds, with continuous development, the expression levels of ZmFATA1/2 and ZmFATB4/6/7 gradually increased (Figure 10). In the late developmental stage, ZmFAT2 showed the highest expression level, followed by ZmFATB6/7. ZmFATB3 showed high expression levels in the early developmental stage, but expression decreased with continuous development. The expression level of ZmFATB1 showed fluctuating changes.
The qRT–PCR analysis results were similar to the transcriptomic analysis. In both the upper and lower parts of seeds, the expression levels of ZmFATA1/2 and ZmFATB4/6 gradually increased with developmental progression (Figure 11 and Figure 12). ZmFATB7 had higher expression levels in the early stage of the upper part (Figure 11J) and higher expression levels in the late stage of the lower part (Figure 12J). During seed formation, the expression levels of ZmFATA3 and ZmFATB1/2/5 in both upper and lower parts showed fluctuating changes (Figure 11 and Figure 12). The expression pattern of ZmFATB3 differed between upper and lower seed regions. In the upper part, ZmFATB3 expression showed a trend of first increasing then decreasing (Figure 11F). In the lower part, its expression first decreased then slowly increased (Figure 12F). These results indicate that ZmFAT genes play important roles in maize seed development, with spatiotemporal differences observed among family members.

4. Discussion

Maize oil is characterized by a high proportion of unsaturated fatty acids and a low proportion of saturated fatty acids. These compositional differences from other plant oils may contribute to the favorable nutritional properties of maize oil [39,40]. Differences in fatty acid composition and content are often regulated by FAT enzymes [41]. The availability of the maize genome sequence enabled the identification and characterization of ZmFATs. In this study, 10 ZmFATs sequences were identified from the maize genome. This is similar to studies in Juglans regia (8 FAT genes) [42] and Arachis hypogaea (21 FAT genes) [16], indicating that ZmFATs is a relatively small gene family. Furthermore, based on amino acid composition and phylogenetic topological analysis, these genes were classified into two subgroups (3 ZmFATAs and 7 ZmFATBs). Moreover, the molecular weights, amino acid compositions, and intron numbers of these ZmFATs exhibited considerable variation among members, consistent with observations in other plant species. Such variation may confer functional diversification to ZmFATs in maize. In addition, we observed that ZmFATBs were divided into two branches in the phylogenetic tree. This may indicate that ZmFATBs have generated functionally distinct classifications due to divergence.
Collinearity analysis is used to reveal the duplication process of homologous genes. Two pairs of collinear genes were identified. Similarly, two collinear gene pairs were also identified in walnut [43]. Additionally, one collinear gene pair was found between maize and rice. Based on these results, we speculate that FAT genes underwent substantial evolutionary changes after the divergence of monocotyledons and dicotyledons. Moreover, this mutation persisted after the divergence of maize and rice.
Cis-acting elements provide insights into gene responses under different environmental conditions and stresses signals. CsbZIP50 enhances drought tolerance in cucumber by directly binding to G box/ABRE cis-acting elements in the CsRD29 promoter to activate its expression [44]. MdMYC2 can bind to G box elements in the MdCBF1 promoter to positively regulate cold tolerance in apple [45]. ABRE cis-acting elements play a role in responsive transcription to the stress-related hormone abscisic acid [45]. Overexpression of the GhGT23 gene can enhance cotton tolerance to salt and drought stress, and this gene can bind to MYB/MBS cis-elements to potentially activate expression of downstream resistance genes [46]. In apple, the transcription factors MdMYB9 and MdMYBPA1 bind to MBS elements in the promoters of target genes to activate MdANS and MdUFGT expression, while mdm-miR858 contributes to anthocyanin accumulation by targeting MdMYB9 and MdMYBPA1 [47]. This study found that most ZmFATs contain G box, ABRE, MYB, and MBS cis-acting elements. We speculate that ZmFATs play roles in stress resistance in maize by responding to environmental stimuli and hormonal changes. Two ZmFATs possess functions in monocarboxylic acid biosynthetic process, fatty acid metabolic process, fatty acid biosynthetic process, thiolester hydrolase activity, purine fatty acid synthase activity, adenine transferring groups other than amino–acyl groups, and acyltransferase activity. The functional activities of these thiolesterases, acyltransferases, and synthases determine the carbon chain length and proportion of unsaturated fatty acids synthesized in maize [48,49]. This result also underscores the limitation of GO analysis alone, as functional annotation can be incomplete or biased by database curation. Therefore, complementary evidence, including expression profiling and future biochemical validation, will be required to fully elucidate the biological roles of the ZmFAT family.
Multiple functional genes cooperate and complement each other and are regulated by multiple different miRNAs [50,51,52]. We found that ZmFATA1/2 interact with multiple other ZmFATs. Moreover, ZmFATA3 and ZmFATB6 may be regulated by more miRNAs. We speculate that these genes play more important roles in fatty acid synthesis.
The ZmFAT family likely play essential roles in maize seed development by regulating fatty acid metabolic pathways. FATs terminate fatty acid synthesis by hydrolyzing acyl–ACP thioester bonds, releasing free fatty acids and ACP, and providing substrates for subsequent lipid metabolism [7]. This enzyme plays key roles in plant lipid storage and membrane system construction by regulating fatty acid chain length and release rate [8,9,10]. Our results demonstrated that ZmFATA1/2 and ZmFATB4/6/7 consistently exhibited high expression in both the upper and lower parts of maize seeds throughout development (Figure 9 and Figure 10), highlighting their critical functions in lipid storage. Furthermore, we also found that the expression levels of ZmFATA1/2 and ZmFATB4/6 gradually increased with developmental progression (Figure 9, Figure 10, Figure 11 and Figure 12). This may be due to massive lipid accumulation during late seed formation. ZmFATA7 exhibited opposite temporal dynamic expression characteristics in the upper and lower parts, reflecting its important role in early fat storage in the upper part. Collectively, these findings indicate that ZmFATA1/2 and ZmFATB4/6/7 are key genes contributing to lipid storage during maize seed development.

