Genome-Wide Characterization of the MADS-Box Gene Family in Radish (Raphanus sativus L.) and Assessment of Its Roles in Flowering and Floral Organogenesis

Li, Chao; Wang, Yan; Xu, Liang; Nie, Shaoping; Chen, Yinglong; Liang, Dongyi; Sun, Xiaochuan; Karanja, Benard; Luo, Xiaobo; Liu, Liwang

doi:10.3389/fpls.2016.01390

Cited by 48 publications

(54 citation statements)

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“…Class E genes (PeMADS8/10/11/12/13) were expressed in all the floral organs ( Fig. 8B-E) which is in accordance with earlier reports on class E genes [RsMADS017/023 in R. sativus (Li et al 2016), BdMADS11/26 in B. distachyon, EpMADS6 in E. pusilla (Lin et al 2016) and OMADS6/11 in Oncidium Gower Ramsey (Chang et al 2009)]. These results suggest that class E genes are required for the functioning of all floral whorls.…”

Section: Discussionsupporting

confidence: 92%

“…The expression of PeMADS2/5/6 (class B) genes in petals was in conformity with class B genes of E. pusilla (EpMADS14/15/16) (Lin et al 2016) and B. distachyon (BdMADS5) (Wei et al 2014). All genes of class E of P. equestris were found to be upregulated in petals which is in concordance with expression of DcSEP1 in Dendrobium crumenatum (Xu et al 2006), PhaMADS7 in Phalaenopsis 'Athens' (Acri-Nunes-Miranda and Mondragón-Palomino 2014) and RsMADS033 in R. sativus (Li et al 2016). Furthermore, the remaining two class B genes, PeMADS3 and PeMADS4 expressed in labellum, as also reported for genes in E. pusilla (EpMADS13/14/16) (Lin et al 2016) and Oncidium Gower Ramsey (OMADS8) (Chang et al 2010).…”

Section: Discussionsupporting

confidence: 66%

“…PeMADS22 (class A) gene had high expression in petals (Fig. 8B), similar to expression of DOMADS1 in Dendrobium (Yu and Goh 2000) and RsMADS68 in R. sativus (Li et al 2016). All the genes of class B exhibited high expression in flower, similar to their expression in C. sativus (CsMADS21/22/23) (Hu and Liu 2012).…”

Section: Discussionsupporting

confidence: 57%

“…The C class genes are also reported to have a role in fruit formation of P. persica (PpeMADS11/24/45) (Wells et al 2015). Class D genes (PeMADS38, PeMADS7) were expressed in gynostemium, thus resembling the expression pattern of other class D genes of RsMADS047 in R. sativus (Li et al 2016), BdMAD2 in B. distachyon (Wei et al 2014) and EpMADS23 in E. pusilla (Lin et al 2016). The E class genes (PeMADS12 and PeMADS10) have comparable expression pattern with VvMADS5 of V. vinifera (Boss et al 2002).…”

Section: Discussionmentioning

confidence: 87%

“…The androecium (whorl 3) and gynoecium (whorl 4) in orchids are fused to form gynostemium. Theoretically, whorl 3 is controlled by Class B, C, and E. PeMADS4 (class B) gene and PeMADS24/25 (class C) genes had high expression in gynostemium and was comparable with class B genes PpeMADS56 of P. persica (Wells et al 2015) and RsMADS078 of R. sativus (Li et al 2016) in stamens, and with class C genes CeMADS1 of Cymbidium ensifoliumin gynostemium (Wang et al 2011), RsMADS036 in R. sativus stamens (Li et al 2016) and OMADS4 in Oncidium Gower Ramsey column (Hsu et al 2010). Chen et al (2012) reported that, PeMADS1 ectopic expression mutants turned petals to gynostemium-like structures.…”

Section: Discussionmentioning

confidence: 97%

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Tracing the footprints of the ABCDE model of flowering inPhalaenopsis equestris(Schauer) Rchb.f. (Orchidaceae)

et al. 2019

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Orchids are indispensable to the floriculture industry due to their unique floral organization. The flowers have two outer whorls of tepals including a lip (labellum), and two inner whorls, pollinia and gynostemiun (column). The floral organization and development is controlled at the molecular level, mainly by the MADS-box gene family, comprising homeotic genes divided into type I and type II groups. The type I group has four subgroups , Mα, Mβ, Mγ, and Mδ, playing roles in seed, embryo, and female reproductive organ development; the type II group genes form classes A, B, C, D, and E, which are a part of the MIKC C subgroup with specific roles in florigenesis and organization. The coordinated functioning of these classes regulates the development of various floral whorls. The availability of genome and transcriptome sequence data for Phalaenopsis equestris offers an opportunity to validate the ABCDE model of flower development. Hence, this study sought to characterize the MADS-box gene family and elucidate of the ABCDE model. A total of 48 identified MADS-box proteins, including 20 type I [Mα (12), Mγ (8)] and 28 type II [MIKC C (27), MIKC* (1)] members, were characterized for physico-chemical features and domains and motifs organization. The exon-intron distribution and the upstream cis-regulatory elements in the promoter regions of MADS-box genes were also analysed. The discrete pace of duplication events in type I and type II genes suggested differential evolutionary constraints between groups. The correlation of spatio-temporal expression pattern with the presence of specific cis-regulatory elements and putative proteinprotein interaction within the different classes of MADS-box gene family endorse the ABCDE model of floral development.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 66%

