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Article

Genome-Wide Identification of MADS-box Family Genes and Analysis of Their Expression Patterns in the Common Oat (Avena sativa L.)

by
Man Zhang
1,
Chun-Long Wang
1,
Yuan Jiang
2,
Bo Feng
1,
Hai-Xiao Dong
2,
Hao Chen
2,
Xue-Ying Li
1,
Xiao-Hui Shan
2,
Juan Tian
1,
Wei-Wei Xu
1,
Ya-Ping Yuan
2,*,
Chang-Zhong Ren
1,* and
Lai-Chun Guo
1,*
1
Key Laboratory of Biotechnology of Jilin Province, Baicheng Academy of Agricultural Science, Baicheng 137000, China
2
Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun 130000, China
*
Authors to whom correspondence should be addressed.
Agronomy 2025, 15(10), 2286; https://doi.org/10.3390/agronomy15102286
Submission received: 14 July 2025 / Revised: 31 August 2025 / Accepted: 23 September 2025 / Published: 26 September 2025
(This article belongs to the Section Crop Breeding and Genetics)
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Versions Notes

Abstract

The MADS-box gene family is a large family of transcription factors, and its members are widely distributed in the plant kingdom. Members of this family are well known to be crucial regulators of many biological processes and environmental responses. In this study, bioinformatics methods were employed to analyze the MADS-box gene family members in the common oat, focusing on their phylogenetic relationships, gene structures, conserved motifs, evolutionary relationships, promoter analysis and responses to photoperiod and abiotic stress. A total of 175 MADS-box genes were detected in Avena sativa, which were categorized into Type I and Type II. Type II members exhibited more complex gene structures, while each subfamily showed similar gene structures and motifs. Evolutionary analysis identified 138 segmental duplication events and revealed strong syntenic conservation with Triticum aestivum (337 collinear gene pairs). Four categories of cis-elements were detected in the promoter regions of the AsMADS-box genes. qRT-PCR analysis revealed that the expression of six Type II AsMADS-box genes varied in response to ABA, GA, drought and salt. Furthermore, 23 AsMADS-box members were potentially associated with heading date when the common oat plants were exposed to different photoperiod conditions. The overexpression of chr4D_AsMADS95 in Arabidopsis thaliana led to early flowering under long-day and short-day photoperiod conditions, likely associated with a significant increase in the expression levels of flowering-related genes in transgenic plants. These findings will provide useful information for future studies on stress responses and increase our understanding of the network that regulates flowering in the common oat.

1. Introduction

Transcription factors (TFs) constitute a major class of proteins that regulate the expression of target genes by binding to specific cis-acting elements in promoter regions [1]. MADS-box genes are one of the largest families of plant transcription factors in eukaryotes [2]. Each MADS-box protein contains a characteristic MADS domain in its N-terminus that is composed of 56 to 58 amino acids. This domain is capable of recognizing and binding to CArG-box [CC(A/T)6GGG, CC(A/T)7G and C(A/T)8G] cis-regulatory elements, thereby regulating the expression of specific genes [3,4]. Based on gene structures and evolutionary relationships, the MADS-box TF family is normally classified into two distinct groups: Type I (M-type) and Type II (MIKC-type) [5,6]. The Type I subfamily is characterized by a simple gene structure, usually containing only one or two exons. This subfamily can be further subdivided into three clades, namely, Mα, Mβ, and Mγ [7]. At present, the functional characterization of Type I genes in plants remains limited, although recent studies have suggested that these genes play roles in regulating female gametophyte and endosperm development in Arabidopsis thaliana, Triticum aestivum and Glycine max [8,9,10]. Compared with Type I, Type II proteins exhibit relatively more complex gene structures. Studies of MADS-box genes have shown that they typically have 6 to 8 exons. The Type II subfamily, also known as MIKC-type MADS-box genes, can be further classified into the MIKC* and MIKCC subgroups in Triticum aestivum and Setaria italica [11,12]. Compared with MIKC* proteins, MIKCC proteins are characterized by a shorter I domain and a more conserved K domain [13]. Phylogenetic analysis has shown that MIKCC proteins can be classified into at least 14 distinct subclades, namely AGAMOUS (AG)/STK, AGAMOUS-LIKE16 (AGL6), AGL12, AGL17, Bsister (GGM13), FLC, AP1 (SQUA), AP3 (DEF), PI (GLO), OsMADS32-like, SVP (StMADS11), SOC1 (TM3), TM8, and SEP from angiosperms [12,13]. To date, a total of 62 Type I and 46 Type II genes have been identified and characterized in Arabidopsis thaliana. Among these Type II genes, 39 MIKCC-type genes were further classified into 12 subgroups based on their phylogenetic relationships [14]. In Oryza sativa, the MIKCC-type genes can be divided into 14 subgroups. Within these subgroups, the OsMADS32-like clade was exclusively identified in monocotyledons and is absent in dicotyledons [12,15,16].
In recent studies, MADS-box genes, particularly MIKCC-type genes, have been implicated in various aspects of plant reproductive development [16,17]. In Arabidopsis thaliana, overexpression of the SVP gene results in late flowering. Further studies revealed that the SVP gene can directly bind to the promoters of SOC1 and FT to decrease their transcriptional levels [18,19]. However, knockout of OsMADS50, which is an Arabidopsis thaliana homologue of SVP, by CRISPR/Cas9 technology delays flowering time, and influences grain size and yield under long-day conditions [20]. The sequence of AGL24 is highly similar to that of SVP, but its protein performs the opposite function during the flowering process. Ectopic expression of AGL24 can promote early flowering, while the SVP gene show delayed flowering [21]. Mutations of OsMADS14, an AP1 MADS-box gene in Oryza sativa, result in a shrunken and chalky grain phenotype. Moreover, the AP1 class of genes is closely associated with bud differentiation [22]. In Arabidopsis thaliana, the disruption of AtSEP3 and AtAP1 interaction resulted in extended vegetative growth, increased size and number of rosette leaves, and modifications in floral structures [23]. In addition, several other MIKCC-type genes, such as the thermosensory flowering regulator FLOWERING LOCUS M (FLM) and AGL6, have been shown to be involved in flowering time. In Arabidopsis thaliana, different FLOWERING LOCUS M (FLM) isoforms (FLM-β and FLM-δ) form a heterodimeric complex with SHORT VEGETATIVE PHASE (SVP) in response to different temperatures. This complex formation was determined in a dosage- and binding affinity-dependent manner, controlling ambient temperature-responsive flowering [24]. The transcriptional repressor AGL6 promotes floral transition by directly suppressing EARLY FLOWERING 3 (ELF3), which in turn directly represses FT expression [25].
In the plant drought response, overexpression of MADS23 confers significant drought tolerance in transgenic rice plants. Studies have demonstrated that under drought conditions, OsMADS11 was shown to activate the transcription of OsNCED2, OsNCED3, OsNCED4, and OsP5CR that are key components for ABA and proline biosynthesis, thereby improving drought tolerance [26]. The flowering repressor SVP is induced by drought stress and directly regulates the expressions of CYP707A1, CYP707A3 and AtBG1, thereby influencing ABA levels and enhancing drought resistance [27]. The retrotransposon insertion within the first intron of the Arabidopsis thaliana FLOWERING LOCUS C (FLC) leads to an adaptive response to herbicides by affecting the balance between coding and non-coding transcripts in response to stress [28]. Moreover, in Actinidia chinensis, a MADS-box gene with homology to Arabidopsis thaliana FLC was induced by cold and correlated with epigenetic changes to control budbreak [29].
Common oat (Avena sativa L.) is a significant cereal crop, with its cultivated area exceeding 8 million hectares worldwide in 2023 [30]. It contains significant amounts of soluble dietetic fiber, beta-glucans, fat-soluble vitamin E and polyunsaturated fatty acid [31]. Due to its exceptional nutritional value, the demand for the common oat for both human consumption and animal feed has significantly increased in recent years. However, as an important cereal and forage crop, the cultivation of the common oat is limited by various environmental factors, such as drought, salinity and photoperiod [32]. Among these factors, photoperiod is a major determinant that regulates the transition from the vegetative stage to the reproductive stage. Heading date of the common oat was hastened by exposure to a long-day photoperiod. Through transcriptomic analysis, our previous study provided comprehensive insights into the molecular mechanisms underlying how photoperiod-sensitive common oat plants respond to different photoperiods conditions [32]. Based on functional enrichment analysis and identification of transcription factors, our findings revealed that several flowering pathways, including the photoperiod, plant hormone, circadian clock and sugar metabolism pathways, as well as various transcription factors, are critical for controlling flowering time in the common oat [32]. Some studies have reported that several transcription factors, such as MADS-box genes, can regulate flowering time through various pathways, including the photoperiodic pathway and hormonal pathways, as well as through crosstalk with these pathways [33]. In Triticum aestivum, the MADS-box transcription factor TaSOC1 modulates flowering by disrupting the interaction between two other MADS-box flowering promoters, TaVRN1 and TaVRT2, in both the vernalization and photoperiod pathways [34]. Recently, MADS-box transcription factors have been identified and functionally characterized in several crop species, including Arabidopsis thaliana, Oryza sativa, Triticum aestivum, Hordeum vulgare and Zea mays [14,15,16,35,36]. A total of sixteen MADS-box genes have been identified in the common oat using the Hidden Markov Model [37]. However, the comprehensive identification and elucidation of the functional roles of MADS-box genes in response to photoperiod and stress have not been reported in the common oat. Our previous studies revealed that Baiyan 2, a common oat cultivar bred by the Baicheng Academy of Agricultural Science, exhibits strong sensitivity to photoperiods during flowering, and flowering was inhibited under short-day conditions and induced under long-day conditions [32,38]. However, the functional characterization of MADS-box family members in response to photoperiod has yet to be performed in the common oat.
In this study, the MADS-box genes in the common oat genome were systematically characterized through bioinformatics methods. The phylogenetic relationships, physical and chemical properties, gene structures, conserved motifs, chromosomal distributions, the cis-acting elements in promoter regions, and gene duplication events were comprehensively analysed. RNA-seq was conducted to investigate the expression patterns of AsMADS-box genes in response to stress treatment and different photoperiod conditions. Notably, for the first time, we propose a model by which AsMADS-box genes regulate flowering in the common oat under long-day photoperiod conditions. Thus, our analysis is the first comprehensive study on AsMADS-box genes, and it provides a basis for further research on the biological functions of these genes in the common oat.

