Identification and bioinformatics analysis of MADS-box family genes containing K-box domain in maize

Authors

  • Wang YINXIA College of Agronomy, Gansu Agricultural University, Lanzhou 730070; Gansu Provincial Key Laboratory of Aridland Crop, Lanzhou 730070; Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070 (CN)
  • Ji XIANGZHUO College of Agronomy, Gansu Agricultural University, Lanzhou 730070; Gansu Provincial Key Laboratory of Aridland Crop, Lanzhou 730070; Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070 (CN)
  • Zhuang ZELONG College of Agronomy, Gansu Agricultural University, Lanzhou 730070; Gansu Provincial Key Laboratory of Aridland Crop, Lanzhou 730070; Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070 (CN)
  • Zhang YUNFANG College of Agronomy, Gansu Agricultural University, Lanzhou 730070; Gansu Provincial Key Laboratory of Aridland Crop, Lanzhou 730070; Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070 (CN)
  • Peng YUNLING College of Agronomy, Gansu Agricultural University, Lanzhou 730070; Gansu Provincial Key Laboratory of Aridland Crop, Lanzhou 730070; Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070 (CN)

DOI:

https://doi.org/10.15835/nbha51413253

Keywords:

bioinformatics analysis, gene expression analysis, K-box domain, MADS-box gene family, maize

Abstract

The MADS-box family genes are involved in the development of plant roots, leaves, flowers, and fruits, and play a crucial role in plant growth and development. Studying MADS-box genes with K-box domain is crucial to distinguish different types of MADS-box genes. This study systematically analysed the genomic structural information of maize MADS-box family members containing the K-box Domain at the genome-wide level using the maize (Zea mays) B73 genome as the reference sequence, and provided insight into the biological functions of the maize MADS-box family containing the K-box domain. According to the findings, 52 MADS-box family genes with K-box domain were identified and divided into 4 subgroups. The distribution of motif in the same subgroup was found to be relatively conservative, and all of them had MADS-box conserved domain and K-box domain. Gene structure analysis showed that the introns and exons of the same subgroup genes have similar gene structure, and different types of genes containing the K-box domain showed different exon/intron structure characteristics. Chromosome mapping showed that 52 genes containing the K-box domain were unevenly distributed on the 10 chromosomes of maize, most of which were distributed at both ends of the chromosome and a small number of genes were distributed near the centromere. Based on the analysis of cis-acting elements of it up-stream promoter, it was found that MADS-box family genes may be involved in light response, IAA, GA, ABA, and LTR signal pathways, indicating that they play a certain role in stress response and hormone signal transduction. The expression analysis of genes with the K-box domain in maize leaves treated with auxin and gibberellin revealed that MADS-box genes may have a regulatory effect on certain plant hormones. Through the identification and bioinformatics analysis of MADS-box family genes containing the K-box domain, it is helpful to further study the function and pathway of MADS-box family genes, and provide a theoretical basis for further re-search for the molecular mechanism of maize growth and development.

References

Arora R, Agarwal P, Ray S, Singh A, Singh V, … Kapoor S (2007). MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8(1):242-252. https://doi.org/10.1186/1471-2164-8-242

Boden S A, Østergaard L (2019). How can developmental biology help feed a growing population. Development 146(3):dev172965. https://doi.org/10.1242/dev.172965

Brumos J, Robles LM, Yun J, Vu T C, Jackson S, Alonso JM, … Stepanova AN (2018). Local auxin biosynthesis is a key regulator of plant development. Developmental Cell 47(3):306-318. https://doi.org/10.1016/j.devcel.2018.09.022

Cheng H, Qin L, Lee S, Fu X, Richards DE, Cao D, … Peng J (2004). Gibberellin regulates Arabidopsis floral development via suppression of DELLA protein function. Development 131(5):1055-1064. https://doi.org/10.1242/dev.00992

Cui YL, Zhang L, Huang MR (2003). Research progress of MADS box genes in plants. Chinese Journal of Biological Engineering 23(9):50-54. https://doi.org/10.3969/j.issn.1671-8135.2003.09.012

Du C (2021). Function and application of the WRKY transcription factor superfamily in plant response to stresses. Pratacultural Science 38(7):14-21. https://doi.org/10.11829/j.issn.1001-0629.2020-0662

