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Article

Genome-Wide Identification and Expression Analysis Under Abiotic Stress of the Lipoxygenase Gene Family in Maize (Zea mays)

by
Sinan Li
,
Shuai Hou
,
Yuanqing Sun
,
Minghao Sun
,
Yan Sun
,
Xin Li
,
Yunlong Li
,
Luyao Wang
,
Quan Cai
,
Baitao Guo
and
Jianguo Zhang
*
Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
*
Author to whom correspondence should be addressed.
Genes 2025, 16(1), 99; https://doi.org/10.3390/genes16010099
Submission received: 10 December 2024 / Revised: 13 January 2025 / Accepted: 16 January 2025 / Published: 18 January 2025
(This article belongs to the Special Issue Genetics of Abiotic Stress Tolerance in Plants Volume II)
Browse Figures
Versions Notes

Abstract

:
Background/Objectives: Abiotic stresses impose significant constraints on crop growth, development, and yield. However, the comprehensive characterization of the maize (Zea mays) lipoxygenase (LOX) gene family under stress conditions remains limited. LOXs play vital roles in plant stress responses by mediating lipid oxidation and signaling pathways. Methods: In this study, 13 ZmLOX genes were identified in maize and characterized to explore their functions under abiotic stresses. Results: Phylogenetics revealed that ZmLOX genes share evolutionary origins with LOX genes in Arabidopsis and rice. Promoter analysis identified cis-acting elements associated with growth, light response, hormone signaling, and stress response, indicating their diverse biological roles. Gene Ontology (GO) and KEGG enrichment analyses showed that ZmLOX genes are involved in jasmonic acid metabolism, lipid signaling, and photosynthetic processes, while protein–protein interaction (PPI) analysis positioned ZmLOX proteins as central hubs in stress-related regulatory networks. Differential expression and qRT-PCR analyses revealed stress-specific (including heat, drought, salt, and cold) expression patterns, with ZmLOX2 and ZmLOX13 showing key roles in drought and cold tolerance, respectively. Conclusions: These findings provide new insights into the regulatory functions of ZmLOX genes, offering potential targets for enhancing maize resilience to abiotic stresses and improving agricultural productivity.

1. Introduction

A lipoxygenase (LOX) is a kind of peroxide dioxygenase that contains non-heme ferritin, does not contain sulfur, and is composed of a single polypeptide chain. It is widely found in plants and animals. LOXs are widely found in plants and initiate the synthesis of a series of cyclic or aliphatic compounds, which is often referred to as the LOX pathway or the octadecanoic pathway [1]. LOX pathway metabolites in plants have a wide range of physiological functions. These metabolites play an active role in plant growth and development and defense response to stress, such as inducing cell senescence and death, mechanical damage, and biotic and abiotic stresses [2,3].
LOX proteins contain a non-heme iron as the catalytic component of the active center, and its active state is the oxidized ferric ion (Fe3+). One water molecule and five (the five ligands are oxygen on the carboxyl group of isoleucine or valine at the carbon terminus, nitrogen on two histidine residues of α-helix 9, nitrogen on one histidine residue of α-helix 18, and an oxygen atom on the distal end of asparagine or serine residues of α-helix 18) amino acid residues are used as ligands to form a six-coordinated octahedral structure with the non-heme iron [4]. LOX proteins generally contain about 38 conserved amino acid residues, of which histidine is essential for LOX to bind iron ions and plays an important role in the catalytic activity of LOX [5].
The LOX can be divided into 9-LOX and 13-LOX according to the oxygenation sites catalyzed by LOX, but some LOXs can be oxygenated at both sites to produce two products; this LOX is called 9/13-LOX, such as OsLOX1 in rice (Oryza sativa) and LOXN2 in pea (Pisum sativum L.) [6,7]. Previous studies have shown that LOX plays an important role in plant growth and development and stress [8,9]. In plants, 9-LOX mainly plays a role in organ development and fruit-ripening processes [1], and 13-LOX is mainly involved in the defense response to biotic and abiotic stresses [10,11]. For example, 17 LOX genes were identified in potato (Solanum tuberosum), of which two StLOX genes (encoding 13-LOX protein) were involved in salt stress response [12]. In addition, 72 LOX genes were identified in cultivated peanuts (Arachis hypogaea) and wild peanuts (Arachis duranensis and Arachis ipaensis), and overexpression of AhLOX29 in Arabidopsis (Arabidopsis thaliana) enhanced drought stress resistance [13]. A total of 64 LOX genes were identified in cotton, and cotton with silencing of GhLOX12 and GhLOX13 showed increased sensitivity to salt stress [14]. LOX family genes have been identified and analyzed in a variety of plants, including potato, peanut, melon (Cucumis melo L.), pear (Pyrus bretschneideri), kiwi (Actinidia chinensis), cucumber (Cucumis sativus L.), passionflower (Passiflora edulis), diploid woodland strawberry (Fragaria vesca), artemisia annua (Artemisia annua L.), foxtail millet (Setaria italica), jujube (Ziziphus jujuba), sorghum (Sorghum bicolor L.), cotton, pepper (Capsicum annuum L.), tea plant (Camellia sinensis), peach tree (Prunus persica), poplar (Populus), Arabidopsis, and rice [12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]. Most of these LOX family genes play roles in fruit aroma formation and stress response.
As one of the most extensively cultivated crops globally, maize holds immense theoretical and practical importance for mining stress-resistant genes. Previous studies have identified LOX genes in maize [30]; however, a comprehensive investigation of the maize LOX gene family is lacking. To address this knowledge gap, we conducted a genome-wide identification and analysis of maize LOX genes, encompassing fundamental gene information, chromosomal positioning, gene structure, encoded protein motifs, phylogenetic relationships, and collinearity. Additionally, we examined the transcriptomic data of all ZmLOX genes under abiotic stress conditions and verified expression patterns using qRT-PCR. Our study sheds light on the evolutionary history and functional diversification within the maize LOX gene family, establishing a theoretical foundation for further elucidating the regulatory mechanisms underpinning plant stress tolerance. By systematically characterizing this critical gene family, our findings contribute to the broader understanding of stress resistance in maize and pave the way for future research and applications in crop improvement.