2. Materials and Methods

2.1. Plant Growth and Treatments

For photoperiod analysis, seeds of the common oat cultivar Baiyan 2 were sown in plastic pots in the greenhouse. All plants were kept in the greenhouse for two weeks under short-day conditions (10 h light at 24 °C and 14 h dark at 20 °C) with 8000 lux light intensity. When the plants were at the first leaf fully expanded stage, half of the plants were shifted to long-day conditions (14 h light at 24 °C and 10 h dark at 20 °C). The photoperiod treatments were applied from 8:00 a.m. to 10 p.m. for long-day conditions, and from 8:00 a.m. to 6:00 p.m. for short-day conditions. The uppermost unfolded leaves were collected at 10:00 a.m. under the 30/40/50-long day treatments, with three replicates, and each replicate was pooled from 3 plants. The SD samples were also collected at the same time. The RNA-seq data under long-day and short-day photoperiods were obtained in our previous study, and the NCBI accession number was PRJNA997076 [32].
For hormone and stress treatments, healthy seeds of the common oat cultivar Baiyan 2 were sterilized with 75% ethanol for 2 min, followed by rinsing with ddH2O at least 5 times. The sterilized seeds were placed on moist filter paper in dishes and incubated for 24 h in the dark. After germination, the seedlings in the dishes were transferred to a growth chamber and maintained for 10 days at 24 °C with 14 h light/10 h dark and 8000 lx. At the two-leaf stage, the seedlings were subjected to ABA (100 μM), GA (200 μM), PEG-6000 (20%) or NaCl (200 mM) treatment. Leaf samples were immediately frozen in liquid nitrogen at 0, 3, 6, and 12 h and stored at −80 °C refrigerator for subsequent qRT-PCR experiments. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (AK251456) was used as the endogenous reference gene. Each sample consisted of three individual plants and had three biological replicates.
In this study, Arabidopsis thaliana (ecotype Columbia-0) was used for genetic transformation. Wild-type (WT) and transgenic seedlings were grown in the sterilized growth medium consisting of vermiculite and turfy soil (3:1). After 3 days of treatment in the dark at 4 °C, the plants were transferred to growth chambers under both LD (16 h light/8 h dark) and SD (8 h light/16 h dark) photoperiod conditions at 21 ± 1 °C with a light intensity of 6000 lux. The flowering time was determined by recording the number of days from sowing until bolting and the number of rosette leaves at the bolting stage, with at least 15 plants per line [39].

2.2. Retrieval of Genome Sequences

Genome sequence data for Avena sativa were obtained from GrainGenes (https://wheat.pw.usda.gov/jb?data=/ggds/oat-ot3098v2-pepsico, accessed on 6 June 2024) [40]. The sequences of the MADS-box proteins from Arabidopsis thaliana and Brachypodium distachyon were downloaded from The Arabidopsis Information Resource (TAIR) database (https://www.arabidopsis.org/, accessed on 6 June 2024) and the Phytozome v13 (https://phytozome-next.jgi.doe.gov/, accessed on 6 June 2024), respectively. The MADS-box genes of Oryza sativa and wheat were obtained from previous reports [41,42].

2.3. Identification of AsMADS-box Genes in the Common Oat and Analysis of Their Chromosomal Location

Three strategies were used to confirm the common oat MADS-box gene family. The MADS-box protein sequences of four plant species, namely, Arabidopsis thaliana, Oryza sativa, Brachypodium distachyon and wheat were used as queries to search against the common oat genome using the BLAST program version 2.9.0 with an E-value threshold ≤ 10 × 10−10. Moreover, the above sequences were also input into the Genewise software (v2.1.1) to search against the common oat genome with an E-value threshold ≤ 10 × 10−5 and identity ≥ 80%. Additionally, the HMM profile of the SRF-TF domain (PF00319) obtained from the Pfam database was used to search against the common oat genome protein sequences using the HMM search tool (v3.0), with an E-value < 1 × 10−5. All the identified MADS-box genes were verified with the public databases, including the National Center for Biotechnology Information Conserved Domain Database (NCBI-CDD) and Pfam, to confirm their reliability and integrity [43].
The chromosomal positions of the identified AsMADS-box genes were retrieved from the common oat genome annotation files, and chromosome mapping was conducted using TBtools-II (v2.310) software [44].

2.4. Phylogenetic Analysis of MADS-box Proteins

Multiple sequence alignment of all the MADS-box protein sequences from Arabidopsis thaliana, Oryza sativa and Avena sativa was performed using MAFFT software (version 7) with the FFT-NS-2 algorithm [45]. The phylogenetic tree was constructed using IQ-TREE software version 2.2.0 [46]. The JTT + G4 model was applied for the MADS-box protein sequences of the three species, whereas the LG + G4 model was used for the common oat MADS-box protein sequences. The generated trees were visualized using the iTOL tool (http://itol.embl.de/, accessed on 18 June 2024) [47].

2.5. Analysis of the Physicochemical Properties, Gene Structure, and Conserved Motif and Domains of the MADS-box TFs

The physical and chemical parameters of AsMADS-box proteins, including protein length, molecular weight, isoelectric point, grand average of hydropathicity (GRAVY) and instability index, were computed with the ProtParam tool of ExPASy (https://web.expasy.org/protparam/, accessed on 18 June 2024). The subcellular localizations of AsMADS-box proteins were predicted with the online Plant-PLoc server v2.0 (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/, accessed on 18 June 2024) [48]. The gene structure information of AsMADS-box genes was extracted from the common oat genome annotation file. The conserved domains were predicted using the National Center for Biotechnology Information Conserved Domain Database (NCBI-CDD) [43]. The conserved motifs were identified using the MEME Suite Version 5.5.8, with a total of 20 motif sets, minimum motif width of 6, and maximum motif width of 50 (https://meme-suite.org/meme/tools/meme, accessed on 25 June 2024). The gene structures, conserved domains and conserved motif features were drawn using TBtools-II (v2.310) software [44].

2.6. Prediction of Gene Duplication and Cis-Acting Regulatory Elements

The prediction of gene duplication events in AsMADS-box genes was performed using the Multiple Collinearity Scan toolkit (MCScanX) in TBtools-II (v2.310) software [49]. Synteny relationships among AsMADS-box genes were visualized with Circos software version S2 based on the following criteria: sequence identity ≥ 75%, E-value ≤ 1 × 10−10, and alignment coverage ≥ 0.75. The synteny relationships of AsMADS-box genes between the common oat genome and those of the other four plant species (Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon and Triticum aestivum) was analysed using the MCScanX2 program [49,50] and visualized using the TBtools-II (v2.310) software [44]. The nonsynonymous (ka)/synonymous substitution (ks) values for all the gene pairs were calculated using KaKs_calculator software version 3.0 to assess selective pressures [51].
The 2000-bp promoter regions of AsMADS-box family members were analysed to predict the cis-regulatory elements with the online tool PlantCARE website (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 25 July 2024). The sequence analysis was visualized with TBtools-II (v2.310) software [44].

2.7. Prediction of Putative microRNAs Targeting AsMADS-box Genes

The CDS sequences of AsMADS-box were submitted to the online psRNATarget software version 2 (https://www.zhaolab.org/psRNATarget/analysis, accessed on 15 September 2025), with all parameters maintained at their default settings. Moreover, the Cytoscape software (version 3.10.3) was employed to generate and visualize the interaction net work between the predicted miRNAs and AsMADS-box targeting genes.

2.8. Analysis of AsMADS-box Expression Profiles Based on Transcriptome Sequencing

RNA extraction, library construction, and Illumina RNA sequencing were performed by Biomarker Technologies Company (Beijing, China). The expression levels of AsMADS-box genes were determined by calculating the fragments per kilobase of transcript per million mapped reads (FPKM) values with StringTie software version 1.2.3 [52]. Differentially expressed genes were identified using DESeq2 with the thresholds of |log2Fold Change|≥1 and false discovery rate (FDR) ≤ 0.05 [53]. The gene expression profiles were visualized using TBtools-II (v2.310) software [44].

2.9. Overexpression Plasmid Construction

The coding sequence of chr4D_AsMADS95 was amplified and inserted into the pDONR207 vector using the Minerva Super Fusion Cloning Kit (US Everbright Inc., Suzhou, China). The resulting construct was further inserted into the overexpression vector pEarleyGate 101 under the control of the 35S promoter by LR clonase (Invitrogen, Waltham, MA, USA). The recombinant plant vector was subsequently transformed into Agrobacterium tumefaciens (strain GV3101) and subsequently into Arabidopsis thaliana (Col-0) plants using the floral dip transformation method [54].

2.10. Validation of AsMADS-box Gene Expression by qRT-PCR

The first-strand cDNA that was used in qRT-PCR analyses was synthesized using RT mix with DNase (All-in-One) (R2028L, US Everbright Inc., Suzhou, China). The qRT-PCR amplification primers were designed using the Primer Premier 5.0. The qRT-PCR amplification was performed using Fast Super EvaGreen®qPCR Master Mix (S2008, US Everbright Inc., Suzhou, China) on an Eco RealTime PCR System (England). The amplification reaction was conducted in five steps: 95 °C for 10 min; 40 cycles of 95 °C for 15 s and 60 °C for 34 s; 95 °C for 15 s; 60 °C for 1 min; and 95 °C for 15 s. For each gene, three biological replicates, each with three technical replicates were performed under identical conditions. The experimental data were analysed using the 2–ΔΔCt method as described by Livak and Schmittgen [55]. The primers for qRT-PCR are listed in Table S1.