Duan K, Li L, Hu P, Xu SP, Xu ZH, Xue HW (2006). A brassinolide-suppressed rice MADS-box transcription factor, OsMDP1, has a negative regulatory role in BR signaling. The Plant Journal for Cell and Molecular Biology 47(4):519-531. https://doi.org/10.1111/j.1365-313X.2006.02804.x

Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, … Bateman A (2016). The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research 44(D1):D279-D285. https://doi.org/10.1093/nar/gkv1344

Gao HH, Zhang YX, Hu SW, Guo Y (2017). Genome-wide survey and phylogenetic analysis of MADS-box gene family in Brassica napus. Journal of Integrative Plant Biology 52(006):699-712. https://doi.org/10.11983/CBB16244

Gou J, Strauss SH, Tsai CJ, Fang K, Chen YR, Jiang XG, … Busov VB (2010). Gibberellins regulate lateral root formation in Populus through interactions with auxin and other hormones. Plant Cell 22(3):623-639. https://doi.org/10.1105/tpc.109.073239

Gramzow L, Theissen G (2010). A hitchhiker's guide to the MADS world of plants. Genome Biology 11(6):214. https://doi.org/10.1186/gb-2010-11-6-214

Guo R, Tu M, Wang X, Zhao J, Wan R, Li Z, … Wang XP (2016). Ectopic expression of a grape aspartic protease gene, AP13, in Arabidopsis thaliana improves resistance to powdery mildew but increases susceptibility to Botrytis cinerea. Plant Science 248:17-27. https://doi.org/10.1016/j.plantsci.2016.04.006

Harris F, Eagles HA, Virgona JM, Martin P J, Condon JR, Angus J F (2017). Effect of VRN1 and PPD1 genes on anthesis date and wheat growth. Crop and Pasture Science 68:195-201. https://doi.org/10.1071/CP16420

Heuer S, Hansen S, Bantin J, Brettschneider R, Kranz E, Lörz H, … Dresselhaus T (2001). 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 Physiology 127(1):33-45. https://doi.org/10.1104/pp.127.1.33

Hu JY, Chen Z, Hu FC, Luo ZW, Nian YW, He F, … Zhang ZL (2017). Bioinformatics analysis of MADS-box gene family in pineapples. Genomics and Applied Biology 36(8):3042-3052. https://doi.org/10.13417/j.gab.036.003042

Huang F, Chi YJ, Yu DY (2012). Research progress of MADS-box gene in plants. Journal of Nanjing Agricultural University 35(5):9-18. https://doi.org/10.7685/j.issn.1000-2030.2012.05.002

Jia JT, Zhao PC, Cheng LQ, Yuan GX, Yang WG, Liu S, … Li XX (2018). MADS-box family genes in sheepgrass and their involvement in abiotic stress responses. BMC Plant Biology 18(1):42-51. https://doi.org/10.1186/s12870-018-1259-8

Jiao ZX, Li JC, Niu JS (2017). Analysis of MIKC- type MADS- box gene family in Wheat (Triticum aestivum). Journal of Agricultural Biotechnology 025(011):1756-1769. https://doi.org/10.3969/j.issn.1674-7968.2017.11.003

Li C (2016). Characterization of MADS-box transcription factor gene family and biological functional validation of RsFLC and miR172 in radish (Raphanus sativus L.). MSc Dissertation, Nanjing Agricultural University, Nanjing.

Li C, Lin H, Chen A, Lau M, Jernstedt J, Dubcovsky J (2019). Wheat VRN1, FUL2 and FUL3 play critical and redundant roles in spikelet development and spike determinacy. Development 146(14): dev175398. https://doi.org/10.1242/dev.175398

Liu M, Fu Q, Ma Z, Sun W, Huang L, Wu Q, … Chen H (2019). Genome-wide investigation of the MADS gene family and dehulling genes in tartary buckwheat (Fagopyrum tataricum). Planta 249(5):1301-1318. https://doi.org/10.1007/s00425-019-03089-3

Ljung K (2013). Auxin metabolism and homeostasis during plant development. Development 140(5):943-950. https://doi.org/10.1242/dev.086363

Lv SH, Meng Z (2007). Gene duplication and functional diversity of MADS-box gene family. Bulletin of Botany 24(1):60-70. https://doi.org/10.3969/j.issn.1674-3466.2007.01.005

Ma H, Yanofsky MF, Meyerowitz EM (1991). AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes. Genes & Development 5(3):484-495. https://doi.org/10.1101/gad.5.3.484

Ma H, Zhang ZJ, Luo SP (2006). Research progress of MADS-box gene in plants. Bulletin of Biotechnology 2006(06):14-18. https://doi.org/10.3969/j.issn.1002-5464.2006.06.004

Ma J, Yang Y, Luo W, Yang C, Ding P Y, Liu YX, … Lan XJ (2017). Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.). PLoS One 12(7):181-189. https://doi.org/10.1371/journal.pone.0181443

Ma XL (2022). Bioinformatics analysis and expression analysis of MADS-box and type Ⅲ PRX gene family in Millet under drought stress. MSc Dissertation, Hebei normal University of Science and Technology, Hebei.

