Genome-Wide Analysis and the Expression Pattern of the MADS-Box Gene Family in

Overview

Journal Plants (Basel)

Date 2021 Oct 23

PMID 34685993

Citations 7

Authors

Ze-Yuan Mi

Qian Zhao

Chan Lu

Qian Zhang

Lin Li

Shuai Liu

Shi-Qiang Wang

Zhe-Zhi Wang

Jun-Feng Niu

Affiliations

Soon will be listed here.

Abstract

(Thunb. ex A. Murray) Rchb. f., a species of the perennial herb Orchidaceae, has potent anti-inflammatory and antiviral biological activities. MADS-box transcription factors play critical roles in the various developmental processes of plants. Although this gene family has been extensively investigated in many species, it has not been analyzed for . In total, 45 MADS-box genes were identified from in this study, which were classified into five subfamilies (Mδ, MIKC, Mα, Mβ, and Mγ). Meanwhile, the highly correlated protein domains, motif compositions, and exon-intron structures of were investigated according to local databases. Chromosome distribution and synteny analyses revealed that segmental duplication and homologous exchange were the main expansion mechanisms. Further, RT-qPCR analysis revealed that had different expression patterns in response to various stress treatments. Our results provide a potential theoretical basis for further investigation of the functions of MADS genes during the growth of .

Citing Articles

Insights into genetics of floral development in Amborella trichopoda Baill. through genome-wide survey and expression analysis of MADS-Box transcription factors.

Parajuli S, Adhikari B, Nepal M Sci Rep. 2025; 15(1):5297.

PMID: 39939686 PMC: 11822109. DOI: 10.1038/s41598-025-88880-x.

Genome-wide identification of a MADS-box transcription factor family and their expression during floral development in Coptis teeta wall.

Duan S, Yu J, Baldwin T, Yuan Y, Xiang G, Cui R BMC Plant Biol. 2024; 24(1):1023.

PMID: 39468440 PMC: 11520390. DOI: 10.1186/s12870-024-05714-0.

Genome-wide identification and expression analysis of the gene family in sweet orange () infested with pathogenic bacteria.

Yang X, Zhang M, Xi D, Yin T, Zhu L, Yang X PeerJ. 2024; 12:e17001.

PMID: 38436028 PMC: 10909352. DOI: 10.7717/peerj.17001.

Genome-wide identification and expression analysis of the C2H2-zinc finger transcription factor gene family and screening of candidate genes involved in floral development in Wall. (Ranunculaceae).

Duan S, Zhao Y, Yu J, Xiang G, Xiao L, Cui R Front Genet. 2024; 15:1349673.

PMID: 38317660 PMC: 10839097. DOI: 10.3389/fgene.2024.1349673.

Genome-wide analysis of the MADS-box gene family in Lonicera japonica and a proposed floral organ identity model.

Lin Y, Qi X, Wan Y, Chen Z, Fang H, Liang C BMC Genomics. 2023; 24(1):447.

PMID: 37553575 PMC: 10408238. DOI: 10.1186/s12864-023-09509-9.

References

Brown L, Yang S, Hair A, Galanis A, Sharrocks A . Molecular characterization of a zebrafish TCF ETS-domain transcription factor. Oncogene. 2000; 18(56):7985-93. DOI: 10.1038/sj.onc.1203197. View

Wu Y, Ke Y, Wen J, Guo P, Ran F, Wang M . Evolution and expression analyses of the MADS-box gene family in Brassica napus. PLoS One. 2018; 13(7):e0200762. PMC: 6053192. DOI: 10.1371/journal.pone.0200762. View

Yang Y, Jack T . Defining subdomains of the K domain important for protein-protein interactions of plant MADS proteins. Plant Mol Biol. 2004; 55(1):45-59. DOI: 10.1007/s11103-004-0416-7. View

Pelaz S, Ditta G, Baumann E, Wisman E, Yanofsky M . B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature. 2000; 405(6783):200-3. DOI: 10.1038/35012103. View

Bailey T, Williams N, Misleh C, Li W . MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006; 34(Web Server issue):W369-73. PMC: 1538909. DOI: 10.1093/nar/gkl198. View