3. Results

3.1. Identification and Chromosomal Location of AsMADS-box Genes

Based on the latest released common oat genome, a total of 175 AsMADS-box family members were identified. The NCBI-CDD search further revealed that 98 (56%) encode MADS-box proteins and 77 (44%) encode MADS and K-box proteins (Table S2). The AsMADS-box family genes were systematically named from AsMADS001 to AsMADS175, with each name prefixed by chromosome and subgenome. Analysis of the physical and chemical properties revealed that the protein length of the AsMADS-box family members ranged from 81 to 255 bp, the molecular weight varied from 9.08 kDa to 71.25 kDa, and the pI ranged from 4.34 to 10.95 (Table S3). A total of 173 out of 175 AsMADS-box proteins were located in the nucleus. The remaining two genes, chr2C_AsMADS39 and chr7C_AsMADS147, were predicted to localize to the peroxisome and cytoplasm, respectively (Table S3). Chromosome localization analysis revealed that 172 AsMADS-box family members were unevenly distributed on all 21 chromosomes of the common oat, with three additional members located on an unknown chromosome. The distribution of these genes exhibited significant variations among chromosomes. Notably, chromosome 7D contained the greatest number of these genes (16), whereas chromosome 3A had the fewest, with only 2 genes (Figure 1).

3.2. Phylogenetic Analysis of AsMADS-box Genes

Comparative phylogenetic analyses of MADS-box genes between Oryza sativa and Avena sativa (Figure S1), as well as between Triticum aestivum and Avena sativa (Figure S2), distinguished Avena sativa genes into Type I and Type II (Table S3).
To investigate the evolutionary relationship of AsMADS-box proteins, a phylogenetic tree was constructed using full sequences of all MADS-box proteins from Oryza sativa (75 sequences), Triticum aestivum (300 sequences), and Avena sativa (175 sequences) (Figure 2, Table S3 and S4). Based on phylogenetic analysis using MADS-box proteins from these two species, the Type I AsMADS-box genes were further divided into three subgroups, namely, Mα, Mβ and Mγ, which included 30, 25, and 24 members, respectively. The Type II genes were subdivided into MIKCC and MIKC* subgroups, which included 87 and 9 members, respectively. The MIKCC subgroup could be further divided into twelve evolutionary clades based on the known Oryza sativa and Triticum aestivum MADS-box genes, such as AP3, PI, OsMADS32, Bsister, SOC1, SVP, AG, AGL12, AGL17, AP1, AGL6 and SEP. Among these subgroups, the AGL17 clade contained the greatest number of AsMADS-box genes (16), whereas the AGL6 clade contained the fewest, with only two genes (Table S3).

3.3. Gene Structure Analysis, Conserved Motif and Domain Identification

Twenty conserved motifs were identified in AsMADS-box genes using the MEME program (Figure S3). Motif 1, Motif 3 and Motif 4 were corresponding to the typical MADS domains (Figure 3B). The main motif 1 was found in all AsMADS-box proteins, and most of AsMADS-box proteins had all three motifs. Based on the sequence alignments of these three motifs, several amino acid residues exhibited a high level of conservation. These conserved residues include Met (M), Thr (T), Ala (A), Glu (E), Cys (C), two Gly (G), two Phe (F), three Lys (K), four Arg (R), and four Leu (L) at different positions, which are consistently observed in both Type I and Type II AsMADS-box proteins (Figure S4). Furthermore, certain motifs were specific to particular types of AsMADS-box proteins. For example, Motif 6 and Motif 14 was uniquely present in Type II proteins and corresponded to the K-domain. Motif 5, Motif 10 and Motif 20 were exclusively found in the Mβ subgroup (Figure 3B), indicating that AsMADS-box proteins in the same subgroups exhibit identical motif patterns, and potentially share similar functional roles. Structural diversity in the exon-intron organizations of AsMADS-box genes was analysed by comparisons of genomic DNA and cDNA sequences. Among the Type I AsMADS-box genes, most exhibited simple structures with no introns or only a single intron, except for chr3D_AsMADS58, chr4A_AsMADS62 and chr7D_AsMADS161, which contained 3, 2 and 2 introns, respectively (Figure 3C). Compared with Type I genes, Type II AsMADS-box genes exhibited more complex gene structures. The number of introns in Type II AsMADS-box ranged from 0 to 12, with an average of 6.62. Notably, 86 (49.14%) members contained at least three introns (Figure 3C, Table S3).

3.4. Cis-Regulatory Element Distribution of AsMADS-box Genes

Analysis of the 2000-bp promoter regions from the AsMADS-box genes revealed that the AsMADS-box family members contained four main categories of cis-regulatory elements, including those related to hormone responses, stress responses, light signalling and plant growth and development (Table S5). All the MADS-box promoters contained light-responsive elements, including a GA-motif, GATA-motif, G-box, circadian, Box-4, AE-box, GT1-motif, I-box and MRE. The G-box was present in 163 AsMADS-box genes, with chr4C_AsMADS71 and chr7D_AsMADS166 containing the greatest number (Figure 4 and Table S4). In the stress category, all the MADS-box genes contained drought-induced elements (MYB, MYC and MBS), with chr2C_AsMADS38 containing the greatest number. Seven cis-elements associated with hormonal responses were identified, including elements associated with abscisic acid (ABRE), MeJA (CGTCA-motif and TGACG-motif), auxin (TGA-element-motif), ethylene (ERE), salicylic acid (as-1, TCA-element) and gibberellin (TATC-box, P-box and CARE) (Figure 4). Additionally, among the predicted plant growth and development elements, A-box was the most abundant, suggesting the putative roles of AsMADS-box genes in the seed development process (Figure 4 and Table S5).

3.5. Gene Duplication Analysis and Orthologous Identification Between the Common Oat and the Other Four Species

To investigate the evolutionary relationships of AsMADS-box genes, the duplication events were analysed using MCScanX software. The results revealed that 7 tandem duplication events involving 11 genes occurred on chromosomes 4A, 4C, 5A and 5D. Among these, the gene pairs of chr4C_AsMADS75/chr4C_AsMADS76 and chr4C_AsMADS76/chr4C_AsMADS77 were identified as members of the Mβ subgroup, whereas the pairs of chr5A_AsMADS100/chr5A_AsMADS101, chr5A_AsMADS101/chr5A_AsMADS102, chr5A_AsMADS102/chr5A_AsMADS103 and chr5D_AsMADS117/chr5D_AsMADS118 belonged to the Mγ subgroup. These findings confirm the accuracy of the group classification in the phylogenetic tree. Moreover, a total of 121 AsMADS-box genes were originated from segmental duplication events. Among these genes, chr5D_AsMADS118 had the strongest collinearity relationship with other AsMADS-box genes, including chr5A_AsMADS100, chr5A_AsMADS101, chr5A_AsMADS102 and chr5A_AsMADS103 (Figure 5, and Table S6). These results revealed that segmental duplication events greatly contributed to the expansion of the MADS-box gene family in the common oat.
The syntenic relationships between the common oat and three other plant species, including one eudicot (Arabidopsis thaliana), and three monocots (Oryza sativa, Brachypodium distachyon and Triticum aestivum), were further studied to elucidate the evolutionary relationships among the five plant species. Overall, 25, 107, 105, and 337 MADS-box collinear gene pairs were identified between Avena sativa and Arabidopsis thaliana, Avena sativa and Oryza sativa, Avena sativa and Brachypodium distachyon, and Avena sativa and Triticum aestivum, respectively (Figure 6 and Table S7). More than half of the AsMADS-box genes in the common oat had syntenic counterparts in at least one of the three species, and most of them had syntenic genes in only one species. Notably, 16 AsMADS-box genes had orthologous relationships across all four species (Table S7). The remaining AsMADS-box genes (less than half) lacked syntenic relationships with any of the four species, suggesting that these genes were more conserved members of the AsMADS-box gene family. The estimated Ka/Ks values of syntenic gene pairs were all less than 1 and varied between 0.019 and 0.778, indicating that purifying selection plays a role in their evolutionary process (Table S7).

3.6. MiRNA Prediction of AsMADS-box Genes from the AGL17 Subclade

When predicting the upstream regulator miRNAs of AsMADS-box genes, it was observed that 201 upstream regulator osa-miRNAs belonging to 28 unique families were found for 13 AsMADS-box genes from the AGL17 subclade, including chr6A_AsMADS126, chr2A_AsMADS29, chr2D_AsMADS43, chr4D_AsMADS84, chr4D_AsMADS85, chr5A_AsMADS97, chr5D_AsMADS114, chr6C_AsMADS133, chr6D_AsMADS135, chr6D_AsMADS136, chr7C_AsMADS156, chrun_AsMADS174 and chrun_AsMADS175 (Figure 7 and Table S8). It was observed that 134 members of osa-miR144 targeted the highest up to 13 AsMADS-box genes from the AGL17 subclade by cleaving mRNA and translational inhibition. Among these genes, chr5A_AsMADS97 was targeted most frequently, as much as 38 times (Figure 7 and Table S8). Besides, when the expectation value was less than 2.5, all the upstream regulatory factors were miR444 (Table S8), suggesting that miR444 may have related roles in AsMADS-box genes in from the AGL17 subclade.

3.7. Analysis of AsMADS-box Gene Expression Patterns Under Hormone and Abiotic Stress Conditions

To gain more insight into the functional role of AsMADS-box genes in responses to ABA, GA, salt and drought, six AsMADS-box genes were selected from the Type II group, and their expression profiles were analysed by qRT-PCR (Figure 8). Under ABA treatment, the expression of chr7D_AsMADS159 decreased at 6 h and 12 h. The expression of chr1D_AsMADS24 decreased at 6 h and increased at 12 h. Similarly, the expression of chr4A_AsMADS68 decreased at 3 h and 6 h, followed by an increase at 12 h. Conversely, the expression of chr4C_AsMADS79 increased dramatically at 3 h and 6 h and decreased significantly at 12 h. chr7D_AsMADS157 expression exhibited a greater increase at 3 h and 12 h, but showed a significant decrease at 6 h (Figure 8A). Following GA treatment, the expression of chr1D_AsMADS24 decreased compared with that of the control, and the expression of chr4A_AsMADS68 and chr7D_AsMADS157 increased and peaked at 12 h (Figure 8B). Compared with the control, salt stress caused a decrease in the expression of chr1D_AsMADS24 and chr7D_AsMADS159 at 6 h and an increase in the expression of chr4C_AsMADS79 at 3 h. The expression of both chr1D_AsMADS18 and chr4A_AsMADS68 increased and peaked at 12 h. The expression patterns of chr7D_AsMADS157 decreased first at 6 h and then increased at 12 h (Figure 8C). The expression pattern of chr1D_AsMADS18, chr4C_AsMADS79 and chr7D_AsMADS157 increased under drought treatment, peaking at 12 h. The expression of chr1D_AsMADS24 decreased at 6 h, whereas that of chr4A_AsMADS68 decreased at 3 h, followed by an increase at 12 h (Figure 8D). These qRT-PCR results indicate the complexity and diversity of AsMADS-box gene expression patterns in response to hormone treatments and abiotic stresses, highlighting their potential for use as key targets for improving tolerance to both hormone and stress.