2. Results

2.1. Identification and Analysis of LOX Family Genes in Maize

Arabidopsis LOX protein sequences were compared against the maize protein database using Blastp, and conserved domains of the LOX proteins were identified based on the HMM file. By integrating the results of protein sequence searches and Pfam domain identification, a total of 13 LOX genes were identified in maize. These genes were named from ZmLOX1 to ZmLOX13, following their chromosomal positions. The encoded ZmLOX proteins had amino acid lengths ranging from 850 (ZmLOX7) to 968 (ZmLOX1). Their molecular weights varied between 95.9922 kDa (ZmLOX7) and 108.2720 kDa (ZmLOX1), while the predicted isoelectric points (pI) ranged from 6.0036 (ZmLOX5) to 8.5904 (ZmLOX1). Subcellular localization predictions indicated that ten ZmLOX proteins are located in the cytoplasm, while three are localized to the chloroplast (Table 1).

2.2. Chromosomal Distribution of ZmLOX Genes

Analysis of chromosomal positions revealed that 13 ZmLOX genes were distributed on chromosomes 1, 2, 3, 4, 5, and 10. Chromosome 1 contains the most ZmLOX genes (four genes), chromosome 3 contains three ZmLOX genes, chromosomes 2 and 5 each contain two ZmLOX genes, and chromosomes 4 and 10 each contain the least ZmLOX genes (one gene). Moreover, our analysis revealed that the majority of ZmLOX genes were located in the telomeric regions of the maize chromosomes (Figure 1).

2.3. Characterization of Conserved Motifs and Structural Features in ZmLOX Family

The thirteen maize LOX proteins were categorized into two groups: 9-LOX, comprising six LOX proteins, and 13-LOX, consisting of seven LOX proteins. The 13-LOX group was further subdivided into Type I and Type II 13-LOX (Figure 2a). All identified LOX proteins were classified based on their conserved domains, including the lipoxygenase and PLAT domains (Figure 2b). A total of 15 motifs were identified across the maize ZmLOX proteins. Motifs 3, 4, 8, 9, 10, 13, 14, and 15 were shared by all ZmLOX proteins. ZmLOX5 contained nine motifs, ZmLOX7 contained ten motifs, and ZmLOX1 and ZmLOX2 contained fourteen motifs, while the remaining ZmLOX proteins contained all fifteen motifs (Figure 2c). Structural analysis of the ZmLOX family genes, conducted using genome annotation data, revealed that all ZmLOX genes contained introns (Figure 2d).

2.4. Phylogenetic Analysis of LOX Family Proteins

A phylogenetic tree was constructed based on the protein sequences of LOX family members from maize, Arabidopsis, and rice. The analysis grouped all LOX proteins into three distinct clades: 9-LOX, Type I 13-LOX, and Type II 13-LOX. The 9-LOX group consisted of six maize LOX proteins, two Arabidopsis LOX proteins, and six rice LOX proteins. The Type II 13-LOX group included six maize LOX proteins, four Arabidopsis LOX proteins, and seven rice LOX proteins. The Type I 13-LOX group was the smallest, containing one maize LOX protein and one rice LOX protein (Figure 3). These results highlight the evolutionary relationships and structural divergence of LOX proteins among the three species.

2.5. Collinearity Analysis of LOX Family Genes in Maize

Collinearity analysis was performed on all maize LOX genes to understand the duplication events of ZmLOX. The results show that ZmLOX3 and ZmLOX11, ZmLOX6 and ZmLOX13, and ZmLOX10 and ZmLOX12 have collinearity relationships (Figure 4a). To elucidate the evolutionary mechanism of LOX family genes in maize, we performed a synteny analysis of LOX genes in maize compared with those in Arabidopsis and rice. None of the ZmLOX genes have a synteny relationship with the Arabidopsis LOX genes and rice LOX genes. The results show that one LOX gene has a synteny relationship between Arabidopsis and rice (Figure 4b).

2.6. Cis-Acting Element Analysis of ZmLOX’s Promoters

To identify and characterize the cis-regulatory elements, we analyzed the 1500 bp upstream sequences of the coding regions for all 13 ZmLOX genes. The discovered cis-acting elements were visualized using TBtools software (Figure 5). Our analysis revealed the presence of twenty-one distinct cis-regulatory motifs within the promoter regions of the ZmLOX gene family, categorized into five light-responsive elements, five plant growth and development elements, six phytohormone-related elements, and five stress-related elements. Notably, all ZmLOX promoters were enriched with plant developmental elements (e.g., TATA box) and light-responsive elements (e.g., CAAT box). Among them, the promoters of ZmLOX7 and ZmLOX8 exhibited a higher abundance of light-responsive elements, while the promoters of ZmLOX4, ZmLOX8, ZmLOX11, and ZmLOX13 contained more stress-responsive elements, suggesting diverse regulatory roles under varying environmental conditions.

2.7. GO and KEGG Annotation of ZmLOX Genes

As shown in Figure 6, the results of Gene Ontology (GO) enrichment analysis (Figure 6a), encompass three categories: biological processes (BPs), cellular components (CCs), and molecular functions (MFs). Key enriched terms include processes such as “jasmonic acid biosynthetic process,” “response to wounding,” and “anther dehiscence” under BPs, components like “chloroplast thylakoid” and “plastid thylakoid” under CCs, and activities such as “dioxygenase activity” and “oxidoreductase activity” under MFs. The results highlight significant enrichment of terms related to jasmonic acid metabolism, lipid oxidation, and thylakoid-related components, suggesting these pathways play a critical role in the function of ZmLOX genes. The KEGG pathway enrichment analysis (Figure 6b) highlights two significantly enriched pathways: α-linolenic acid metabolism and linoleic acid metabolism, critical in lipid metabolism.

2.8. Protein–Protein Interaction Network of ZmLOX in Maize

To explore potential regulatory mechanisms of ZmLOX in maize, a protein–protein interaction (PPI) network was constructed. As shown in Figure 7, This PPI network analysis illustrates the interactions between key proteins. Prominent nodes, such as members of the ZmLOX family (e.g., ZmLOX5 and ZmLOX7), act as central hubs with high connectivity, suggesting their pivotal roles in regulatory or signaling pathways. In addition to ZmLOX proteins, a total of 40 proteins were identified as interacting partners of ZmLOX, and these proteins are likely to play important roles in the pathways where ZmLOX exerts its functions.

