Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships

Da, Zhao; Chen, Zheng; Xu, Lei; Zhang, Lijun; Zou, Quan

doi:10.3390/genes12121956

Cited by 21 publications

(24 citation statements)

References 74 publications

(88 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…MADS-box gene family are ubiquitous in plants and have been identified in more than 40 species, such as Arabidopsis (109 genes) ( Kofuji et al, 2003 ), rice (75 genes) ( Arora et al, 2007 ), cucumber (43 genes) ( Hu and Liu, 2012 ), soybean (163 genes) ( Fan et al, 2013 ), peach (79 genes) ( Wells et al, 2015 ), chinese cabbage (167 genes) ( Saha et al, 2015 ), banana (96 genes) ( Liu et al, 2017 ), pineapple (48 genes) ( Zhang et al, 2020 ), maize (75 genes) ( Zhao D. et al, 2021 ), musa balbisiana (97 genes) ( Lakhwani et al, 2022 ). In this study, 89 MADS-box genes were identified in kiwifruit, which is the same as foxtail millet (89 genes) ( Lai et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Genome-wide analysis of MADS-box gene family in kiwifruit (Actinidia chinensis var. chinensis) and their potential role in floral sex differentiation

Luo²,

Wang³

et al. 2022

Front. Genet.

View full text Add to dashboard Cite

Kiwifruit (Actinidia chinensis Planch.) is a functionally dioecious plant, which displays diverse morphology in male and female flowers. MADS-box is an ancient and huge gene family that plays a key role in plant floral organ differentiation. In this study, we have identified 89 MADS-box genes from A. chinensis Red 5 genome. These genes are distributed on 26 chromosomes and are classified into type I (21 genes) and type II (68 genes). Overall, type II AcMADS-box genes have more complex structures than type I with more exons, protein domains, and motifs, indicating that type II genes may have more diverse functions. Gene duplication analysis showed that most collinearity occurred in type II AcMADS-box genes, which was consistent with a large number of type II genes. Analysis of cis-acting elements in promoters showed that AcMADS-box genes are mainly associated with light and phytohormone responsiveness. The expression profile of AcMADS-box genes in different tissues showed that most genes were highly expressed in flowers. Further, the qRT-PCR analysis of the floral organ ABCDE model-related genes in male and female flowers revealed that AcMADS4, AcMADS56, and AcMADS70 were significantly expressed in female flowers. It indicated that those genes may play an important role in the sex differentiation of kiwifruit. This work provided a comprehensive analysis of the AcMADS-box genes and may help facilitate our understanding of the sex differentiation regulatory mechanism in kiwifruit.

show abstract

Section: Discussionmentioning

confidence: 99%

“…Type II MADS-box genes are mainly derived from whole genome duplication ( Airoldi and Davies, 2012 ). In most species, the gene structure of type II MADS-box genes are more complex than type I, such as Arabidopsis ( Kofuji et al, 2003 ), rice ( Arora et al, 2007 ), maize ( Zhao D. et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of MADS-box gene family in kiwifruit (Actinidia chinensis var. chinensis) and their potential role in floral sex differentiation

Luo²,

Wang³

et al. 2022

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…These 72 SmiMADSes could be classi ed into two types according to their phylogenetic relationships with Arabidopsis and rice, as follows: type I (18, Supplementary Table S2) and type II (54). Type I was further categorised into Mα (12), Mβ (2) and Mγ (4). Type II was assigned to MIKC * (6) and MIKC c (48).…”

Section: Discussionmentioning

confidence: 99%

“…The deep study of MADS-box genes is due to their important function in the ower organ. At present, many MADSbox genes have been found in a variety of plants, such as Arabidopsis thaliana 11 , maize 12 , rice 13 , pineapple 14 , Theobroma cacao 15 and Chrysanthemum nankingense 16 . Nonetheless, the number and expression patterns of MADS-box gene family members in different plants are not exactly the same; investigations speci cally focused on S. miltiorrhiza are scarce, thereby hindering the exploration process of S. miltiorrhiza's ower development pattern.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and ABCE-class proposal of the MADS-box gene family in Salvia miltiorrhiza Bunge