3.8. Expression Analysis of AsMADS-box Genes Under in Long-Day and Short-Day Conditions

The transcriptome data were analysed to investigate the response of AsMADS-box genes in Baiyan 2 to a long-day photoperiod in the floral organ primordium differentiation stage (30 LD), the booting stage (40 LD) and the heading date stage (50 LD). The results revealed that 60 AsMADS-box genes were differentially expressed (Table S9). With the threshold criteria of |log2(Fold Change)| ≥ 1 and FDR ≤ 0.05, 23 AsMADS-box genes exhibited significant changes in expression at different developmental stages. A heatmap was constructed to visualize these changes (Figure 8). Among these genes, the expression levels of the chr1D_AsMADS17/chr2A_AsMADS26/chr2C_AsMADS35/chr2D_AsMADS46/chr3C_AsMADS51/chr4A_AsMADS66/chr4A_AsMADS67/chr4C_AsMADS71/chr4D_AsMADS91/chr4D_AsMADS95/chr7C_AsMADS148 genes were significantly induced (Figure 9A), whereas those of the chr1C_AsMADS13/chr1C_AsMADS15/chr2A_AsMADS31/chr2C_AsMADS36/chr2D_AsMADS41/chr4A_AsMADS68/chr4C_AsMADS79/chr6C_AsMADS130/chr7A_AsMADS138/chr7C_AsMADS147/chr7D_AsMADS157/chr7D_AsMADS162 genes were significantly downregulated under the long-day period conditions compared with the short-day period conditions (Figure 9B). These observations suggest the potential role of these MADS-box genes in regulating the heading date of the common oat under long-day conditions. In addition, 13 significantly expressed AsMADS-box genes, including chr1C_AsMADS15/chr2A_AsMADS26/chr2C_AsMADS35/chr2D_AsMADS41/chr2D_AsMADS46/chr4A_AsMADS66/chr4A_AsMADS67/chr4C_AsMADS79/chr4D_AsMADS91/chr7A_AsMADS138/chr7C_AsMADS148/chr7D_AsMADS157/chr7D_AsMADS162, were members of seven segmentally duplicated AsMADS-box gene pairs (Table S6). These genes exhibited similar expression patterns in Baiyan 2 under long-day photoperiod conditions, suggesting their similar roles in the flowering regulatory network.

3.9. chr4D_AsMADS95 Promotes Flowering Under LD and SD Photoperiod Conditions

To assess the potential role of chr4D_AsMADS95 in the regulation of flowering time, chr4D_AsMADS95-overexpressing and wild-type Arabidopsis thaliana plants were examined under LD and SD photoperiod conditions. Statistical analysis of flowering time and rosette leaf number revealed that chr4D_AsMADS95-overexpressing plants flowered earlier and produced fewer rosette leaves than the wild-type plants under both LD and SD conditions. Under long-day conditions, chr4D_AsMADS95-overexpressing plants flowered 5–7 days earlier than wild-type plants (Figure 10A,B). Wild-type Arabidopsis thaliana produced an average of 12 rosette leaves before flowering, whereas the overexpression plants required only 8 rosette leaves on average (Figure 10C). Under short-day conditions, chr4D_AsMADS95-overexpressing plants flowered 15–20 days earlier than wild-type plants (Figure 10D,E), and they produced significantly fewer rosette leaves, with a reduction of 12–16 leaves (Figure 10F). Together, these results indicate that chr4D_AsMADS95 positively regulates flowering time in Arabidopsis thaliana. To investigate the molecular mechanisms underlying the early flowering phenotype in chr4D_AsMADS95-overexpressing Arabidopsis thaliana lines, we examined the expression levels of six key flowering-related genes in both the wild-type and corresponding overexpression lines under LD and SD conditions. Compared with those in the wild-type plants, the expression levels of AtFT, AtAP1 and AtFUL were significantly greater in all three chr4D_AsMADS95-overexpressing lines under LD and SD conditions (Figure 10G). In addition, the expression level of AtSOC1 also significantly increased in the chr4D_AsMADS95-overexpressing lines under LD conditions (Figure 10H). These findings are consistent with the early-flowering phenotype observed in the chr4D_AsMADS95-overexpressing lines.

4. Discussion

Common oat, an important cereal crop cultivated worldwide, serves as a valuable source of proteins, lipids, vitamins, minerals, and antioxidants, which has led to increased interest from the food, pharmaceutical, and cosmetic industries [56]. However, the molecular mechanisms underlying the common oat development remain poorly understood. Functional studies of MADS-box proteins have revealed their crucial role in plant development and stress responses, particularly in floral organ differentiation, flowering time regulation, and fruit development and ripening. The MADS-box gene family has been characterized in many plant species, including Arabidopsis thaliana, Oryza sativa, and Gossypium raimondii. However, the understanding of MADS-box genes in the common oat remains limited. In this study, we employed three methods to identify members of the MADS-box gene family in the common oat and further explored the potential roles of these genes in flowering time regulation and responses to abiotic stress.

4.1. The AsMADS-box Gene Family Has Undergone Significant Expansion in the Common Oat

In this study, a total of 175 AsMADS-box genes was identified in the common oat via genome-wide analysis, including 79 Type I and 96 Type II genes. The number of MADS-box genes in the common oat were greater than that reported for several other plant species, including Arabidopsis thaliana (66 members), Oryza sativa (34 members) [57], dioecious spinach (54 members) [58], Camellia oleifera (86 members) [59], Beta vulgaris (48 members) [60], Paeonia ostii (110 members) [61], Lumnitzera littorea (63 members) [62], Cucumis sativus (48 members) [63] and Lathyrus sativus (46 members) [64], but less than those in Triticum aestivum (180 members) [65]. Our analysis revealed that there was no obvious correlation between plant genome size and the number of MADS-box genes. Previous studies have reported that the main driving forces of MADS-box gene family expansion are tandem duplication and segmental duplication. In Primulina huaijiensis, 61 PhuMADS-box genes were derived from segmental duplication events, whereas only one gene pair was associated with a tandem duplication event [66]. Gene duplication analysis demonstrated that segmental duplication was the primary driving force of the expansion of the MADS-box genes in Ricinus communis [67]. Our gene duplication analysis indicated that segmental duplication was the driving force behind the expansion of the MADS-box gene family in the common oat, which particularly occurred more often in Type II genes. This pattern was consistent with observations in Oryza sativa, where more Tpye II genes were found in segmental duplications. These duplication events occurred in the common oat MADS-box gene family play novel functional roles, thereby enhancing the environmental adaptability of the common oat.

4.2. AsMADS-box Genes May Be Involved in Hormone Signalling and Abiotic Stress Responses

Cis-acting regulatory elements (CREs) are noncoding DNA sequences within the promoter regions to which transcription factors bind to control the transcription of target genes. Characterization of CREs is essential for gaining deeper insights into the mechanism within gene regulatory networks. Consistent with previous studies, various hormone response elements, such as elements related to auxin, abscisic acid, gibberellin, ethylene, and salicylic acid, were identified among the common oat MADS-box genes, potentially suggesting their involvement in many hormone regulatory pathways. ABRE is an important cis-acting element in ABA signalling pathways. In this study, all the AsMADS-box genes were found to contain ABREs, suggesting that these MADS-box genes may participate in the response to ABA. Furthermore, our qRT-PCR results revealed that 5 AsMADS-box genes might play key roles in the ABA signalling pathway according to the up- and downregulation of their expression. Previous studies have revealed that MADS-box genes contribute to the regulation of plant stress tolerance. For example, the overexpression of CaMADS in Arabidopsis thaliana plants increased tolerance to cold, salt and osmotic stress [68]. The rice transcription factor OsMADS57 enhances salt tolerance in transgenic Arabidopsis thaliana and Oryza sativa plants [69]. Furthermore, the overexpression of PvMADS31 in transgenic plants can increase their tolerance to drought and salinity [70]. Our results revealed that the transcription of all 6 AsMADS-box genes significantly changed in response to short-term salt and drought treatment. The qRT-PCR results provide strong evidence for the crucial involvement of the common oat MADS-box genes in response to salt and drought. Furthermore, these cis-elements likely contribute to the adaptation of the common oat to these adverse environments.
MicroRNAs, small non-coding RNA molecules, were associated with various developmental processes and responses to environmental stimuli [71]. In Oryza sativa, the miR444 gene family has been shown to target certain MADS-box transcription factors. For instance, OsMADS27, a major miR444 target, regulates the expression of nitrate transporters, as well as key genes including expansins, and those involved in auxin signalling, thereby promoting root growth [72]. In this study, 201 unique miRNAs from Oryza sativa were identified, targeting 13 AsAMADS-box genes of the AGL17 subclade. Among these, osa-miR444 was found to target up to 13 AsAMADS-box genes of the AGL17 subclade. These results suggest that miR444 may have related roles in these AsAMADS-box genes, suggesting a potentially conserved role in the regulation of MADS-box genes across different species.