2.9. Differential Expression and Expression Profiling of ZmLOX Genes Based on Transcriptome Data

To analyze the differential expression and expression profiling of ZmLOX genes, volcano and heatmap plots were constructed. Figure 8a presents multiple volcano plots comparing the differential expression of ZmLOX genes across four group comparisons (C1-C2, C1-T1, C2-T2, T1-T2, same treatment or same sample type). ZmLOX genes are categorized as upregulated (Up, |log2FoldChange| > 1, and adj. p < 0.05), downregulated (Down, |log2FoldChange| > 1, and adj. p < 0.05), or non-significant (NS, |log2FoldChange| < 1, or adj. p < 0.05), with key genes such as ZmLOX2 and ZmLOX13 displaying significant expression changes across multiple comparisons. ZmLOX8 and ZmLOX9 display significant downregulated in C1-C2 and T1-T2, indicating that these exhibited expression specificity in different maize varieties. ZmLOX4 was upregulated in the treatment group, indicating that it is the cold-responsive gene in different maize varieties. In addition, referring to Figure 8b, the results indicate that genes ZmLOX2 and ZmLOX13 are likely to be specifically differentially expressed in cold-tolerant variety 2 under cold treatment.

2.10. Expression Analysis of ZmLOX Family Genes Under Abiotic Stress Using qRT-PCR

To analyze the responsiveness of ZmLOX genes to different abiotic stresses, including heat, drought, salt, and cold stress, the relative expression levels of ZmLOX genes were analyzed using qRT-PCR. As shown in Figure 9, seven ZmLOX genes exhibit significantly upregulated expression patterns in response to heat stress; except for ZmLOX5, the other six genes reach their highest relative expression levels at 24 h under heat stress. Six genes show significant responsive expression under drought stress, particularly ZmLOX2, which is upregulated nearly 70-fold after 24 h of drought treatment. Similarly, six genes display significant responsive expression patterns under salt stress; except for ZmLOX9, the other five ZmLOX genes are significantly upregulated after 12 h. Regarding cold stress, twelve ZmLOX genes show significant responsive expression patterns; except for ZmLOX2 and ZmLOX11, the other ten genes exhibit an expression pattern that first increases and then decreases under cold stress.

3. Discussion

Maize is a kind of food crop that is widely grown in the world. Environmental conditions such as temperature, humidity, light, moisture, and biodiversity vary greatly in different planting areas. Therefore, maize is often faced with stresses such as cold, heat, drought, salt, diseases, and pests in actual agricultural production [31]. When plants are stressed, the intracellular reactive oxygen species (ROS), such as H2O2 and O2−·, will rise sharply. These excessive ROS can cause excessive oxidation of cells and damage the intracellular protein structure, which seriously affects the biological function of cells [32]. Lipoxygenase (LOX) enzymes facilitate the oxidation of polyunsaturated fatty acids, producing oxylipins via enzymatic or non-enzymatic pathways that play crucial roles in fatty acid metabolism [33]. In plants, LOX genes are often upregulated under stress conditions and play a regulatory role in enhancing tolerance to abiotic stresses. For instance, PgLOX3 in ginseng (Panax ginseng) has been shown to positively regulate drought tolerance [34]. In rapeseed (Brassica campestris), various LOX genes respond to drought and heat stress [35]. In soybean (Glycine max), LOX-silenced plants exhibited reduced singlet oxygen (1O2) formation under osmotic stress and promoted root growth compared to wild-type plants [36]. Furthermore, when AfLOX4, a gene from Amorpha fruticosa L., was overexpressed in tobacco (Nicotiana tabacum), it considerably improved the plant’s resilience to NaHCO3 and drought stress conditions. [37].
Studies have demonstrated that LOX activity increases progressively with drought stress duration in maize (Zea mays L.). However, a comprehensive analysis of the LOX gene family under these conditions remains to be elucidated [2]. In plants, genes usually exist in the form of gene families. By identifying the LOX gene family in maize and investigating its structural features and expression profiles under various stress conditions, we gain an important understanding of the possible functions these genes may play. Preliminary predictions of their functions under stress are crucial for understanding their contribution to stress tolerance, offering a foundation for improving maize resistance to environmental challenges. In this study, a total of thirteen ZmLOX family genes were identified in maize, of which six encode 9-LOX, one encodes Type I 13-LOX, and six encode Type II 13-LOX (Table 1). The 13 ZmLOX genes were randomly distributed on different chromosomes, and the distribution on the same chromosome was also uneven, with most ZmLOX genes distributed at both ends of the chromosome (Figure 1). This phenomenon, observed in most gene family studies [12,13,14,19,20,21,23,24,25,27,29], suggests that many ZmLOX genes might be highly expressed and functionally active in maize. In this study, we analyzed the structure of ZmLOX genes and the conserved motifs of their encoded proteins (Figure 2), constructed a phylogenetic tree of ZmLOX proteins (Figure 3), and examined collinearity among ZmLOX genes in maize (Figure 4). The phylogenetic analysis revealed that ZmLOX proteins are grouped with LOX proteins from Arabidopsis and rice, indicating conserved evolutionary relationships. Additionally, synteny analysis showed that LOX genes in maize, Arabidopsis, and rice share syntenic relationships, suggesting that these genes may have originated from a common ancestor and persisted through evolutionary processes. Examination of the cis-regulatory elements within the promoter regions of ZmLOX genes uncovered a high prevalence of motifs related to plant growth, development, and responsiveness to light stimuli (Figure 4). This suggests that LOX genes might play a crucial role in plant growth and development, possibly acting as essential regulatory factors in these processes. In addition, the presence of hormone response type and stress response type elements in the promoter of the ZmLOX gene suggests that the ZmLOX family genes may have hormone or stress response functions. This pattern is similar to the cis-acting elements of LOX genes identified in cotton [14]. The GO and KEGG pathway enrichment analyses (Figure 6) provided key insights into the functional roles of ZmLOX genes. The significant enrichment of GO terms related to jasmonic acid metabolism, lipid oxidation, and thylakoid-associated components underscores the involvement of ZmLOX genes in critical biological processes, including stress responses and photosynthesis. Similarly, the identification of α-linolenic acid and linoleic acid metabolism pathways through KEGG enrichment highlights the importance of lipid signaling in ZmLOX-mediated functions. Complementing these findings, the PPI network (Figure 7) identified ZmLOX proteins as central hubs with extensive connectivity, interacting with 40 other proteins. These results suggest that ZmLOX proteins are pivotal in regulatory and signaling networks, mediating stress responses and other vital functions.
When exposed to stressful environments, plants frequently display alterations in gene expression patterns as an adaptive mechanism to cope with adverse conditions, potentially leading to improved stress resilience [38]. Analysis of transcriptomic datasets from stress-exposed maize populations enabled the examination of ZmLOX gene expression profiles under diverse environmental challenges (Figure 8). Additionally, the relative expression levels of all ZmLOX genes were validated under these stress conditions using qRT-PCR analysis (Figure 9). The expression profiling analyses in Figure 8 and Figure 9 further delineate the regulatory roles of ZmLOX genes under various conditions. Differential expression analysis (Figure 8) revealed that ZmLOX genes, such as ZmLOX2 and ZmLOX13, exhibit specific upregulation in cold-tolerant maize varieties under cold treatment, suggesting their critical roles in cold tolerance mechanisms. Meanwhile, qRT-PCR data (Figure 9) demonstrated that ZmLOX genes respond distinctly to abiotic stresses, with several genes showing significant upregulation in response to heat, drought, salt, and cold stresses. Consistent with previous studies, differential accumulation of LOX has been observed among maize genotypes with varying degrees of salt/alkali sensitivity [3]. Additionally, in peanut (Arachis hypogaea L.), LOX genes have been demonstrated to be inducible by various biotic stresses [13]. Notably, ZmLOX2 exhibited a nearly 70-fold upregulation under drought stress, and ten genes displayed transient expression peaks under cold stress, possibly reflecting a delayed participation in cold-responsive pathways. These results collectively underscore the diverse and stress-specific regulatory functions of ZmLOX genes, providing a foundation for further exploration of their roles in maize stress tolerance.