5. Conclusions

In this study, a comprehensive genome-wide analysis was performed to characterize the FAT gene families in maize, resulting in the identification of 3 ZmFATA and 7 ZmFATB genes. The ZmFATs clustered into different branches in the phylogenetic tree. The gene structures and encoded protein lengths showed considerable differences. ZmFATs contained two pairs of collinear genes within the species. Moreover, as monocotyledonous plants, maize and rice shared one gene pair. The expression of ZmFATs was regulated by light signals and extensively involved in plant growth and development. Furthermore, ZmFATs are potentially involved in the regulation of fatty acid metabolism. Members exhibited interaction relationships and were potentially regulated by 14 miRNAs. ZmFATA1/2 and ZmFATB4/6/7 consistently maintained high expression levels in both the upper and lower parts of maize seeds. The expression levels of ZmFATA1/2 and ZmFATB4/6 gradually increased with developmental progression.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes16091035/s1, Table S1: The primer sequences of FAT genes; Table S2: GO functional annotation.

Author Contributions

J.Z., S.L. (Sinan Li) and X.L. designed the research strategy and conceived and supervised the project; Y.L., S.H., and Y.S. wrote the manuscript; S.L. (Shujun Li), M.S. and B.G. analyzed the data; L.W. and Q.C. performed the experiments and drew the figures. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by Innovation Project of Heilongjiang Academy of Agricultural Sciences: CX25JC06/CX23ZD05/CX23JQ04; Research Business Fee Project of Provincial Research Institutes under the Finance Department of Heilongjiang Province: CZKYF2025-1-B002/CZKYF2024-1-C010; The earmarked fund for CARS-02-07; Major Special Project of Agricultural Biological Breeding: 2022ZD0400504; Key Research and Development Program of Heilongjiang Province: GA22B002.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Phylogenetic tree of FATs proteins from maize, Arabidopsis, and soybean. The same shapes and background colors represent proteins from the same plant. Subgroups are marked with different colored text and dashed lines on the right side.
Figure 1. Phylogenetic tree of FATs proteins from maize, Arabidopsis, and soybean. The same shapes and background colors represent proteins from the same plant. Subgroups are marked with different colored text and dashed lines on the right side.
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Genes 16 01035 g002
Figure 2. Phylogenetic tree, motif patterns, and gene structure of ZmFATs. Different colored blocks represent different motifs, UTRs, and CDS. Black lines in the right panel represent introns.
Figure 2. Phylogenetic tree, motif patterns, and gene structure of ZmFATs. Different colored blocks represent different motifs, UTRs, and CDS. Black lines in the right panel represent introns.
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Genes 16 01035 g003
Figure 3. Collinearity among ZmFATs homologous genes. Gray lines as background represent the collinearity of genes across the whole genome, and colored lines are used to connect ZmFATs pairs with collinear relationships.
Figure 3. Collinearity among ZmFATs homologous genes. Gray lines as background represent the collinearity of genes across the whole genome, and colored lines are used to connect ZmFATs pairs with collinear relationships.
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Genes 16 01035 g004
Figure 4. Collinearity among FATs between maize and Arabidopsis/rice. Gray lines as background connect collinear genes in genomes of different species, and red lines connect FATs gene pairs with collinearity between different species.