Cui

Guo

Chen³

et al. 2022

Preprint

View full text Add to dashboard Cite

MADS-box transcription factors, as the heart of the classic ABCE model of floral development, play critical roles in several aspects of plant flowering. In recent years, to comprehensively utilise and improve the added value of Chinese herbal medicine, the non-medicinal part (flower) development of Salvia miltiorrhiza Bunge has been promoted, thereby focusing the attention of researchers on the flower organ of S. miltiorrhiza. However, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of S. miltiorrhiza genome sequencing. This work systematically characterised S. miltiorrhiza MADS-box genes (SmiMADSes) and predicted those likely involved in the floral development of this medicinal plant. Seventy-two MADS-box genes were identified in the S. miltiorrhiza genome and categorised into MIKC*, MIKCc, Mα, Mβ and Mγ groups based on phylogeny. Genomic localisation analysis revealed that these genes were evenly localised on 10 genome scaffolds. The expression profiles of all the SmiMADSes were analysed in four organs and four flower tissues, as well as in the three stages of floral development. Transcripts for 13 genes accumulated preferentially in flowers. SmiMADS44 was specifically expressed in stems. SmiMADS57 and SmiMADS31 showed specific expressions in roots and leaves, respectively. Based on transcriptome data and homology with functionally validated ABCE class genes in Arabidopsis, a prediction was made to gain insight into ABCE-class SmiMADSes that were strongly expressed in all flowering stages of S. miltiorrhiza, including the following: SmiMADS65 and SmiMADS67 of A-class; SmiMADS26, SmiMADS28 and SmiMADS29 of B-class; SmiMADS45, SmiMADS50 and SmiMADS51 of C-class; and SmiMADS70, SmiMADS71 and SmiMADS72 of E-class. The results of this study lay a foundation for the further exploration of molecular and regulatory mechanisms controlling floral organ development and provide a basis for the selection of candidate genes for functional validation studies.

show abstract

“…In addition, MIKC-type genes are also involved in root ( AGL14 and AGL21 ) ( Garay-Arroyo et al., 2013 ; Yu et al., 2014 ) and seed development ( SHP1/2 , FUL ) ( Ferrandiz et al., 2000 ; Liljegren et al., 2000 ). To date, the MADS-box TFs have been systematically investigated in dicotyledon plants, such as tomato ( Solanum lycopersicum L.) ( Wang et al., 2019 ), potato ( Solanum tuberosum L.) ( Shao et al., 2021 ), B. rapa ( Duan et al., 2015 ), B. oleracea ( Sheng et al., 2019 ), and B. napus ( Wu et al., 2018 ; Zhou et al., 2022 ), and monocotyledon plants, such as maize ( Zea mays L. ) ( Zhao et al., 2021a ), wheat ( Triticum aestivum L.) ( Ma et al., 2017 ; Schilling et al., 2020 ), Foxtail Millet ( Setaria italica ) ( Zhao et al., 2021b ), and rice ( Oryza sativa ) ( Arora et al., 2007 ). However, there have been no reports on the identification of MADS-box genes in three species of U’s triangle: B. nigra , B. juncea , and B. carinata .…”

Section: Introductionmentioning

confidence: 99%

Systematic analysis of MADS-box gene family in the U’s triangle species and targeted mutagenesis of BnaAG homologs to explore its role in floral organ identity in Brassica napus

et al. 2023

View full text Add to dashboard Cite

MADS-box transcription factors play an important role in regulating floral organ development and participate in environmental responses. To date, the MADS-box gene family has been widely identified in Brassica rapa (B. rapa), Brassica oleracea (B. oleracea), and Brassica napus (B. napus); however, there are no analogous reports in Brassica nigra (B. nigra), Brassica juncea (B. juncea), and Brassica carinata (B. carinata). In this study, a whole-genome survey of the MADS-box gene family was performed for the first time in the triangle of U species, and a total of 1430 MADS-box genes were identified. Based on the phylogenetic relationship and classification of MADS-box genes in Arabidopsis thaliana (A. thaliana), 1430 MADS-box genes were categorized as M-type subfamily (627 genes), further divided into Mα, Mβ, Mγ, and Mδ subclades, and MIKC-type subfamily (803 genes), further classified into 35 subclades. Gene structure and conserved protein motifs of MIKC-type MADS-box exhibit diversity and specificity among different subclades. Comparative analysis of gene duplication events and syngenic gene pairs among different species indicated that polyploidy is beneficial for MIKC-type gene expansion. Analysis of transcriptome data within diverse tissues and stresses in B. napus showed tissue-specific expression of MIKC-type genes and a broad response to various abiotic stresses, particularly dehydration stress. In addition, four representative floral organ mutants (wtl, feml, aglf-2, and aglf-1) in the T0 generation were generated by editing four AGAMOUS (BnaAG) homoeologs in B. napus that enriched the floral organ variant phenotype. In brief, this study provides useful information for investigating the function of MADS-box genes and contributes to revealing the regulatory mechanisms of floral organ development in the genetic improvement of new varieties.

show abstract

Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships

Cited by 21 publications

References 74 publications

Genome-wide analysis of MADS-box gene family in kiwifruit (Actinidia chinensis var. chinensis) and their potential role in floral sex differentiation

Genome-wide analysis of MADS-box gene family in kiwifruit (Actinidia chinensis var. chinensis) and their potential role in floral sex differentiation

Genome-wide identification and ABCE-class proposal of the MADS-box gene family in Salvia miltiorrhiza Bunge

Systematic analysis of MADS-box gene family in the U’s triangle species and targeted mutagenesis of BnaAG homologs to explore its role in floral organ identity in Brassica napus

Contact Info

Product

Resources

About