4. Materials and Methods

4.1. Plant Materials and Treatments

Maize material of the genotype T641 was utilized in this research. These maize materials were cultivated in a light incubator (MGC-100, Shanghai Yiheng Scientific Instrument Co., Ltd.) under a photoperiod of 16 h of light and 8 h of darkness at 25 °C until the three-leaf stage. For heat stress, the plant growth temperature was set to 35 °C. For drought stress, the cleaned maize roots were soaked with a 10% PEG6000 solution. For salt stress, the cleaned maize roots were soaked with 100 mmol/L NaCl solution. For cold stress, the plant growth temperature was set to 5 °C. The sampling time points were 0 h, 6 h, 12 h, 24 h, and 48 h, with three biological replicates established for each group.

4.2. Identification of LOX Family Genes in Maize

To identify LOX family members in maize, we employed a multi-step approach utilizing various bioinformatics tools and databases. First, we acquired the LOX hidden Markov model (HMM) file (PF00305) from the InterPro database (https://www.ebi.ac.uk/interpro/, accessed on 10 November 2024). We then obtained the maize genome data, including genome annotations and protein sequences, from the Phytozome database (https://phytozome-next.jgi.doe.gov/, accessed on 15 November 2024). Using the hmmsearch software (v3.3.1), we scanned the maize protein sequences against the LOX HMM file to detect potential ZmLOX genes. In parallel, we retrieved LOX protein sequences from Arabidopsis through the TAIR database (https://www.arabidopsis.org/, accessed on 15 November 2024) and performed a comparative analysis against the maize protein dataset using Blastp (v2.13.0). By integrating results from these complementary approaches, we compiled a comprehensive list of putative LOX family members in maize. To validate the presence of conserved domains, we submitted the corresponding protein sequences to multiple domain structure databases, including InterPro, SMART (http://smart.embl-heidelberg.de, accessed on 18 November 2024), and Conserved Domain Database (CDD, https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, accessed on 18 November 2024).

4.3. Chromosome Distribution Analysis of ZmLOX Genes

To investigate the genomic distribution of ZmLOX genes, we retrieved data on their chromosomal locations and the lengths of all 10 maize chromosomes from the maize genome annotation file. Using TBtools version 1.098765, we performed data processing and generated visual representations of the results.

4.4. Motif and Domain Analysis of ZmLOX Proteins

The conserved motifs of ZmLOX proteins were identified using MEME software (v4.12) based on their protein sequences. The parameters were set as follows: a maximum motif length of 100 amino acids, a minimum motif length of 6 amino acids, 15 motifs identified, and 10,000 iterations [39]. Information on conserved domains was retrieved from the CDD database.

4.5. Gene Structure Analysis of ZmLOX Genes

The coding sequences (CDSs) and untranslated regions (UTRs) of maize ZmLOX family genes were identified based on the maize genome annotation files. These elements were analyzed and visualized using the ggplot2 (v3.5.1) and gggenomes (v1.01) packages.

4.6. Phylogenetic Analysis of LOX Family Members

Protein sequences of LOX family members from maize, Arabidopsis, and rice were obtained from the Phytozome database. A phylogenetic tree was constructed using the Neighbor-Joining method [40], with Clustal W employed for sequence alignment. The parameters included the Poisson substitution model and a bootstrap value of 1000. We employed the ggtree package to generate a graphical representation of LOX family evolutionary relationships [41].

4.7. Collinearity Analysis of Maize LOX Family Genes

Genome sequence files and gene structure annotation files for maize, Arabidopsis, and rice were retrieved from the Phytozome database. Duplication events within the ZmLOX family were analyzed by aligning the maize whole-genome sequence using TBtools software. Synteny relationships of LOX genes among maize, Arabidopsis, and rice were determined by comparing the genome sequences of Arabidopsis and rice with that of maize using TBtools and jcvi [42].

4.8. Cis-Acting Element Analysis of ZmLOX Gene Promoters

To identify potential regulatory elements influencing ZmLOX gene expression, we extracted the 1500 bp sequences upstream of the coding DNA sequence (CDS) for each ZmLOX gene from the maize genome database. These putative promoter regions were then submitted to the PlantCARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html, accessed on 18 November 2024) for in silico prediction of cis-acting elements.

4.9. GO and KEGG Analysis

To investigate the potential functions of ZmLOX genes, we conducted functional annotation using the eggNOG-mapper tool [43]. This tool assigns Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to gene products. The resulting annotations were statistically summarized and visualized using the clusterProfiler package in R [44]. This analysis provided insights into the molecular functions, biological processes, cellular components, and metabolic pathways associated with ZmLOX genes.

4.10. PPI Network Analysis

For protein–protein interaction (PPI) network analysis, all ZmLOX protein sequences were submitted to the STRING database (https://string-db.org/, accessed on 20 November 2024) with the species set to maize (Z. mays). Potential interacting proteins were identified, and the results were downloaded. Proteins with the top 40 confidence scores were selected, and the PPI network was visualized using the ggraph (v2.1.0) package.