Mandel MA, Yanofsky MF (1995). The Arabidopsis AGL8 MADS box gene is expressed in inflorescence meristems and is negatively regulated by APETALA1. Plant Cell 7(11):1763-1771. https://doi.org/10.1105/tpc.7.11.1763

Martínez-Ainsworth NE, Tenaillon MI (2016). Superheroes and masterminds of plant domestication. Comptes Rendus Biologies 339(7-8):268-273. https://doi.org/10.1016/j.crvi.2016.05.005

Melzer R, Verelst W, Theißen G (2009). The class E floral homeotic protein SEPALLATA3 is sufficient to loop DNA in ‘floral quartet’-like complexes in vitro. Nucleic Acids Research 37(1):144-157. https://doi.org/10.1093/nar/gkn900

Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, Abe H (2003). Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant Journal 34(2):137-148. https://doi.org/10.1046/j.1365-313x.2003.01708.x

Ogawa M, Hanada A, Yamauchi Y, Kuwahara A, Kamiya Y, Yamaguchi S (2003). Gibberellin Biosynthesis and Response during Arabidopsis Seed Germination. Plant Cell 15(7):1591-1604. https://doi.org/10.1105/tpc.011650

Ren XY, Vorst O, Fiers MW, Stiekema WJ, Nap JP (2006). In plants, highly expressed genes are the least compact. Trends in Genetics 22(10):528-532. https://doi.org/10.1016/j.tig.2006.08.008

Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R, Jermiin Lars S, … Melzer Rainer (2020). Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. New Phytologist 225(1):511-529. https://doi.org/10.1111/nph.16122

Schilling S, Pan S, Kennedy A, Melzer R (2018). MADS-box genes and crop domestication: the jack of all traits. Journal of Experimental Botany 69(7):1447-1469. https://doi.org/10.1093/jxb/erx479

Schmitz J, Franzen R, Ngyuen TH, Garcia-Maroto F, Pozzi C, Salamini F, … Rohde W (2000). Cloning, mapping and expression analysis of barley MADS-box genes. Plant Molecular Biology 42(6):899-913. https://doi.org/10.1023/a:1006425619953

Schwarz-Sommer Z, Huijser P, Nacken W, Saedler H, Sommer H (1990). Genetic control of flower development by homeotic genes in antirrhinum majus. Science (New York, N.Y.) 250(4983):931-936. https://doi.org/10.1126/science.250.4983.931

Shao SQ, Li BY, Zhang ZT, Zhou Y, Jiang J, Li XB (2010). Expression of a cotton MADS-box gene is regulated in anther development and in response to phytohormone signaling. Journal of Genetics and Genomics 37(12):805-816. https://doi.org/10.1016/S1673-8527(09)60098-9

Shinwari ZK, Nakashima K, Miura S, Kasuga M, Seki M, YamaguchiShinozaki K, … Shinozaki K (1998). An arabidopsis gene family encoding DRE/CRT binding proteins involved in low-temperature-responsive gene expression. Biochemical and Biophysical Research Communications 250(1):161-170. https://doi.org/10.1006/bbrc.1998.9267

Shu Y, Yu D, Wang D, Guo D, Guo C (2013). Genome-wide survey and expression analysis of the MADS-box gene family in soybean. Molecular Biology Reports 40(6):3901-3911. https://doi.org/10.1007/s11033-012-2438-6

Song M, Zhang Y, Jia Q, Huang S, An R, Chen N, … Hu S (2023). 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. Front Plant Science 13:1115513. https://doi.org/10.3389/fpls.2022.1115513

Teale WD, Paponov IA, Palme K (2006). Auxin in action: signalling, transport and the control of plant growth and development. Nature Reviews Molecular Cell Biology 7(11):847-859. https://doi.org/10.1038/nrm2020

