Genome-wide study of flowering-related MADS-box genes family in Cardamine hirsuta

BACKGROUND: Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE: To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS: The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS: The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC *: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS: This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.

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Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid

BMC Plant Biology ◽

10.1186/s12870-019-1836-5 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 4

Author(s):

Chunmei He ◽

Can Si ◽

Jaime A. Teixeira da Silva ◽

Mingzhi Li ◽

Jun Duan

Keyword(s):

Seed Germination ◽

Mads Box ◽

Mads Box Genes ◽

Genome Wide

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Genome-Wide Diversity of MADS-Box Genes in Bread Wheat is Associated with its Rapid Global Adaptability

Frontiers in Genetics ◽

10.3389/fgene.2021.818880 ◽

2022 ◽

Vol 12 ◽

Author(s):

Qasim Raza ◽

Awais Riaz ◽

Rana Muhammad Atif ◽

Babar Hussain ◽

Iqrar Ahmad Rana ◽

...

Keyword(s):

Gene Family ◽

Bread Wheat ◽

Phylogenetic Analyses ◽

Rapid Evolution ◽

Wheat Genome ◽

Fine Tuning ◽

Yield Potential ◽

Mads Box ◽

Mads Box Genes ◽

Genome Wide

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. Here, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more rapid evolution was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that could accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.

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Genome-Wide Analysis of MIKCC-Type MADS Box Genes in Grapevine

PLANT PHYSIOLOGY ◽

10.1104/pp.108.131052 ◽

2008 ◽

Vol 149 (1) ◽

pp. 354-369 ◽

Cited By ~ 131

Author(s):

José Díaz-Riquelme ◽

Diego Lijavetzky ◽

José M. Martínez-Zapater ◽

María José Carmona

Keyword(s):

Mads Box ◽

Mads Box Genes ◽

Genome Wide Analysis ◽

Genome Wide

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A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]

BMC Plant Biology ◽

10.1186/s12870-015-0436-2 ◽

2015 ◽

Vol 15 (1) ◽

pp. 41 ◽

Cited By ~ 44

Author(s):

Christina E Wells ◽

Elisa Vendramin ◽

Sergio Jimenez Tarodo ◽

Ignazio Verde ◽

Douglas G Bielenberg

Keyword(s):

Prunus Persica ◽

Mads Box ◽

Mads Box Genes ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

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Identification and characterization of MADS-box gene family in pigeonpea, their wild relatives and comparative phylogenetic analysis with grain legumes.

10.31220/osf.io/wsh8q ◽

2020 ◽

Author(s):

Kuldeep Kumar ◽

Harsha Srivastava ◽

Antara Das ◽

Kishor U. Tribhuvan ◽

Kumar Durgesh ◽

...

Keyword(s):

Single Copy ◽

Grain Legumes ◽

Wild Relatives ◽

Mads Box ◽

Mads Box Genes ◽

Genome Wide ◽

The Status ◽

Mads Box Gene ◽

Comparative Phylogenetic Analysis

Abstract MADS-box genes are classes of transcription factors involved in various physiological and developmental processes in plants. Here, genome wide identification of MADS-box genes was done in Cajanus cajan, identifying 102 members, classified into two different groups based on their gene structure. The gene based phylogeny of C. cajan MADS-box genes, and some grain legumes was developed to detect their gene homologs in C. cajan. The status of all these genes was analyzed in three wild relatives i.e. C. scarabaeoides, C. platycarpus and C. cajanifolius. A total of 41 MADS-box genes were found to be missing in wild type cultivars hinting towards their role in domestication and evolution. Single copy of Flowering locus C (FLC) and Short vegetative phase (SVP), while three copies of Suppressor of activation of Constans 1 (SOC1) was found to be present. One SOC1 gene i.e. CcMADS1.5 was found to be missing in all wild relatives, also forming separate clade in phylogeny, revealing its origin through duplication followed by divergence, and role in domestication. Expression profiling of major MADS-box genes involved in flowering was done in different tissues viz vegetative meristem vegetative leaf, reproductive meristem and reproductive bud. Gene based time tree of FLC and SOC1 gene dictates their divergence from Arabidopsis before 71 and 23 million year ago (mya) respectively. This study provides valuable insights into the functions, characteristics and evolution of MADS-box proteins in grain legumes with emphasis on C. cajan, which may help in further characterizing these genes.

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Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis

PeerJ ◽

10.7717/peerj.8019 ◽

2019 ◽

Vol 7 ◽

pp. e8019 ◽

Cited By ~ 1

Author(s):

Yanshu Qu ◽

Changwei Bi ◽

Bing He ◽

Ning Ye ◽

Tongming Yin ◽

...