4.3. AsMADS-box Genes Can Participate in Responses Associated with Flowering in the Common Oat Under Long-Day and Short-Day Conditions

Photoperiod, which is a major environmental factor, significantly regulates flowering time in plant species. When the day length exceeds 12 h, oat can flower normally. However, under a short-day photoperiod (day length shorter than 12 h), most oat cultivars fail to flower and produce seeds, resulting in a lower oat yield and quality. Research in Arabidopsis thaliana and Oryza sativa has revealed that MADS-box genes play significant roles in flowering time. AGL79 positively regulates flowering time in Arabidopsis thaliana by interacting with SOC1 and repressing TFL1 expression [73]. The overexpression of AGL19 in Arabidopsis thaliana causes early flowering via the strong upregulation of FT [74]. In Oryza sativa, flowering is regulated by OsMADS56, which is tightly controlled by an intronic lncRNA, namely, RIFLA, that is transcribed from the first intron of the OsMADS56 gene [75]. OsMADS22 interacts with OsMADS50 to antagonistically control a series of downstream flowering-related genes, including OsMADS14, RFT1, Ehd1, Hd3a and OsMADS1 [20]. Additional studies in other plants have shown that many MADS-box transcription factors are associated with regulation of flowering time in response to photoperiod. In Brassica napus, BnaC09.FUL overexpression results in early flowering, whereas BnaFUL mutation causes delayed flowering [76]. The overexpression of BjuAGL18-1L in Brassica juncea and Arabidopsis thaliana leads to late flowering, whereas BjuAGL18-1S overexpression results in early flowering [77]. GmMADS66, which is a homologous gene of the SOC1-like subfamily from Glycine max, induces early flowering in transgenic Arabidopsis thaliana plants through a photoperiod-dependent pathway [78]. However, the role of MADS-box genes in Avena sativa remains to be further investigated. In this study, 11 upregulated DEGss and 12 downregulated DEGs belonging to the MADS-box gene family were identified under long-day conditions compared with short-day conditions. Several common oat MADS-box genes that are homologous to those in Arabidopsis thaliana and other plant species have been characterized in previous studies [22,23,24,25,26,27,28,29]. With the combination of previous findings and our results in this study, we propose a model for the regulation of flowering by AsMADS-box genes in the common oat under LD conditions (Figure S5). In the model, expression of the MADS-box genes chr1D_AsMADS17/chr2A_AsMADS26/chr2C_AsMADS35/chr2D_AsMADS46/chr3C_AsMADS51/chr4A_AsMADS66/chr4A_AsMADS67/chr4C_AsMADS71/chr4D_AsMADS91/chr6C_AsMADS130/chr7C_AsMADS147/chr7C_AsMADS148/chr7D_AsMADS162 may be induced, and chr1C_AsMADS13/chr1C_AsMADS15/chr2A_AsMADS31/chr2C_AsMADS36/chr2D_AsMADS41/chr4A_AsMADS68/chr4C_AsMADS79/chr7D_AsMADS157 may negatively regulate flowering. However, up- and downstream AsMADS-box genes are still unknown. Further efforts are thus needed to elucidate the roles of AsMADS-box genes in flowering under LD conditions. Functional verification revealed that one of the DEGs, namely, chr4D_AsMADS95, promoted flowering under both long-day and short-day photoperiod conditions. Our phenotypic results are consistent with previous findings in Oryza sativa [79]. These findings strongly suggest that AsMADS-box genes may play a significant role in regulating heading date in response to different photoperiods in Avena sativa. However, further studies are essential to fully elucidate the roles of other genes that are involved in this process.
Overall, our study conducted an extensive analysis of the MADS-box gene family in the common oat. Our findings will not only offer valuable insights for improving the productivity and adaptation of the common oat cultivars under different environments, but also lay a strong foundation for functional studies of the MADS-box gene family across plant species in the future.

5. Conclusions

This study provides the first comprehensive analysis of the MADS-box gene family in the common oat. Here, a total of 175 AsMADS-box genes were detected, and their phylogenetic relationships, gene structures, conserved motifs, gene duplication events and cis-acting regulatory elements were systematically characterized in the common oat. Expression profiles by qRT-PCR revealed that the AsMADS-box genes were involved in hormone regulation and various abiotic stress responses. Transcriptome analysis revealed that AsMADS-box genes responded significantly to different photoperiods. Functional characterization revealed that chr4D_AsMADS95 promoted flowering under both long-day and short-day photoperiod conditions. This study identified candidate genes for further investigations on the regulation of stress tolerance and heading date in the common oat.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agronomy15102286/s1, Figure S1: Comparative phylogenetic tree of MADS-box genes between Oryza sativa and Avena sativa. M- and MIKC-type genes were highlighted with blue and red colour nodes, respectively. Figure S2: Comparative phylogenetic tree of MADS-box genes between Triticum aestivum and Avena sativa. M- and MIKC-type genes were highlighted with blue and red colour nodes, respectively. Figure S3: Sequence logos for seven identified conserved motifs in AsMADS-box proteins. Figure S4: Sequence alignment of MADS domains from MADS-box proteins in the common oat. Figure S5: MADS-box genes involved in the regulatory network for the flowering time of the common oat under LD conditions. The clock at the top designates the circadian clock. Red arrows represent induction, and green T-bars represent suppression. Table S1: Sequences of the primers that were used for qRT-PCR. Table S2: Putative protein domains identified in the common oat MADS-box genes through NCBI conserved domain database. Table S3. Overview of identified MADS-box genes from Avena sativa. Table S4: The MADS-box genes identified from Oryza sativa and Triticum aestivum in this study. Table S5: Detailed information about the cis-acting elements in the promoter regions of MADS-box genes from Avena sativa. Table S6: Detailed information about syntenic MADS-box gene pairs. Table S7: Ka/Ks values of MADS-box collinear gene pairs between the common oat and four other plant species. Table S8: The putative miRNA of AsMADS-box genes from the AGL17 subclade. Table S9: Transcript levels (FPKM values) of 58 AsMADS-box genes in Baiyan 2 at three developmental stages under long-day and short-day photoperiods.

Author Contributions

Conceptualization, L.-C.G., C.-Z.R. and Y.-P.Y.; methodology, M.Z.; software, M.Z., H.-X.D.; validation, L.-C.G., C.-Z.R. and Y.-P.Y.; formal analysis, M.Z., C.-L.W., Y.J. and H.-X.D.; investigation, M.Z., C.-L.W., Y.J. and H.-X.D.; resources, L.-C.G. and C.-Z.R.; data curation, M.Z.; writing—original draft preparation, M.Z., C.-L.W., Y.J. and H.-X.D.; writing—review and editing, M.Z., C.-L.W., Y.J., H.-X.D., B.F., H.C., X.-Y.L., X.-H.S., J.T., W.-W.X., L.-C.G., C.-Z.R. and Y.-P.Y.; supervision, L.-C.G., C.-Z.R. and Y.-P.Y.; project administration, L.-C.G., C.-Z.R. and Y.-P.Y. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the China Agriculture Research System of the Ministry of Finance and Ministry of Agriculture and Rural Affairs (CARS07 to C.R.), the Jilin Development and Reform Commission Project, Research and Application of Key Technologies in Oat Molecular Breeding (2021FGWCXNLJSSZ04), the Baicheng Science and Technology Development Program (202211) and Inner Mongolia Autonomous Region Biological Breeding Technology Innovation Center-Creation of new forage germplasm and breeding and promotion of new varieties (2024NSZC03).