Terzaghi W B, Cashmore A R (1995). Light-Regulated Transcription. Annual review of plant biology 46(1):445-474. https://doi.org/10.1146/annurev.pp.46.060195.002305

Theißen G, Rümpler F, Gramzow L (2018). Array of MADS-box genes: facilitator for rapid adaptation. Trends in Plant Science 23(7):563-576. https://doi.org/10.1016/j.tplants.2018.04.008

Wan ZT, Lu M, Wu SS, Mi YL, Zhai JW (2021). Identification and expression analysis of the MIKC-type MADS-box gene family in Cannabis sativa L. Acta Pharmaceutica Sinica 56(11):3173-3183. https://doi.org/10.16438/j.0513-4870.2021-0892

Wang LN (2010). Molecular cloning, expression profile and function analysis of MADS-box genes in cotton. MSc Dissertation, Chinese Academy of Agricultural Sciences, Beijing.

Wang X, Guo XB, Wang CY, Hou YJ, Yi J (2009). Advances of MADS-box genes in plant. Anhui Agricultural Sciences 37(35):17372-17375. https://doi.org/10.13989/j.cnki.0517-6611.2009.35.027

Wang Y, Mu YX, Wang J (2021). Advances in the regulation of plant floral organ development by MADS-box gene family. Zhejiang Journal of Agricultural Sciences 33(06):1149-1158. https://doi.org/10.3969/j.issn.1004-1524.2021.06.21

Wei KF, Zhang W (2018). Transcriptome-wide identification and expression profiling of the MADS-box gene family in Hylocereus Undatus. Journal of Minnan Normal University (Nat. Sci.) 004:31-38. https://doi.org/10.16007/j.cnki.issn2095-7122.2018.04.008

Wei M, Wang Y, Pan R, Li W (2018). Genome-Wide identification and characterization of MADS-box family genes related to floral organ development and stress resistance in hevea brasiliensis Müll. Arg. Forests 9(6):304-315. https://doi.org/10.3390/f9060304

Wei N, Li YP, Ma YT, Liu WX (2022). Genome-wide identification of TCP gene families in Alfalfa and analysis of their expression patterns under drought stress. Prataculturae Science 31(01):118-130. https://doi.org/10.11686/cyxb2021189

Yang W, Lou X, Li J, Pu M, Mirbahar A A, Liu D, … Zhang A (2017). Cloning and functional analysis of MADS-box genes, TaAG-A and TaAG-B, from a Wheat K-type cytoplasmic male sterile line. Front Plant Science 8:1081. https://doi.org/10.3389/fpls.2017.01081

Yun KY, Park MR, Mohanty B, Herath V, Xu FY, Mauleon R, … Bruskiewich R (2010). Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant Biology 10(1):1-29. https://doi.org/10.1186/1471-2229-10-16

Zhang Y, Wang J Q, Yu ZJ, Xu Q, Zhang L, Pan YX (2022). Bioinformatics analysis of MIKC-type MADS-box gene family in legumes. Chinese Journal of Oil Crop Sciences 44(04):798-809. https://doi.org/10.19802/j.issn.1007-9084.2021175

Zhao D, Chen Z, Xu L, Zhang L, Zou Q (2021). Genome-Wide analysis of the MADS-Box gene family in Maize: gene structure, evolution, and relationships. Genes 12(12):1956. https://doi.org/10.3390/genes12121956

Zhao W, Zhang LL, Xu ZS, Fu L, Pang HX, Ma YZ, … Min DH (2021). 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 Science 12:659474. https://doi.org/10.3389/fpls.2021.659474

Zhao Y, Li X, Chen W, Peng X, Cheng X, Zhu S, … Cheng B (2011). Whole-genome survey and characterization of MADS-box gene family in maize and sorghum. Plant Cell, Tissue and Organ Culture (PCTOC) 105(2):159-173. https://doi.org/10.1007/s11240-010-9848-8

Published

2023-11-16

How to Cite

YINXIA, W., XIANGZHUO, J., ZELONG, Z., YUNFANG, Z., & YUNLING, P. (2023). Identification and bioinformatics analysis of MADS-box family genes containing K-box domain in maize. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 51(4), 13253. https://doi.org/10.15835/nbha51413253

Issue

Section

Research Articles
CITATION
DOI: 10.15835/nbha51413253

Most read articles by the same author(s)