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Evolutionary Analysis ◽

Mads Box ◽

Mads Box Genes ◽

Floral Organogenesis ◽

Functional Studies ◽

Genome Wide ◽

Development Processes ◽

Mads Box Gene

MADS-box genes encode transcription factors that participate in various plant growth and development processes, particularly floral organogenesis. To date, MADS-box genes have been reported in many species, the completion of the sequence of the willow genome provides us with the opportunity to conduct a comprehensive analysis of the willow MADS-box gene family. Here, we identified 60 willow MADS-box genes using bioinformatics-based methods and classified them into 22 M-type (11 Mα, seven Mβ and four Mγ) and 38 MIKC-type (32 MIKCc and six MIKC*) genes based on a phylogenetic analysis. Fifty-six of the 60 SsMADS genes were randomly distributed on 19 putative willow chromosomes. By combining gene structure analysis with evolutionary analysis, we found that the MIKC-type genes were more conserved and played a more important role in willow growth. Further study showed that the MIKC* type was a transition between the M-type and MIKC-type. Additionally, the number of MADS-box genes in gymnosperms was notably lower than that in angiosperms. Finally, the expression profiles of these willow MADS-box genes were analysed in five different tissues (root, stem, leave, bud and bark) and validated by RT-qPCR experiments. This study is the first genome-wide analysis of the willow MADS-box gene family, and the results establish a basis for further functional studies of willow MADS-box genes and serve as a reference for related studies of other woody plants.

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Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (Callicarpa americana)

Plants ◽

10.3390/plants10091805 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1805

Author(s):

Tareq Alhindi ◽

Ayed M. Al-Abdallat

Keyword(s):

Gene Family ◽

Type I ◽

Distribution Analysis ◽

Type Ii ◽

Mads Box ◽

Mads Box Genes ◽

Floral Organogenesis ◽

Genome Wide ◽

Organ Identity ◽

Mads Box Gene

The MADS-box gene family encodes a number of transcription factors that play key roles in various plant growth and development processes from response to environmental cues to cell differentiation and organ identity, especially the floral organogenesis, as in the prominent ABCDE model of flower development. Recently, the genome of American beautyberry (Callicarpa americana) has been sequenced. It is a shrub native to the southern region of United States with edible purple-colored berries; it is a member of the Lamiaceae family, a family of medical and agricultural importance. Seventy-eight MADS-box genes were identified from 17 chromosomes of the C. americana assembled genome. Peptide sequences blast and analysis of phylogenetic relationships with MADS-box genes of Sesame indicum, Solanum lycopersicum, Arabidopsis thaliana, and Amborella trichopoda were performed. Genes were separated into 32 type I and 46 type II MADS-box genes. C. americana MADS-box genes were clustered into four groups: MIKCC, MIKC*, Mα-type, and Mγ-type, while the Mβ-type group was absent. Analysis of the gene structure revealed that from 1 to 15 exons exist in C. americana MADS-box genes. The number of exons in type II MADS-box genes (5–15) greatly exceeded the number in type I genes (1–9). The motif distribution analysis of the two types of MADS-box genes showed that type II MADS-box genes contained more motifs than type I genes. These results suggested that C. americana MADS-box genes type II had more complex structures and might have more diverse functions. The role of MIKC-type MADS-box genes in flower and fruit development was highlighted when the expression profile was analyzed in different organs transcriptomes. This study is the first genome-wide analysis of the C. americana MADS-box gene family, and the results will further support any functional and evolutionary studies of C. americana MADS-box genes and serve as a reference for related studies of other plants in the medically important Lamiaceae family.

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Genome-wide analysis of the MADS-box gene family in cucumber

Genome ◽

10.1139/g2012-009 ◽

2012 ◽

Vol 55 (3) ◽

pp. 245-256 ◽

Cited By ~ 62

Author(s):

Lifang Hu ◽

Shiqiang Liu

Keyword(s):

Gene Family ◽

Tandem Duplication ◽

Tissue Expression ◽

Mads Box ◽

Mads Box Genes ◽

Motif Analysis ◽

Genome Wide Analysis ◽

Genome Wide ◽

Cucumber Genome ◽

Mads Box Gene

MADS-box transcription factors are known to be involved in many important processes during plant growth and development. To date, few cucumber MADS-box genes and little tissue expression profiling have been reported. Recent completion of the cucumber whole-genome sequencing has allowed genome-wide analysis of the MADS-box gene family in cucumber as well as its comparison with other species. Here, we performed comprehensive analyses of the 43 cucumber MADS-box genes and compared them with those in Arabidopsis, poplar, and grapevine. The phylogenetic analysis showed that most cucumber members were comparable with those in other species, with the exception of AG members. At the same time, the three subfamilies FLC, AGL12, and Bs were absent in the cucumber genome. The conserved motif analysis revealed that most motifs outside the MADS domain were distributed only in specific groups. The analysis of chromosomal localization suggested that tandem duplication might contribute to the MADS-box gene expansion. Expression analysis revealed that 42 of 43 cucumber MADS-box members were expressed in multiple plant tissues, thereby implying their various roles in plants.

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