4.11. Expression Analysis of ZmLOX Genes

Transcriptome data (PRJNA1090631) were obtained from the NCBI database (https://www.ncbi.nlm.nih.gov/, accessed on 20 November 2024) to analyze the expression patterns of ZmLOX genes under cold stress conditions. Gene expression quantification was performed using the featureCounts package [45], while differential expression analysis was carried out with Trinity [46]. Volcano plots depicting differentially expressed genes were created using the ggplot2 package, and heatmaps of gene expression were visualized with the pheatmap (v1.0.12) package.

4.12. qRT-PCR Analysis

To analyze the expression patterns of ZmLOX genes, we first isolated total RNA from maize leaves using the RNA Mini Kit (Youcan Bio, Shanghai, China). Reverse transcription was performed utilizing a cDNA synthesis kit. We designed qRT-PCR primers specific to each ZmLOX gene using the NCBI Primer Design tool, and the primer sequences are listed in Table S1. The qRT-PCR assays were performed using qPCR SYBR Green Master Mix (Youcan Bio, Shanghai, China), with a reaction protocol consisting of an initial denaturation step at 95 °C for 5 min, followed by 40 cycles of 95 °C for 10 s, 60 °C for 20 s, and 72 °C for 20 s. We determined the relative expression levels of ZmLOX genes using the 2−∆∆Ct method, with the maize actin gene serving as an internal reference for normalization [47]. All experiments were performed in three biological replicates for each sample.

4.13. Statistical Analyses

All statistical analyses in this study were performed using SPSS software (version 22). Experimental data were tested for significance using a one-way or two-way analysis of variance (ANOVA), depending on the experimental design. Post hoc comparisons were conducted using Tukey’s HSD (Honestly Significant Difference) test for a one-way ANOVA or Bonferroni correction for a two-way ANOVA, to identify significant differences between groups. A p-value of less than 0.05 was considered statistically significant. Data are expressed as mean ± standard deviation (SD) unless otherwise specified.

5. Conclusions

This study identified and characterized 13 ZmLOX genes in maize, uncovering their evolutionary conservation, structural features, and roles in stress responses. Promoter analyses revealed cis-acting elements linked to growth, light response, hormone signaling, and stress adaptation, suggesting diverse biological functions. Functional enrichment and PPI analyses highlighted the involvement of ZmLOX genes in jasmonic acid metabolism, lipid signaling, and photosynthesis, with ZmLOX proteins acting as regulatory hubs in stress pathways. Expression profiling and qRT-PCR confirmed stress-specific expression patterns, with ZmLOX2 and ZmLOX13 playing key roles in drought and cold tolerance. These findings provide a basis for leveraging ZmLOX genes to enhance maize resilience to abiotic stresses.

Supplementary Materials

The following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/genes16010099/s1. Table S1. qRT-PCR primers for ZmLOXs.