Tian Y, Dong Q, Ji Z, Chi F, Cong P, Zhou Z . Genome-wide identification and analysis of the MADS-box gene family in apple. Gene. 2014; 555(2):277-90. DOI: 10.1016/j.gene.2014.11.018. View

Damveld R, Arentshorst M, Franken A, vanKuyk P, Klis F, Van Den Hondel C . The Aspergillus niger MADS-box transcription factor RlmA is required for cell wall reinforcement in response to cell wall stress. Mol Microbiol. 2005; 58(1):305-19. DOI: 10.1111/j.1365-2958.2005.04827.x. View

Sun C, Yu J, Wen L, Guo Y, Sun X, Hao Y . Chrysanthemum MADS-box transcription factor CmANR1 modulates lateral root development via homo-/heterodimerization to influence auxin accumulation in Arabidopsis. Plant Sci. 2017; 266:27-36. DOI: 10.1016/j.plantsci.2017.09.017. View

Parenicova L, de Folter S, Kieffer M, Horner D, Favalli C, Busscher J . Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell. 2003; 15(7):1538-51. PMC: 165399. DOI: 10.1105/tpc.011544. View

10.

Tang Y, Wang J, Bao X, Wu Q, Yang T, Li H . Genome-wide analysis of Jatropha curcas MADS-box gene family and functional characterization of the JcMADS40 gene in transgenic rice. BMC Genomics. 2020; 21(1):325. PMC: 7187513. DOI: 10.1186/s12864-020-6741-7. View

11.

de Bodt S, Raes J, Van de Peer Y, Theissen G . And then there were many: MADS goes genomic. Trends Plant Sci. 2003; 8(10):475-83. DOI: 10.1016/j.tplants.2003.09.006. View

12.

Heuer S, Hansen S, Bantin J, Brettschneider R, Kranz E, Lorz H . The maize MADS box gene ZmMADS3 affects node number and spikelet development and is co-expressed with ZmMADS1 during flower development, in egg cells, and early embryogenesis. Plant Physiol. 2001; 127(1):33-45. PMC: 117960. DOI: 10.1104/pp.127.1.33. View

13.

Wei B, Zhang R, Guo J, Liu D, Li A, Fan R . Genome-wide analysis of the MADS-box gene family in Brachypodium distachyon. PLoS One. 2014; 9(1):e84781. PMC: 3890268. DOI: 10.1371/journal.pone.0084781. View

14.

Ng M, Yanofsky M . Function and evolution of the plant MADS-box gene family. Nat Rev Genet. 2001; 2(3):186-95. DOI: 10.1038/35056041. View

15.

Sommer H, Beltran J, Huijser P, Pape H, Lonnig W, Saedler H . Deficiens, a homeotic gene involved in the control of flower morphogenesis in Antirrhinum majus: the protein shows homology to transcription factors. EMBO J. 1990; 9(3):605-13. PMC: 551713. DOI: 10.1002/j.1460-2075.1990.tb08152.x. View

16.

Kobayashi K, Maekawa M, Miyao A, Hirochika H, Kyozuka J . PANICLE PHYTOMER2 (PAP2), encoding a SEPALLATA subfamily MADS-box protein, positively controls spikelet meristem identity in rice. Plant Cell Physiol. 2009; 51(1):47-57. PMC: 2807174. DOI: 10.1093/pcp/pcp166. View

17.

Xu D, Pan Y, Chen J . Chemical Constituents, Pharmacologic Properties, and Clinical Applications of . Front Pharmacol. 2019; 10:1168. PMC: 6838137. DOI: 10.3389/fphar.2019.01168. View

18.

Hu B, Jin J, Guo A, Zhang H, Luo J, Gao G . GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2014; 31(8):1296-7. PMC: 4393523. DOI: 10.1093/bioinformatics/btu817. View

19.

Hurst L . The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 2002; 18(9):486. DOI: 10.1016/s0168-9525(02)02722-1. View

20.

Duan W, Song X, Liu T, Huang Z, Ren J, Hou X . Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage). Mol Genet Genomics. 2014; 290(1):239-55. DOI: 10.1007/s00438-014-0912-7. View