Data Availability Statement

Data are contained within the article and Supplementary Materials.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Yu, H.; Xia, L.; Zhu, J.; Xie, X.; Wei, Y.; Li, X.; He, X.; Luo, C. Genome-wide analysis of the MADS-box gene family in mango and ectopic expression of MiMADS77 in Arabidopsis results in early flowering. Gene 2025, 935, 149054. [Google Scholar] [CrossRef]
  2. Riechmann, J.L.; Heard, J.; Martin, G.; Reuber, L.; Jiang, C.; Keddie, J.; Adam, L.; Pineda, O.; Ratcliffe, O.J.; Samaha, R.R.; et al. Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes. Science 2000, 290, 2105–2110. [Google Scholar] [CrossRef]
  3. Niels, A.; Suzanne, D.B.; Hilda, V.M.; Angenent, G.C.; Van, D.A.D.J. Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana. BMC Plant Biol. 2018, 18, 131. [Google Scholar] [CrossRef] [PubMed]
  4. Käppel, S.; Eggeling, R.; Rümpler, F.; Groth, M.; Melzer, R.; Theißen, G. DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq. Plant Mol. Biol. 2021, 105, 543–557. [Google Scholar] [CrossRef] [PubMed]
  5. Ghorbani Marghashi, M.; Bagheri, H.; Gholami, M. Genome-wide study of flowering-related MADS-box genes family in Cardamine hirsuta. 3 Biotech 2020, 10, 518. [Google Scholar] [CrossRef]
  6. Duan, K.; Fu, H.; Fang, D.; Wang, K.; Zhang, W.; Liu, H.; Sahu, S.K.; Chen, X. Genome-wide analysis of the MADS-box gene family in Holoparasitic Plants (Balanophora subcupularis and Balanophora fungosa var. globosa). Front. Plant Sci. 2022, 13, 846697. [Google Scholar] [CrossRef] [PubMed]
  7. Kaufmann, K.; Melzer, R.; Theissen, G. MIKC-type MADS-domain proteins: Structural modularity, protein interactions and network evolution in land plants. Gene 2005, 347, 183–198. [Google Scholar] [CrossRef]
  8. Paul, P.; Joshi, S.; Tian, R.; Diogo Junior, R.; Chakrabarti, M.; Perry, S.E. The MADS-domain factor AGAMOUS-Like 18 promotes somatic embryogenesis. Plant Physiol. 2022, 188, 1617–1631. [Google Scholar] [CrossRef]
  9. Zhang, J.; Zhang, Z.; Zhang, R.; Yang, C.; Zhang, X.; Chang, S.; Chen, Q.; Rossi, V.; Zhao, L.; Xiao, J.; et al. Type I MADS-box transcription factor TaMADS-GS regulates grain size by stabilizing cytokinin signalling during endosperm cellularization in wheat. Plant Biotechnol. J. 2024, 22, 200–215. [Google Scholar] [CrossRef]
  10. Zhang, A.; He, H.; Li, Y.; Wang, L.; Liu, Y.; Luan, X.; Wang, J.; Liu, H.; Liu, S.; Zhang, J.; et al. MADS-box subfamily gene GmAP3 from glycine max regulates early flowering and flower development. Int. J. Mol. Sci. 2023, 24, 2751. [Google Scholar] [CrossRef]
  11. Schilling, S.; Kennedy, A.; Pan, S.; Jermiin, L.S.; Melzer, R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: Pervasive duplications, functional conservation and putative neofunctionalization. New Phytol. 2020, 225, 511–529. [Google Scholar] [CrossRef]
  12. Zhao, W.; Zhang, L.L.; Xu, Z.S.; Fu, L.; Pang, H.X.; Ma, Y.Z.; Min, D.H. Genome-wide analysis of MADS-Box genes in foxtail millet (Setaria italica L.) and functional assessment of the role of SiMADS51 in the drought stress response. Front. Plant Sci. 2021, 12, 659474. [Google Scholar] [CrossRef] [PubMed]
  13. Qin, Y.; Zhu, G.P.; Li, F.D.; Wang, L.; Chen, C.; Zhao, H. MIKC-type MADS-box gene family discovery and evolutionary investigation in Rosaceae Plants. Agronomy 2023, 13, 1695. [Google Scholar] [CrossRef]
  14. Duan, W.; Song, X.; Liu, T.; Huang, Z.; Ren, J.; Hou, X.; Li, Y. Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage). Mol. Genet. Genom. 2015, 290, 239–255. [Google Scholar] [CrossRef]
  15. Parenicová, L.; de Folter, S.; Kieffer, M.; Horner, D.S.; Favalli, C.; Busscher, J.; Cook, H.E.; Ingram, R.M.; Kater, M.M.; Davies, B.; et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world. Plant Cell 2003, 15, 1538–1551. [Google Scholar] [CrossRef] [PubMed]
  16. Tian, J.; Gao, L. Evolutionary Dynamics and expression divergence of the MADS-Box gene family during recent speciation of AA-genome Oryza Species. Plants 2025, 14, 379. [Google Scholar] [CrossRef]
  17. Tahmasebi, S.; Jonoubi, P.; Majdi, M.; Majd, A.; Heidari, P. Genome-wide characterization and expression profiling of MADS-box family genes during organ development and drought stress in Camelina sativa L. Sci. Rep. 2025, 15, 9327. [Google Scholar] [CrossRef]
  18. Bouché, F.; Lobet, G.; Tocquin, P.; Périlleux, C. FLOR-ID: An interactive database of flowering-time gene networks in Arabidopsis thaliana. Nucleic Acids Res. 2015, 44, D1167–D1171. [Google Scholar] [CrossRef]
  19. Meng, Q.; Gao, Y.N.; Cheng, H.; Liu, Y.; Yuan, L.N.; Song, M.R.; Li, Y.R.; Zhao, Z.X.; Hou, X.F.; Tan, X.M.; et al. Molecular mechanism of interaction between SHORT VEGETATIVE PHASE and APETALA1 in Arabidopsis thaliana. Plant Physiol. Biochem. 2025, 220, 109512. [Google Scholar] [CrossRef]
  20. Wang, D.; Chai, Y.; Chen, S. OsMADS22 interacts with OsMADS50 to regulate floral transition in rice. Biochem. Biophys. Res. Commun. 2025, 757, 151607. [Google Scholar] [CrossRef]
  21. Chen, H.; Zhang, H.; Wang, D.; Wang, Y.; Jiang, H.; Chen, J. Integrative transcriptome and metabolome analyses reveal the molecular mechanism of re-flowering induction in Hydrangea macrophylla. J. Plant Physiol. 2025, 308, 154492. [Google Scholar] [CrossRef]
  22. Feng, T.; Wang, L.; Li, L.; Liu, Y.; Chong, K.; Theißen, G.; Meng, Z. OsMADS14 and NF-YB1 cooperate in the direct activation of OsAGPL2 and Waxy during starch synthesis in rice endosperm. New Phytol. 2022, 234, 7–92. [Google Scholar] [CrossRef]
  23. Tan, X.M.; Li, Y.R.; Song, M.R.; Yuan, L.N.; Zhao, Z.X.; Liu, Y.; Meng, Q.; Huang, X.; Ma, Y.Y.; Xu, Z.Q. The molecular mechanism of interaction between SEPALLATA3 and APETALA1 in Arabidopsis thaliana. Plant Direct 2025, 9, e70052. [Google Scholar] [CrossRef] [PubMed]
  24. Jin, S.; Kim, S.Y.; Susila, H.; Nasim, Z.; Youn, G.; Ahn, J.H. FLOWERING LOCUS M isoforms differentially affect the subcellular localization and stability of SHORT VEGETATIVE PHASE to regulate temperature-responsive flowering in Arabidopsis. Mol. Plant 2022, 15, 1696–1709. [Google Scholar] [CrossRef] [PubMed]
  25. Lee, K.; Yoon, H.; Seo, P.J. The AGL6–ELF3–FT circuit controls flowering time in Arabidopsis. Plant Signal Behav. 2024, 19, 2358684. [Google Scholar] [CrossRef] [PubMed]
  26. Li, X.; Yu, B.; Wu, Q.; Min, Q.; Zeng, R.; Xie, Z.; Huang, J. OsMADS23 phosphorylated by SAPK9 confers drought and salt tolerance by regulating ABA biosynthesis in rice. PLoS Genet. 2021, 17, e1009699. [Google Scholar] [CrossRef]
  27. Wang, Z.; Wang, F.; Hong, Y.; Yao, J.; Ren, Z.; Shi, H.; Zhu, J. The flowering repressor SVP confers drought resistance in Arabidopsis by regulating abscisic acid catabolism. Mol. Plant 2018, 11, 1184–1197. [Google Scholar] [CrossRef]
  28. Raingeval, M.; Leduque, B.; Baduel, P.; Edera, A.; Roux, F.; Colot, V.; Quadrana, L. Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide. Nat. Plants 2024, 10, 1672–1681. [Google Scholar] [CrossRef]
  29. Voogd, C.; Brian, L.A.; Wu, R.; Wang, T.; Allan, A.C.; Varkonyi-Gasic, E. A MADS-box gene with similarity to FLC is induced by cold and correlated with epigenetic changes to control budbreak in kiwifruit. New Phytol. 2022, 233, 2111–2126. [Google Scholar] [CrossRef]
  30. FAO. Available online: http://faostat.fao.org (accessed on 19 August 2025).
  31. Jiang, P.; Kang, Z.; Zhao, S.; Meng, N.; Liu, M.; Tan, B. Effect of dynamic high-pressure microfluidizer on physicochemical and microstructural properties of whole-grain oat pulp. Foods 2023, 12, 2747. [Google Scholar] [CrossRef]
  32. Zhang, M.; Jiang, Y.; Dong, H.; Shan, X.; Tian, J.; Sun, M.; Ma, F.; Ren, C.; Yuan, Y. Transcriptomic response for revealing the molecular mechanism of oat flowering under different photoperiods. Front. Plant Sci. 2023, 14, 1279107. [Google Scholar] [CrossRef] [PubMed]
  33. Feng, Z.; Zhang, Q.; Li, Y.; Hao, P.B.; Wei, H.L.; Fu, X.K.; Lu, J.H.; Ma, L.; Yu, S.X.; Wang, H.T. GhGAI interacts with GhAP1 and regulates flowering pathway in upland cotton. Ind. Crops Prod. 2023, 192, 116110. [Google Scholar] [CrossRef]
  34. Luo, X.; Liu, B.; Xie, L.; Wang, K.; Xu, D.; Tian, X.; Xie, L.; Li, L.; Ye, X.; He, Z.; et al. The TaSOC1-TaVRN1 module integrates photoperiod and vernalization signals to regulate wheat flowering. Plant Biotechnol. J. 2024, 22, 635–649. [Google Scholar] [CrossRef]
  35. Wang, F.; Zhou, Z.; Zhu, L.; Gu, Y.; Guo, B.; Lv, C.; Zhu, J.; Xu, R. Genome-wide analysis of the MADS-box gene family involved in salt and waterlogging tolerance in barley (Hordeum vulgare L.). Front. Plant Sci. 2023, 14, 1178065. [Google Scholar] [CrossRef]
  36. Zhao, D.; Chen, Z.; Xu, L.; Zhang, L.; Zou, Q. Genome-wide analysis of the MADS-Box gene family in maize: Gene structure, evolution, and relationships. Genes 2021, 12, 1956. [Google Scholar] [CrossRef]
  37. Nan, J.; An, J.; Yang, Y.; Zhao, G.; Yang, X.; Liu, H.; Han, B. Genome-wide identification of the MADS-box gene family in Avena sativa and its role in photoperiod-insensitive oat. PeerJ 2024, 12, e16759. [Google Scholar] [CrossRef] [PubMed]
  38. Zhang, M.; Jiang, Y.; Dong, H.; Shan, X.; Chen, H.; Li, X.; Wang, C.; Ba, S.; Li, J.; Guo, L.; et al. Comparative transcriptome analysis of oat varieties with different flowering performances under a short-day photoperiod. BMC Plant Biol. 2025, 25, 622. [Google Scholar] [CrossRef]
  39. Cui, J.; Li, Y.; Liu, H.; Jiang, X.; Zhang, L.; Dai, H.; Wang, X.; He, F.; Li, M.; Kang, J. Genome-wide identification and expression analysis of CBF/DREB1 gene family in Medicago sativa L. and functional verification of MsCBF9 affecting flowering time. BMC Plant Biol. 2025, 25, 87. [Google Scholar] [CrossRef]
  40. Kamal, N.; Tsardakas Renhuldt, N.; Bentzer, J.; Gundlach, H.; Haberer, G.; Juhász, A.; Lux, T.; Bose, U.; Tye-Din, J.A.; Lang, D.; et al. The mosaic oat genome gives insights into a uniquely healthy cereal crop. Nature 2022, 606, 113–119. [Google Scholar] [CrossRef] [PubMed]
  41. Arora, R.; Agarwal, P.; Ray, S.; Singh, A.K.; Singh, V.P.; Tyagi, A.K.; Kapoor, S. MADS-box gene family in rice: Genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genom. 2007, 8, 242. [Google Scholar] [CrossRef]
  42. Raza, Q.; Riaz, A.; Atif, R.M.; Hussain, B.; Rana, I.A.; Ali, Z.; Budak, H.; Alaraidh, I.A. Genome-wide diversity of MADS-Box genes in bread wheat is associated with its rapid global adaptability. Front. Genet. 2022, 12, 818880. [Google Scholar] [CrossRef]
  43. Lu, S.N.; Wang, J.Y.; Chitsaz, F.; Derbyshire, M.K.; Geer, R.C.; Gonzales, N.R.; Gwadz, M.; Hurwitz, D.I.; Marchler, G.H.; Song, J.S.; et al. CDD/SPARCLE: The conserved domain database in 2020. Nucleic Acids Res. 2019, 48, D265–D268. [Google Scholar] [CrossRef] [PubMed]
  44. Chen, C.; Wu, Y.; Li, J.; Wang, X.; Zeng, Z.; Xu, J.; Liu, Y.; Feng, J.; Chen, H.; He, Y.; et al. TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining. Mol. Plant 2023, 16, 1733–1742. [Google Scholar] [CrossRef] [PubMed]
  45. Katoh, K.; Standley, D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef]
  46. Nguyen, L.T.; Schmidt, H.A.; von Haeseler, A.; Minh, B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2014, 32, 268–274. [Google Scholar] [CrossRef]
  47. Letunic, I.; Bork, P. Interactive tree of life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics 2007, 23, 127–128. [Google Scholar] [CrossRef] [PubMed]
  48. Chou, K.C.; Shen, H.B. Plant-mPLoc: A top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS ONE 2010, 5, e11335. [Google Scholar] [CrossRef]
  49. Krzywinski, M.; Schein, J.; Birol, I.; Connors, J.; Gascoyne, R.; Horsman, D.; Jones, S.J.; Marra, M.A. Circos: An information aesthetic for comparative genomics. Genome Res. 2009, 19, 1639–1645. [Google Scholar] [CrossRef]
  50. Wang, Y.; Tang, H.; Debarry, J.D.; Tan, X.; Li, J.; Wang, X.; Lee, T.H.; Jin, H.; Marler, B.; Guo, H.; et al. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2021, 40, e49. [Google Scholar] [CrossRef]
  51. Zhang, Z.; Li, J.; Zhao, X.Q.; Wang, J.; Wong, G.K.; Yu, J. KaKs calculator: Calculating Ka and Ks through model selection and model averaging. Genom. Proteom. Bioinform. 2006, 4, 259–263. [Google Scholar] [CrossRef]
  52. Trapnell, C.; Williams, B.A.; Pertea, G.; Mortazavi, A.; Kwan, G.; van Baren, M.J.; Salzberg, S.L.; Wold, B.J.; Pachter, L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28, 511–515. [Google Scholar] [CrossRef]
  53. Love, M.I.; Huber, W.; Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014, 15, 550. [Google Scholar] [CrossRef] [PubMed]
  54. Clough, S.J.; Bent, A.F. Floral dip: A simplified method for Agrobacterium mediated transformation of Arabidopsis thaliana. Plant J. 1998, 16, 735–743. [Google Scholar] [CrossRef]
  55. Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25, 402–408. [Google Scholar] [CrossRef]
  56. Kumari, A.; Kumar, M.; Tyagi, A.; Maheshwari, C.; Meena, N.L. Nutritional Composition of Oats and Its Comparison with Other Major Cereal Crops. Oat (Avena sativa), 1st ed.; CRS Press: Boca Raton, FL, USA, 2024; pp. 69–103. [Google Scholar]
  57. Abdullah-Zawawi, M.R.; Ahmad-Nizammuddin, N.F.; Govender, N.; Harun, S.; Mohd-Assaad, N.; Mohamed-Hussein, Z.A. Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice. Sci. Rep. 2021, 11, 19678. [Google Scholar] [CrossRef]
  58. Fatima, M.; Ma, X.; Zhang, J.; Ming, R. Genome-wide analysis of MADS-box genes and their expression patterns in unisexual flower development in dioecious spinach. Sci. Rep. 2024, 14, 18635. [Google Scholar] [CrossRef] [PubMed]