Author Contributions

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

Funding

This work was supported by the National Key Research and Development Program of China: 2021YFD1201001; the Research Business Fee Project of Provincial Research Institutes under the Finance Department of Heilongjiang Province: CZKYF2024-1-C010; the earmarked fund for CARS-02-07; and the Innovation Project of Heilongjiang Academy of Agricultural Sciences: CX23ZD05.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The raw sequencing reads were deposited at the National Center for Biotechnology Information Sequence Read Archive (https://submit.ncbi.nlm.nih.gov/subs/sra/, accessed on 15 September 2024) under Project Accession Number PRJNA1090631.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Porta, H.; Rocha-Sosa, M. Plant lipoxygenases. Physiological and molecular features. Plant Physiol. 2002, 130, 15–21. [Google Scholar] [CrossRef] [PubMed]
  2. Anjum, S.A.; Ashraf, U.; Tanveer, M.; Khan, I.; Hussain, S.; Shahzad, B.; Zohaib, A.; Abbas, F.; Saleem, M.F.; Ali, I. Drought induced changes in growth, osmolyte accumulation and antioxidant metabolism of three maize hybrids. Front. Plant Sci. 2017, 8, 69. [Google Scholar] [CrossRef] [PubMed]
  3. Rohman, M.M.; Talukder, M.; Hossain, M.; Uddin, M.; Amiruzzaman, M.; Biswas, A.; Ahsan, A.; Chowdhury, M. Saline sensitivity leads to oxidative stress and increases the antioxidants in presence of proline and betaine in maize (‘Zea mays’ L.) inbred. Plant Omics 2016, 9, 35–47. [Google Scholar]
  4. Brash, A.R. Lipoxygenases: Occurrence, functions, catalysis, and acquisition of substrate. J. Biol. Chem. 1999, 274, 23679–23682. [Google Scholar] [CrossRef] [PubMed]
  5. Steczko, J.; Donoho, G.P.; Clemens, J.C.; Dixon, J.E.; Axelrod, B. Conserved histidine residues in soybean lipoxygenase: Functional consequences of their replacement. Biochemistry 1992, 31, 4053–4057. [Google Scholar] [CrossRef]
  6. Wang, R.; Shen, W.; Liu, L.; Jiang, L.; Liu, Y.; Su, N.; Wan, J. A novel lipoxygenase gene from developing rice seeds confers dual position specificity and responds to wounding and insect attack. Plant Mol. Biol. 2008, 66, 401–414. [Google Scholar] [CrossRef]
  7. Veronico, P.; Giannino, D.; Melillo, M.T.; Leone, A.; Reyes, A.; Kennedy, M.W.; Bleve-Zacheo, T. A novel lipoxygenase in pea roots. Its function in wounding and biotic stress. Plant Physiol. 2006, 141, 1045–1055. [Google Scholar] [CrossRef]
  8. Kolomiets, M.V.; Hannapel, D.J.; Chen, H.; Tymeson, M.; Gladon, R.J. Lipoxygenase is involved in the control of potato tuber development. Plant Cell 2001, 13, 613–626. [Google Scholar] [CrossRef]
  9. Porta, H.; Figueroa-Balderas, R.E.; Rocha-Sosa, M. Wounding and pathogen infection induce a chloroplast-targeted lipoxygenase in the common bean (Phaseolus vulgaris L.). Planta 2008, 227, 363–373. [Google Scholar] [CrossRef]
  10. López, M.A.; Vicente, J.; Kulasekaran, S.; Vellosillo, T.; Martínez, M.; Irigoyen, M.L.; Cascón, T.; Bannenberg, G.; Hamberg, M.; Castresana, C. Antagonistic role of 9-lipoxygenase-derived oxylipins and ethylene in the control of oxidative stress, lipid peroxidation and plant defence. Plant J. 2011, 67, 447–458. [Google Scholar] [CrossRef]
  11. Vellosillo, T.; Martínez, M.; Lopez, M.A.; Vicente, J.; Cascon, T.; Dolan, L.; Hamberg, M.; Castresana, C. Oxylipins produced by the 9-lipoxygenase pathway in Arabidopsis regulate lateral root development and defense responses through a specific signaling cascade. Plant Cell 2007, 19, 831–846. [Google Scholar] [CrossRef] [PubMed]
  12. Zhu, J.; Chen, L.; Li, Z.; Wang, W.; Qi, Z.; Li, Y.; Liu, Y.; Liu, Z. Genome-Wide Identification of LOX Gene Family and Its Expression Analysis under Abiotic Stress in Potato (Solanum tuberosum L.). Int. J. Mol. Sci. 2024, 25, 3487. [Google Scholar] [CrossRef] [PubMed]
  13. Mou, Y.; Sun, Q.; Yuan, C.; Zhao, X.; Wang, J.; Yan, C.; Li, C.; Shan, S. Identification of the LOX gene family in peanut and functional characterization of AhLOX29 in drought tolerance. Front. Plant Sci. 2022, 13, 832785. [Google Scholar] [CrossRef] [PubMed]
  14. Shaban, M.; Ahmed, M.M.; Sun, H.; Ullah, A.; Zhu, L. Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses. BMC Genom. 2018, 19, 1–13. [Google Scholar] [CrossRef] [PubMed]
  15. Zhang, C.; Jin, Y.; Liu, J.; Tang, Y.; Cao, S.; Qi, H. The phylogeny and expression profiles of the lipoxygenase (LOX) family genes in the melon (Cucumis melo L.) genome. Sci. Hortic. 2014, 170, 94–102. [Google Scholar] [CrossRef]
  16. Li, M.; Li, L.; Dunwell, J.M.; Qiao, X.; Liu, X.; Zhang, S. Characterization of the lipoxygenase (LOX) gene family in the Chinese white pear (Pyrus bretschneideri) and comparison with other members of the Rosaceae. BMC Genom. 2014, 15, 444. [Google Scholar] [CrossRef]
  17. Zhang, B.; Chen, K.; Bowen, J.; Allan, A.; Espley, R.; Karunairetnam, S.; Ferguson, I. Differential expression within the LOX gene family in ripening kiwifruit. J. Exp. Bot. 2006, 57, 3825–3836. [Google Scholar] [CrossRef]
  18. Yang, X.-Y.; Jiang, W.-J.; Yu, H.-J. The expression profiling of the lipoxygenase (LOX) family genes during fruit development, abiotic stress and hormonal treatments in cucumber (Cucumis sativus L.). Int. J. Mol. Sci. 2012, 13, 2481–2500. [Google Scholar] [CrossRef]
  19. Huang, D.; Ma, F.; Wu, B.; Lv, W.; Xu, Y.; Xing, W.; Chen, D.; Xu, B.; Song, S. Genome-wide association and expression analysis of the lipoxygenase gene family in Passiflora edulis revealing pelox4 might be involved in fruit ripeness and ester formation. Int. J. Mol. Sci. 2022, 23, 12496. [Google Scholar] [CrossRef]
  20. Li, Z.; Xie, Q.; Yan, J.; Chen, J.; Chen, Q. Genome-wide identification and characterization of the abiotic-stress-responsive GRF gene family in diploid woodland strawberry (Fragaria vesca). Plants 2021, 10, 1916. [Google Scholar] [CrossRef]
  21. Meng, Y.; Liang, Y.; Liao, B.; He, W.; Liu, Q.; Shen, X.; Xu, J.; Chen, S. Genome-wide identification, characterization and expression analysis of lipoxygenase gene family in Artemisia annua L. Plants 2022, 11, 655. [Google Scholar] [CrossRef] [PubMed]
  22. Zhang, Q.; Zhao, Y.; Zhang, J.; Li, X.; Ma, F.; Duan, M.; Zhang, B.; Li, H. The responses of the lipoxygenase gene family to salt and drought stress in foxtail millet (Setaria italica). Life 2021, 11, 1169. [Google Scholar] [CrossRef] [PubMed]
  23. Li, J.; Chen, L.; Chen, P.; Li, Q.; Yang, Q.; Zhang, Y.; Tan, B.; Ye, X.; Zheng, X.; Feng, J. Genome-wide identification and expression of the lipoxygenase gene family in jujube (Ziziphus jujuba) in response to phytoplasma infection. J. Plant Biochem. Biotechnol. 2022, 31, 139–153. [Google Scholar] [CrossRef]