Section: Discussionsupporting

confidence: 57%

Section: Discussionmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 97%

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Tracing the footprints of the ABCDE model of flowering inPhalaenopsis equestris(Schauer) Rchb.f. (Orchidaceae)

et al. 2019

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Genome-wide identification, evolution, and expression characterization of the pepper MADS-box gene family

Gan

Feng

et al. 2022

Preprint

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MADS domain transcription factors play roles throughout the whole lifecycle of plants from seeding to flowering and fruitbearing. However, systematic research into MADS-box genes of the economically important vegetable crop pepper (Capsicum spp.) is still lacking. We identified 174, 207, and 72 MADS-box genes from the genomes of C. annuum, C. baccatum and C. chinense, respectively. These 453 MADS-box genes were divided into type I (Mα, Mβ, Mγ) and type II (MIKC* and MIKCC) based on their phylogenetic relationships. Collinearity analysis identified 144 paralogous genes and 195 orthologous genes in the three pepper species, and 70, 114, and 10 MADS-box genes specific to C. annuum, C. baccatum and C. chinense, respectively. Comparative genomic analysis highlighted functional differentiation among homologous MADS-box genes during pepper evolution. Tissue expression analysis revealed three main expression patterns: highly expressed in roots, stems, leaves and flowers (CaMADS93/CbMADS35/CcMADS58); only expressed in roots; and specifically expressed in flowers (Ca-MADS26/CbMADS31/CcMADS11). This study provides the basis for an in-depth study of the evolutionary features and biological functions of pepper MADS-box genes. Hosted fileessoar.10512212.1.docx available at https://authorea.com/users/542768/articles/601054genome-wide-identification-evolution-and-expression-characterization-of-the-pepper-madsbox-gene-family Core Ideas:• Genome-wide identification identified 454 MADS-box genes from Capsicum spp. Genomes.• Genome-wide identification revealed the evolutionary relationship of MADSbox gene family in Capsicum spp.• Most of the Capsicum MADS-box genes have been amplified on a large scale.• Most of the Capsicum MADS-box genes have undergone purification selection during evolution.• Tissue specific expression patterns of most MADS-box genes indicated their functional diversity. Genome-wide identification, evolution, and expression characterization of the pepper MADS-box gene familyZhicheng Gan,

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CaVIL1, a plant homeodomain gene that promotes flowering in pepper

et al. 2018

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CaVIL1 is a homolog of VIL1, a regulator of vernalization response in Arabidopsis and acts as a flowering promoter in pepper which does not respond to vernalization and photoperiod. As part of our goal to study the genetic and molecular basis of transition to flowering in pepper, we isolated the late-flowering mutant E-2698. Aside from late flowering, multiple pleiotropic alterations of the shoot structure, such as enlarged and distorted leaves, weak apical dominance, and reduced angle of the lateral branches were observed, indicating a broad role for the mutated gene in pepper development. Genetic mapping and sequence analyses revealed that the disrupted gene in E-2698 is the pepper homolog of VERNALIZATION INSENSITIVE 3-LIKE 1 (VIL1) that acts as a regulator of vernalization in Arabidopsis through chromatin modification. The pepper gene, CaVIL1, contains a plant homeodomain motif associated with chromatin modification and a VERNALIZATION INSENSITIVE 3-interacting domain that is truncated in E-2698 and in two other allelic mutants. Because pepper flowering does not respond to vernalization, we postulate that CaVIL1 regulates flowering time via chromatin modification of unknown targets. Expression analysis indicated that CaVIL1 activates the flowering promoter CaFLOWERING LOCUS T and represses the flowering repressor CaAPETALA2. Furthermore, CaVIL1 represses several genes from the FLOWERING LOCUS C (FLC)-LIKE clade that are clustered together in the pepper genome. This indicates their possible involvement in flowering regulation in this species. Our results show that CaVIL1 is a major regulator of flowering and interacts with other flowering promoters and repressors, as well as with FLC-LIKE genes whose function in flowering regulation is not yet known in pepper.

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Genome-Wide Characterization of the MADS-Box Gene Family in Radish (Raphanus sativus L.) and Assessment of Its Roles in Flowering and Floral Organogenesis

Cited by 48 publications

References 84 publications

Tracing the footprints of the ABCDE model of flowering inPhalaenopsis equestris(Schauer) Rchb.f. (Orchidaceae)

Tracing the footprints of the ABCDE model of flowering inPhalaenopsis equestris(Schauer) Rchb.f. (Orchidaceae)

Genome-wide identification, evolution, and expression characterization of the pepper MADS-box gene family

CaVIL1, a plant homeodomain gene that promotes flowering in pepper

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