  59. Zhang, X.; He, W.; Wang, X.; Duan, Y.; Li, Y.; Wang, Y.; Jiang, Q.; Liao, B.; Zhou, S.; Li, Y. Genome-wide analyses of MADS-Box Genes reveal their involvement in seed development and oil accumulation of tea-oil tree (Camellia oleifera). Int. J. Genom. 2024, 2024, 3375173. [Google Scholar] [CrossRef]
  60. Cao, J.; Gong, Y.; Zou, M.; Li, H.; Chen, S.; Ma, C. Genome-wide identification and salt stress response analysis of the MADS-box transcription factors in sugar beet. Physiol. Plant. 2024, 176, e70001. [Google Scholar] [CrossRef] [PubMed]
  61. Yang, X.; Guo, Q.; Liu, S.; Wang, D.; Zuo, D.; Niu, T.; Wei, D.; Guo, L.; Hou, X. Genome-wide characterization of the MADS-box gene family in Paeonia ostii and expression analysis of genes related to floral organ development. BMC Genom. 2025, 26, 49. [Google Scholar] [CrossRef] [PubMed]
  62. Zhang, L.; Yang, Y.; Zhang, Y.; Yang, F. Genome-wide investigation of MADS-box genes in flower development and environmental acclimation of Lumnitzera littorea (Jack) Voigt. Int. J. Mol. Sci. 2025, 26, 1680. [Google Scholar] [CrossRef]
  63. Wang, Z.; Chang, J.; Han, J.; Yin, M.; Wang, X.; Ren, Z.; Wang, L. Genome-wide reidentification and expression analysis of MADS-Box gene family in Cucumber. Int. J. Mol. Sci. 2025, 26, 3800. [Google Scholar] [CrossRef]
  64. Abdelsattar, M.; Nassar, A.E.; Mousa, K.H.; Hussein, A.; El-Baghdady, M.M.S.; Radwan, K.H.; Ibrahim, M.S.; El Allali, A.; Hamwieh, A.; Alsamman, A.M.; et al. Genome-wide identification, characterization, and expression analysis of the MADS-box gene family in grass pea (Lathyrus sativus) under salt stress conditions. BMC Genom. 2025, 26, 519. [Google Scholar]
  65. Ma, J.; Yang, Y.; Luo, W.; Yang, C.; Ding, P.; Liu, Y.; Qiao, L.; Chang, Z.; Geng, H.; Wang, P.; et al. Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.). PLoS ONE 2017, 12, e0181443. [Google Scholar] [CrossRef]
  66. Zhang, J.; Cai, X.; Liu, Q.; Lei, Z.; Feng, C. Genome-wide identification and expression analyses of the MADS-box gene during flowering in Primulina huaijiensis. Plants 2025, 14, 1843. [Google Scholar] [CrossRef]
  67. Sun, J.; Zhou, Z.; Meng, F.; Wen, M.; Liu, A.; Yu, A. Characterization analyses of MADS-box genes highlighting their functions with seed development in Ricinus communis. Front. Plant Sci. 2025, 16, 1589915. [Google Scholar] [CrossRef]
  68. Chen, R.; Ma, J.; Luo, D.; Hou, X.; Ma, F.; Zhang, Y.; Meng, Y.; Zhang, H.; Guo, W. CaMADS, a MADS-box transcription factor from pepper, plays an important role in the response to cold, salt, and osmotic stress. Plant Sci. 2019, 280, 164–174. [Google Scholar] [PubMed]
  69. Wu, J.; Yu, C.; Huang, L.; Gan, Y. A rice transcription factor, OsMADS57, positively regulates high salinity tolerance in transgenic Arabidopsis thaliana and Oryza sativa plants. Physiol. Plant. 2021, 173, 1120–1135. [Google Scholar] [CrossRef]
  70. Mostafa, K.; Yerlikaya, B.A.; Abdulla, M.F.; Aydin, A.; Yerlikaya, S.; Kavas, M. Genome-wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses. Plant Genome 2024, 17, e20432. [Google Scholar]
  71. Chojnacka, A.; Smoczynska, A.; Bielewicz, D.; Pacak, A.; Hensel, G.; Kumlehn, J.; Maciej Karlowski, W.; Grabsztunowicz, M.; Sobieszczuk-Nowicka, E.; Jarmolowski, A.; et al. PEP444c encoded within the MIR444c gene regulates microRNA444c accumulation in barley. Physiol. Plant. 2023, 175, e14018. [Google Scholar] [CrossRef]
  72. Pachamuthu, K.; Hari Sundar, V.; Narjala, A.; Singh, R.R.; Das, S.; Avik Pal, H.C.Y.; Shivaprasad, P.V. Nitrate-dependent regulation of miR444-OsMADS27 signalling cascade controls root development in rice. J. Exp. Bot. 2022, 73, 3511–3530. [Google Scholar]
  73. Yang, H.; Zhang, P.; Guo, D.; Wang, N.; Lin, H.; Wang, X.; Niu, L. Transcriptional repressor AGL79 positively regulates flowering time in Arabidopsis. J. Plant Physiol. 2023, 285, 153985. [Google Scholar] [CrossRef]
  74. Lim, C.J.; Park, K.S.; Ali, A.; Park, J.; Ryou, S.M.; Shen, M.; Khan, H.A.; Bader, Z.E.; Zareen, S.; Bae, M.J.; et al. Negative regulation of floral transition in Arabidopsis by HOS15-PWR-HDA9 complex. Front. Plant Sci. 2023, 13, 1105988. [Google Scholar] [CrossRef]
  75. Shin, W.J.; Nam, A.H.; Kim, J.Y.; Kwak, J.S.; Song, J.T.; Seo, H.S. Intronic long noncoding RNA, RICE FLOWERING ASSOCIATED (RIFLA), regulates OsMADS56-mediated flowering in rice. Plant Sci. 2022, 320, 111278. [Google Scholar] [CrossRef]
  76. Min, Y.; He, S.; Wang, X.; Hu, H.; Wei, S.; Ge, A.; Jiang, L.; Yang, S.; Guo, Y.; Liu, Z.; et al. Transcription factors BnaC09.FUL and BnaC06.WIP2 antagonistically regulate flowering time under long-day conditions in Brassica napus. J. Genet. Genom. 2025, 52, 650–665. [Google Scholar] [CrossRef]
  77. Deng, Q.; Lu, H.; Liu, D.; Huang, Y.; Feng, J.; Wei, D.; Wang, Z.; Tang, Q. Modulation of flowering by an alternatively spliced AGL18-1 transcript in Brassica juncea. Crop J. 2025, 13, 456–467. [Google Scholar] [CrossRef]
  78. Yao, X.; Li, K.; Wang, S.; Ji, X.; Zhang, Y.; Zhu, H. GmMADS66 regulates flowering time under photoperiod dependent pathway in Arabidopsis. Plant Cell Tissue Organ Cult. 2025, 160, 14. [Google Scholar] [CrossRef]
  79. Ma, Y.; Dong, J.; Yang, W.; Chen, L.; Wu, W.; Li, W.; Zhou, L.; Wang, J.; Chen, J.; Yang, T.; et al. OsFLZ2 interacts with OsMADS51 to fine-tune rice flowering time. Development 2022, 149, dev200862. [Google Scholar] [CrossRef]
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Figure 1. Chromosomal locations of AsMADS-box genes. The ruler on the left side of each chromosome indicates the chromosome length in megabases (Mb). Chromosome numbers are labelled at the left of each chromosome. Gene density is represented by coloured bands, ranging from high gene density in red to low gene density in yellow.
Figure 1. Chromosomal locations of AsMADS-box genes. The ruler on the left side of each chromosome indicates the chromosome length in megabases (Mb). Chromosome numbers are labelled at the left of each chromosome. Gene density is represented by coloured bands, ranging from high gene density in red to low gene density in yellow.
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Figure 2. A phylogenetic tree was constructed using the MADS-box protein sequences from Oryza sativa (75 sequences), Triticum aestivum (300 sequences), and Avena sativa (175 sequences).
Figure 2. A phylogenetic tree was constructed using the MADS-box protein sequences from Oryza sativa (75 sequences), Triticum aestivum (300 sequences), and Avena sativa (175 sequences).
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Figure 3. Phylogenetic tree, gene structure and conserved motif analysis of AsMADS-box genes. (A) Phylogenetic relationships of 175 AsMADS-box proteins. (B) Distributions of the identified conserved motifs in AsMADS-box proteins, with different motifs indicated by distinct coloured boxes. The number in the box indicates the label for the corresponding motif. (C) Gene structures of AsMADS-box genes. The green box indicates the coding region (CDS), the grey line indicates the intron, and the yellow box indicates the untranslated region (UTR).
Figure 3. Phylogenetic tree, gene structure and conserved motif analysis of AsMADS-box genes. (A) Phylogenetic relationships of 175 AsMADS-box proteins. (B) Distributions of the identified conserved motifs in AsMADS-box proteins, with different motifs indicated by distinct coloured boxes. The number in the box indicates the label for the corresponding motif. (C) Gene structures of AsMADS-box genes. The green box indicates the coding region (CDS), the grey line indicates the intron, and the yellow box indicates the untranslated region (UTR).
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Figure 4. Cis-regulatory elements (CREs) in the promoter regions of AsMADS-box genes. Different CREs are indicated by different colours.
Figure 4. Cis-regulatory elements (CREs) in the promoter regions of AsMADS-box genes. Different CREs are indicated by different colours.
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Figure 5. Collinearity of AsMADS-box genes. The pink lines inside the circle represent syntenic A. sativa MADS-box gene pairs.
Figure 5. Collinearity of AsMADS-box genes. The pink lines inside the circle represent syntenic A. sativa MADS-box gene pairs.
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Figure 6. Synteny analysis of MADS-box genes between the common oat and four other species: Arabidopsis thaliana, Oryza sativa, Brachypodium distachyon and Triticum aestivum. The grey lines represent collinear blocks in the genomes of the common oat and three other species. The red lines indicate syntenic MADS-box gene pairs.
Figure 6. Synteny analysis of MADS-box genes between the common oat and four other species: Arabidopsis thaliana, Oryza sativa, Brachypodium distachyon and Triticum aestivum. The grey lines represent collinear blocks in the genomes of the common oat and three other species. The red lines indicate syntenic MADS-box gene pairs.
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Figure 7. The relationship between 13 members of the AsMADS-box gene from the AGL17 subclade and miRNAs.
Figure 7. The relationship between 13 members of the AsMADS-box gene from the AGL17 subclade and miRNAs.
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Figure 8. Relative expression profiles of 6 selected Type II AsMADS-box genes after ABA (A), GA (B), salt (C) and drought (D) treatments according to qRT-PCR. Error bars represent the standard error of the mean. Significant differences between the control and treatment groups are indicated with * p ≤ 0.05 and ** p ≤ 0.01.
Figure 8. Relative expression profiles of 6 selected Type II AsMADS-box genes after ABA (A), GA (B), salt (C) and drought (D) treatments according to qRT-PCR. Error bars represent the standard error of the mean. Significant differences between the control and treatment groups are indicated with * p ≤ 0.05 and ** p ≤ 0.01.
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Figure 9. Heatmap showing significant differential expression of AsMADS-box genes in the common oat cultivars under long-day and short-day photoperiod conditions. The colour scale indicates log2(fold-change) values. The red and blue blocks illustrate the increased and decreased expression levels of AsMADS-box genes under the long-day and short-day photoperiod conditions, respectively. Nonsignificant differences are indicated as NA, and is coloured in dark grey.
Figure 9. Heatmap showing significant differential expression of AsMADS-box genes in the common oat cultivars under long-day and short-day photoperiod conditions. The colour scale indicates log2(fold-change) values. The red and blue blocks illustrate the increased and decreased expression levels of AsMADS-box genes under the long-day and short-day photoperiod conditions, respectively. Nonsignificant differences are indicated as NA, and is coloured in dark grey.
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Figure 10. chr4D_AsMADS95 promotes flowering in Arabidopsis thaliana. (A) Early flowering phenotypes of AsMADS095 transgenic lines under LD conditions. Scale bar = 5 cm; (B) Days to bolting and (C) the number of rosette leaves of chr4D_AsMADS95 transgenic lines and WT plants under LD conditions; (D) Early flowering phenotypes of chr4D_AsMADS95 transgenic lines under SD conditions. Scale bar = 5 cm; (E) Days to bolting and (F) the number of rosette leaves of chr4D_AsMADS95 transgenic lines and WT plants under SD conditions. The letters above the bars represent significant differences between the wild-type and chr4D_AsMADS95 transgenic lines, as determined by a two-tailed Student’s t test. (G,H) Relative expression levels of flowering-related genes in chr4D_AsMADS95 transgenic and WT plants under LD (G) and SD (H) conditions. The letters above the bars represent significant differences between the wild-type and chr4D_AsMADS95 transgenic lines, as determined by a two-tailed Student’s t test. The mRNA levels of these flowering-related genes were normalized to those of PP2a as an internal control.
Figure 10. chr4D_AsMADS95 promotes flowering in Arabidopsis thaliana. (A) Early flowering phenotypes of AsMADS095 transgenic lines under LD conditions. Scale bar = 5 cm; (B) Days to bolting and (C) the number of rosette leaves of chr4D_AsMADS95 transgenic lines and WT plants under LD conditions; (D) Early flowering phenotypes of chr4D_AsMADS95 transgenic lines under SD conditions. Scale bar = 5 cm; (E) Days to bolting and (F) the number of rosette leaves of chr4D_AsMADS95 transgenic lines and WT plants under SD conditions. The letters above the bars represent significant differences between the wild-type and chr4D_AsMADS95 transgenic lines, as determined by a two-tailed Student’s t test. (G,H) Relative expression levels of flowering-related genes in chr4D_AsMADS95 transgenic and WT plants under LD (G) and SD (H) conditions. The letters above the bars represent significant differences between the wild-type and chr4D_AsMADS95 transgenic lines, as determined by a two-tailed Student’s t test. The mRNA levels of these flowering-related genes were normalized to those of PP2a as an internal control.
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Zhang, M.; Wang, C.-L.; Jiang, Y.; Feng, B.; Dong, H.-X.; Chen, H.; Li, X.-Y.; Shan, X.-H.; Tian, J.; Xu, W.-W.; et al. Genome-Wide Identification of MADS-box Family Genes and Analysis of Their Expression Patterns in the Common Oat (Avena sativa L.). Agronomy 2025, 15, 2286. https://doi.org/10.3390/agronomy15102286