  24. Shrestha, K.; Pant, S.; Huang, Y. Genome-wide identification and classification of Lipoxygenase gene family and their roles in sorghum-aphid interaction. Plant Mol. Biol. 2021, 105, 527–541. [Google Scholar] [CrossRef]
  25. Sarde, S.J.; Kumar, A.; Remme, R.N.; Dicke, M. Genome-wide identification, classification and expression of lipoxygenase gene family in pepper. Plant Mol. Biol. 2018, 98, 375–387. [Google Scholar] [CrossRef]
  26. Zhu, J.; Wang, X.; Guo, L.; Xu, Q.; Zhao, S.; Li, F.; Yan, X.; Liu, S.; Wei, C. Characterization and alternative splicing profiles of the lipoxygenase gene family in tea plant (Camellia sinensis). Plant Cell Physiol. 2018, 59, 1765–1781. [Google Scholar] [CrossRef]
  27. Guo, S.; Song, Z.; Ma, R.; Yang, Y.; Yu, M. Genome-wide identification and expression analysis of the lipoxygenase gene family during peach fruit ripening under different postharvest treatments. Acta Physiol. Plant. 2017, 39, 111. [Google Scholar] [CrossRef]
  28. Chen, Z.; Chen, X.; Yan, H.; Li, W.; Li, Y.; Cai, R.; Xiang, Y. The lipoxygenase gene family in poplar: Identification, classification, and expression in response to MeJA treatment. PLoS ONE 2015, 10, e0125526. [Google Scholar] [CrossRef]
  29. Umate, P. Genome-wide analysis of lipoxygenase gene family in Arabidopsis and rice. Plant Signal. Behav. 2011, 6, 335–338. [Google Scholar] [CrossRef]
  30. Ogunola, O.F.; Hawkins, L.K.; Mylroie, E.; Kolomiets, M.V.; Borrego, E.; Tang, J.D.; Williams, W.P.; Warburton, M.L. Characterization of the maize lipoxygenase gene family in relation to aflatoxin accumulation resistance. PLoS ONE 2017, 12, e0181265. [Google Scholar] [CrossRef]
  31. Gong, F.; Yang, L.; Tai, F.; Hu, X.; Wang, W. “Omics” of maize stress response for sustainable food production: Opportunities and challenges. Omics A J. Integr. Biol. 2014, 18, 714–732. [Google Scholar] [CrossRef] [PubMed]
  32. Hasanuzzaman, M.; Bhuyan, M.B.; Zulfiqar, F.; Raza, A.; Mohsin, S.M.; Mahmud, J.A.; Fujita, M.; Fotopoulos, V. Reactive oxygen species and antioxidant defense in plants under abiotic stress: Revisiting the crucial role of a universal defense regulator. Antioxidants 2020, 9, 681. [Google Scholar] [CrossRef] [PubMed]
  33. Sofo, A.; Dichio, B.; Xiloyannis, C.; Masia, A. Lipoxygenase activity and proline accumulation in leaves and roots of olive trees in response to drought stress. Physiol. Plant. 2004, 121, 58–65. [Google Scholar] [CrossRef] [PubMed]
  34. Bae, K.-S.; Rahimi, S.; Kim, Y.-J.; Devi, B.S.R.; Khorolragchaa, A.; Sukweenadhi, J.; Silva, J.; Myagmarjav, D.; Yang, D.-C. Molecular characterization of lipoxygenase genes and their expression analysis against biotic and abiotic stresses in Panax ginseng. Eur. J. Plant Pathol. 2016, 145, 331–343. [Google Scholar] [CrossRef]
  35. Rai, A.N.; Mandliya, T.; Kulkarni, P.; Rao, M.; Suprasanna, P. Evolution and transcriptional modulation of lipoxygenase genes under heat, drought, and combined stress in Brassica rapa. Plant Mol. Biol. Report. 2021, 39, 60–71. [Google Scholar] [CrossRef]
  36. Chen, T.; Cohen, D.; Itkin, M.; Malitsky, S.; Fluhr, R. Lipoxygenase functions in 1O2 production during root responses to osmotic stress. Plant Physiol. 2021, 185, 1638–1651. [Google Scholar] [CrossRef]
  37. Zhang, Y.; Wang, K.; Wang, Z.; Li, X.; Li, M.; Zhu, F.; Majeed, Z.; Lan, X.; Guan, Q. The lipoxygenase gene AfLOX4 of Amorpha fruticosa L. is a potential regulator of drought stress tolerance pathways under saline and alkaline conditions. Acta Physiol. Plant. 2023, 45, 72. [Google Scholar] [CrossRef]
  38. Lian, C.; Li, Q.; Yao, K.; Zhang, Y.; Meng, S.; Yin, W.; Xia, X. Populus trichocarpa PtNF-YA9, a multifunctional transcription factor, regulates seed germination, abiotic stress, plant growth and development in Arabidopsis. Front. Plant Sci. 2018, 9, 954. [Google Scholar] [CrossRef]
  39. Lv, R.; Mo, F.; Li, C.; Meng, F.; Zhang, H.; Yu, L.; Cheng, M.; Wang, P.; Liu, S.; Liu, Z. Genome-wide identification of the CLC gene family in tomato (Solanum lycopersicum) and functional analysis of SlCLC8 in salt stress tolerance. Sci. Hortic. 2024, 338, 113754. [Google Scholar] [CrossRef]
  40. Mo, F.; Xue, X.; Meng, L.; Zhang, Y.; Cui, Y.; Liu, J.; Cheng, M.; Wang, P.; Lv, R.; Meng, F. Genome-wide identification and expression analysis of SLAC1 gene family in tomato (Solanum lycopersicum) and the function of SlSLAC1–6 under cold stress. Sci. Hortic. 2023, 313, 111904. [Google Scholar] [CrossRef]
  41. Yu, G. Using ggtree to visualize data on tree-like structures. Curr. Protoc. Bioinform. 2020, 69, e96. [Google Scholar] [CrossRef] [PubMed]
  42. Tang, H.; Krishnakumar, V.; Zeng, X.; Xu, Z.; Taranto, A.; Lomas, J.S.; Zhang, Y.; Huang, Y.; Wang, Y.; Yim, W.C. JCVI: A versatile toolkit for comparative genomics analysis. iMeta 2024, 3, e211. [Google Scholar] [CrossRef] [PubMed]
  43. Huerta-Cepas, J.; Szklarczyk, D.; Heller, D.; Hernández-Plaza, A.; Forslund, S.K.; Cook, H.; Mende, D.R.; Letunic, I.; Rattei, T.; Jensen, L.J. eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019, 47, D309–D314. [Google Scholar] [CrossRef] [PubMed]
  44. Yu, G.; Wang, L.-G.; Han, Y.; He, Q.-Y. clusterProfiler: An R package for comparing biological themes among gene clusters. Omics A J. Integr. Biol. 2012, 16, 284–287. [Google Scholar] [CrossRef]
  45. Liao, Y.; Smyth, G.K.; Shi, W. featureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014, 30, 923–930. [Google Scholar] [CrossRef]
  46. Haas, B.J.; Papanicolaou, A.; Yassour, M.; Grabherr, M.; Blood, P.D.; Bowden, J.; Couger, M.B.; Eccles, D.; Li, B.; Lieber, M. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 2013, 8, 1494–1512. [Google Scholar] [CrossRef]
  47. Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 2001, 25, 402–408. [Google Scholar] [CrossRef]
Genes 16 00099 g001
Figure 1. Chromosome locations of ZmLOX genes. The scale on the left represents the lengths of the chromosomes.The number 1 represents chromosome 1, the number 2 represents chromosome 2, and so on.
Figure 1. Chromosome locations of ZmLOX genes. The scale on the left represents the lengths of the chromosomes.The number 1 represents chromosome 1, the number 2 represents chromosome 2, and so on.
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Figure 2. Characteristic analysis of ZmLOX gene family members. (a) Phylogenetic tree of ZmLOX proteins. (b) Conserved domains of ZmLOX proteins. (c) Motifs analysis of ZmLOX protein. (d) Gene structure analysis of ZmLOX genes.