Figure 4. Collinearity among FATs between maize and Arabidopsis/rice. Gray lines as background connect collinear genes in genomes of different species, and red lines connect FATs gene pairs with collinearity between different species.
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Genes 16 01035 g005
Figure 5. Cis-acting elements in promoters. The number of each element is labeled in the corresponding grid. The background color of grids represents the number of elements.
Figure 5. Cis-acting elements in promoters. The number of each element is labeled in the corresponding grid. The background color of grids represents the number of elements.
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Genes 16 01035 g006
Figure 6. GO annotation analysis of ZmFATs. The horizontal axis represents the proportion of genes annotated with the corresponding functions. The size and color of circles represent the number of genes annotated with functions and −log10 (p-value), respectively.
Figure 6. GO annotation analysis of ZmFATs. The horizontal axis represents the proportion of genes annotated with the corresponding functions. The size and color of circles represent the number of genes annotated with functions and −log10 (p-value), respectively.
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Figure 7. Interaction network of ZmFATs. The size of circles represents popularity. Lines connect genes with correlations. Gradient colors represent the magnitude of correlations.
Figure 7. Interaction network of ZmFATs. The size of circles represents popularity. Lines connect genes with correlations. Gradient colors represent the magnitude of correlations.
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Genes 16 01035 g008
Figure 8. Potential regulation of ZmFATs by miRNAs. Blue triangles represent ZmFATs, and purple circles represent miRNAs. miRNAs and ZmFATs with correlations are connected by black dashed lines.
Figure 8. Potential regulation of ZmFATs by miRNAs. Blue triangles represent ZmFATs, and purple circles represent miRNAs. miRNAs and ZmFATs with correlations are connected by black dashed lines.
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Genes 16 01035 g009
Figure 9. Transcriptomic expression levels of ZmFAT genes in the upper tissue (U) of seeds after pollination. The gradient from blue to red represents gradually increasing expression levels. The horizontal axis represents different sampling stages (4, 5, 6, 8, 10, 12, 16, 20, 24, 28, 32 days after pollination).
Figure 9. Transcriptomic expression levels of ZmFAT genes in the upper tissue (U) of seeds after pollination. The gradient from blue to red represents gradually increasing expression levels. The horizontal axis represents different sampling stages (4, 5, 6, 8, 10, 12, 16, 20, 24, 28, 32 days after pollination).
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Genes 16 01035 g010
Figure 10. Transcriptomic expression levels of ZmFAT genes in the bottom tissue (B) of seeds after pollination. The gradient from blue to red represents gradually increasing expression levels. The horizontal axis represents different sampling stages (4, 5, 6, 8, 10, 12, 16, 20, 24, 28, 32 days after pollination).
Figure 10. Transcriptomic expression levels of ZmFAT genes in the bottom tissue (B) of seeds after pollination. The gradient from blue to red represents gradually increasing expression levels. The horizontal axis represents different sampling stages (4, 5, 6, 8, 10, 12, 16, 20, 24, 28, 32 days after pollination).
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Genes 16 01035 g011