AMA Style

Zhang M, Wang C-L, Jiang Y, Feng B, Dong H-X, Chen H, Li X-Y, Shan X-H, Tian J, Xu W-W, et al. Genome-Wide Identification of MADS-box Family Genes and Analysis of Their Expression Patterns in the Common Oat (Avena sativa L.). Agronomy. 2025; 15(10):2286. https://doi.org/10.3390/agronomy15102286

Chicago/Turabian Style

Zhang, Man, Chun-Long Wang, Yuan Jiang, Bo Feng, Hai-Xiao Dong, Hao Chen, Xue-Ying Li, Xiao-Hui Shan, Juan Tian, Wei-Wei Xu, and et al. 2025. "Genome-Wide Identification of MADS-box Family Genes and Analysis of Their Expression Patterns in the Common Oat (Avena sativa L.)" Agronomy 15, no. 10: 2286. https://doi.org/10.3390/agronomy15102286

APA Style

Zhang, M., Wang, C.-L., Jiang, Y., Feng, B., Dong, H.-X., Chen, H., Li, X.-Y., Shan, X.-H., Tian, J., Xu, W.-W., Yuan, Y.-P., Ren, C.-Z., & Guo, L.-C. (2025). Genome-Wide Identification of MADS-box Family Genes and Analysis of Their Expression Patterns in the Common Oat (Avena sativa L.). Agronomy, 15(10), 2286. https://doi.org/10.3390/agronomy15102286

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