Figure 2. Characteristic analysis of ZmLOX gene family members. (a) Phylogenetic tree of ZmLOX proteins. (b) Conserved domains of ZmLOX proteins. (c) Motifs analysis of ZmLOX protein. (d) Gene structure analysis of ZmLOX genes.
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Figure 3. Phylogenetic tree of LOX proteins in 3 species of plants. Three groups of LOX in different plant species were marked with different shapes: rectangle means A. thaliana, circle means maize, and rhombus means O. sativa.
Figure 3. Phylogenetic tree of LOX proteins in 3 species of plants. Three groups of LOX in different plant species were marked with different shapes: rectangle means A. thaliana, circle means maize, and rhombus means O. sativa.
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Figure 4. Gene duplication analysis of ZmLOX genes. (a) Collinearity analysis of LOX genes in maize. (b) Synteny analysis of LOX genes in maize, Arabidopsis, and rice.
Figure 4. Gene duplication analysis of ZmLOX genes. (a) Collinearity analysis of LOX genes in maize. (b) Synteny analysis of LOX genes in maize, Arabidopsis, and rice.
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Figure 5. Cis-element analysis of ZmLOX promoters.
Figure 5. Cis-element analysis of ZmLOX promoters.
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Figure 6. GO and KEGG enrichment of ZmLOX genes. (a) GO enrichment. (b) KEGG enrichment. The x-axis represents the Rich factor, indicating the proportion of genes associated with each term relative to the background set, while the size of the data points reflects the gene count and the color gradient denotes statistical significance (−log10(p-value)).
Figure 6. GO and KEGG enrichment of ZmLOX genes. (a) GO enrichment. (b) KEGG enrichment. The x-axis represents the Rich factor, indicating the proportion of genes associated with each term relative to the background set, while the size of the data points reflects the gene count and the color gradient denotes statistical significance (−log10(p-value)).
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Figure 7. PPI network between ZmLOX proteins and other proteins in maize. Each node represents a protein and edges indicate their interactions.
Figure 7. PPI network between ZmLOX proteins and other proteins in maize. Each node represents a protein and edges indicate their interactions.
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Figure 8. Expression profiling of ZmLOX genes in cold-sensitive maize and cold-resistant maize under cold treatment. (a) Differential expression of ZmLOX genes; samples mean control samples and treatment groups in differential expression gene analysis. (b) Expression heatmap of ZmLOX genes. C means control groups (25 °C), T means treatment groups (4 °C), and 1 or 2 means cold-sensitive maize and cold-resistant maize.
Figure 8. Expression profiling of ZmLOX genes in cold-sensitive maize and cold-resistant maize under cold treatment. (a) Differential expression of ZmLOX genes; samples mean control samples and treatment groups in differential expression gene analysis. (b) Expression heatmap of ZmLOX genes. C means control groups (25 °C), T means treatment groups (4 °C), and 1 or 2 means cold-sensitive maize and cold-resistant maize.
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Figure 9. The qRT-PCR analysis of 13 ZmLOX genes under four types of abiotic stresses. Error bars represent the standard error of the mean (SEM; n = 3). * indicates significant difference (p < 0.05), ** indicates highly significant difference (p < 0.01), *** indicates highly significant difference (p < 0.001) and **** indicates extremely significant difference (p < 0.0001).
Figure 9. The qRT-PCR analysis of 13 ZmLOX genes under four types of abiotic stresses. Error bars represent the standard error of the mean (SEM; n = 3). * indicates significant difference (p < 0.05), ** indicates highly significant difference (p < 0.01), *** indicates highly significant difference (p < 0.001) and **** indicates extremely significant difference (p < 0.0001).
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Table 1. The information on ZmLOX gene family members.
Table 1. The information on ZmLOX gene family members.
NameIDChrStartEndMW (KDa)LengthHydrophobicitypICell
ZmLOX1Zm00001d02789311694860816955122108.27968−0.338.59Cytoplasm
ZmLOX2Zm00001d0314491190316537190321767105.33956−0.336.73Chloroplast
ZmLOX3Zm00001d033623126904781726905287496.73867−0.326.06Cytoplasm
ZmLOX4Zm00001d0336241269056560269072120100.36887−0.456.63Cytoplasm
ZmLOX5Zm00001d00200024150293415440498.66904−0.296.00Cytoplasm
ZmLOX6Zm00001d00353324710518747109372105.31941−0.447.28Cytoplasm
ZmLOX7Zm00001d041204310535637710535973295.99850−0.448.22Cytoplasm
ZmLOX8Zm00001d0425403171277704171281453100.75892−0.376.68Cytoplasm
ZmLOX9Zm00001d042541317142171717142540199.33884−0.346.81Cytoplasm
ZmLOX10Zm00001d0536754238805319238809230102.06905−0.396.54Chloroplast
ZmLOX11Zm00001d01349351270118012706156100.36887−0.436.83Cytoplasm
ZmLOX12Zm00001d0158525126372618126376084102.87911−0.397.04Chloroplast
ZmLOX13Zm00001d02552410121268606121272616103.6929−0.427.14Cytoplasm
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Li, S.; Hou, S.; Sun, Y.; Sun, M.; Sun, Y.; Li, X.; Li, Y.; Wang, L.; Cai, Q.; Guo, B.; et al. Genome-Wide Identification and Expression Analysis Under Abiotic Stress of the Lipoxygenase Gene Family in Maize (Zea mays). Genes 2025, 16, 99. https://doi.org/10.3390/genes16010099

AMA Style

Li S, Hou S, Sun Y, Sun M, Sun Y, Li X, Li Y, Wang L, Cai Q, Guo B, et al. Genome-Wide Identification and Expression Analysis Under Abiotic Stress of the Lipoxygenase Gene Family in Maize (Zea mays). Genes. 2025; 16(1):99. https://doi.org/10.3390/genes16010099

Chicago/Turabian Style

Li, Sinan, Shuai Hou, Yuanqing Sun, Minghao Sun, Yan Sun, Xin Li, Yunlong Li, Luyao Wang, Quan Cai, Baitao Guo, and et al. 2025. "Genome-Wide Identification and Expression Analysis Under Abiotic Stress of the Lipoxygenase Gene Family in Maize (Zea mays)" Genes 16, no. 1: 99. https://doi.org/10.3390/genes16010099

APA Style

Li, S., Hou, S., Sun, Y., Sun, M., Sun, Y., Li, X., Li, Y., Wang, L., Cai, Q., Guo, B., & Zhang, J. (2025). Genome-Wide Identification and Expression Analysis Under Abiotic Stress of the Lipoxygenase Gene Family in Maize (Zea mays). Genes, 16(1), 99. https://doi.org/10.3390/genes16010099

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