Figure 11. Relative expression levels of ZmFAT genes in the upper tissue of seeds after pollination. The horizontal axis represents different sampling stages (4, 5, 6, 8, 10, 12, 16, 20, 24, 28, 32 days after pollination). Different letters indicate significant differences between treatments (p < 0.05). (A–J) represent the expression levels of different genes, with each panel labeled with the corresponding gene name and figure designation.
Figure 11. Relative expression levels of ZmFAT genes in the upper tissue of seeds after pollination. The horizontal axis represents different sampling stages (4, 5, 6, 8, 10, 12, 16, 20, 24, 28, 32 days after pollination). Different letters indicate significant differences between treatments (p < 0.05). (A–J) represent the expression levels of different genes, with each panel labeled with the corresponding gene name and figure designation.
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Genes 16 01035 g012
Figure 12. Relative expression levels of ZmFAT genes in the lower tissue of seeds after pollination. The horizontal axis represents different sampling stages (4, 5, 6, 8, 10, 12, 16, 20, 24, 28, 32 days after pollination). Different letters indicate significant differences between treatments (p < 0.05). (A–J) represent the expression levels of different genes, with each panel labeled with the corresponding gene name and figure designation.
Figure 12. Relative expression levels of ZmFAT genes in the lower tissue of seeds after pollination. The horizontal axis represents different sampling stages (4, 5, 6, 8, 10, 12, 16, 20, 24, 28, 32 days after pollination). Different letters indicate significant differences between treatments (p < 0.05). (A–J) represent the expression levels of different genes, with each panel labeled with the corresponding gene name and figure designation.
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Table 1. Basic information of maize FAT genes.
Table 1. Basic information of maize FAT genes.
Protein IDNameaaCDSMWpIGRAVY
Zm00001d006080ZmFATA115747116,956.178.68−0.17
Zm00001d021046ZmFATA220360922,119.058.24−0.14
Zm00001d026569ZmFATA3426127847,666.776.37−0.34
Zm00001d029901ZmFATB116048017,915.045.4−0.54
Zm00001d029902ZmFATB214242616,029.888.64−0.75
Zm00001d005148ZmFATB3379113742,303.499.19−0.44
Zm00001d036137ZmFATB423971725,933.468.56−0.08
Zm00001d021004ZmFATB5832499737.4210.29−0.37
Zm00001d045387ZmFATB6434130247,759.839.01−0.39
Zm00001d046454ZmFATB7418125446,396.38.25−0.36
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Li, Y.; Hou, S.; Sun, Y.; Li, S.; Sun, M.; Guo, B.; Wang, L.; Cai, Q.; Li, X.; Li, S.; et al. Comprehensive Characterization of the FATs Gene Family in Maize: Phylogeny, Expression Patterns, and Regulatory Networks. Genes 2025, 16, 1035. https://doi.org/10.3390/genes16091035

AMA Style

Li Y, Hou S, Sun Y, Li S, Sun M, Guo B, Wang L, Cai Q, Li X, Li S, et al. Comprehensive Characterization of the FATs Gene Family in Maize: Phylogeny, Expression Patterns, and Regulatory Networks. Genes. 2025; 16(9):1035. https://doi.org/10.3390/genes16091035

Chicago/Turabian Style

Li, Yunlong, Shuai Hou, Yan Sun, Shujun Li, Minghao Sun, Baitao Guo, Luyao Wang, Quan Cai, Xin Li, Sinan Li, and et al. 2025. "Comprehensive Characterization of the FATs Gene Family in Maize: Phylogeny, Expression Patterns, and Regulatory Networks" Genes 16, no. 9: 1035. https://doi.org/10.3390/genes16091035

APA Style

Li, Y., Hou, S., Sun, Y., Li, S., Sun, M., Guo, B., Wang, L., Cai, Q., Li, X., Li, S., & Zhang, J. (2025). Comprehensive Characterization of the FATs Gene Family in Maize: Phylogeny, Expression Patterns, and Regulatory Networks. Genes, 16(9), 1035. https://doi.org/10.3390/genes16091035

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