Genome-wide analysis and gene expression studies revealed putative homeotic genes with a role in flower formation in sesame (Sesamum indicum L.)
Sesame (Sesamum indicum L.) is an ancient oilseed crop with medicinal and nutritional value. Timely regulation of flowering could increase the sesame crop’s seed productivity potential. To regulate flowering in sesame, it is necessary to identify the genes involved in flower development. Although several homeotic genes with a role in flower development have been identified in model plant species such as Arabidopsis thaliana, Antirrhinum majus, and Petunia hybrida, the homeotic genes in sesame need to be detected. It is hypothesized that a set of homeotic genes is conserved with a role in flower formation in sesame. The study aimed at identifying the homeotic genes through a genome-wide in silico search using the Sesamum genome database and gene expression studies. Our study revealed 23 putative homeotic genes that exhibited MADS domain, a characteristic of the homeotic genes, along with nine putative transcription factors with a role in flower formation. Furthermore, the gene expression studies revealed the five putative ABCDE class of genes –SiAP1, SiAP3, SiAG, SiSTK, and SiSEP3, respectively, as the critical players representing each of the five classes of ABCDE genes in sesame, confirming their function in floral induction and floral organ identity. The homeotic genes identified in this study could be explored further through gene manipulation and complementation studies to understand the mechanism of flowering in sesame.
Annapurna HN, Ramachandran A, Reagan NSR, Pamei I, Ramya KT, Makandar R. Genome-wide analysis and gene expression studies revealed putative homeotic genes with a role in flower formation in sesame (Sesamum indicum L.). J App Biol Biotech 2025. Article in Press. http://doi.org/10.7324/JABB.2026.250381
1. Uzun B, Arslan Ç, Furat ?. Variation in fatty acid compositions, oil content and oil yield in a germplasm collection of sesame (Sesamum indicum L.). J Am Oil Chem Soc. 2008;85:1135-42. https://doi.org/10.1007/s11746-008-1304-0
2. Kouighat M, Guirrou I, El Antari A, El Fechtali M, Bouchyoua A, Nabloussi A. Exploring fatty acid composition, bioactive compounds, and antioxidant properties in oils of newly developed sesame mutant lines in Morocco. J Am Oil Chem Soc. 2025;102:223-37. https://doi.org/10.1002/aocs.12879
3. Hano C, Tungmunnithum D. Plant polyphenols, more than just simple natural antioxidants: Oxidative stress, aging and age-related diseases. Medicines (Basel). 2020;7:26. https://doi.org/10.3390/medicines7050026
4. Dossa K, Niang M, Assogbadjo AE, Cissé N, Diouf D. Whole genome homology-based identification of candidate genes for drought tolerance in sesame (Sesamum indicum L.). Afr J Biotech. 2016;15:1464-75. https://doi.org/10.5897/AJB2016.15420
5. Naik YD, Bahuguna RN, Garcia?Caparros P, Zwart RS, Reddy MS, Mir RR, et al. Exploring the multifaceted dynamics of flowering time regulation in field crops: Insight and intervention approaches. Plant Genome. 2025;18:e70017. https://doi.org/10.1002/tpg2.70017
6. Cho LH, Yoon J, An G. The control of flowering time by environmental factors. Plant J. 2017;90:708-19. https://doi.org/10.1111/tpj.13461
7. Ruelens P, Zhang Z, Van Mourik H, Maere S, Kaufmann K, Geuten K. The origin of floral organ identity quartets. Plant Cell. 2017;29:229-42, https://doi.org/10.1105/tpc.16.00366
8. Meng Q, Gao YN, Cheng H, Liu Y, Yuan LN, Song MR, et al. Molecular mechanism of interaction between short vegetative phase and apetala1 in Arabidopsis thaliana. Plant Physiol Biochem. 2025;220:109512. https://doi.org/10.1016/j.plaphy.2025.109512
9. Yang D, Chen Y, He Y, Song J, Jiang Y, Yang M, et al. Transcriptome analysis reveals association of E-class AmMADS-Box genes with petal malformation in Antirrhinum majus L. Int J Mol Sci. 2025;26:4450. https://doi.org/10.3390/ijms26094450
10. Bednarczyk D, Skaliter O, Kerzner S, Masci T, Shklarman E, Shor E, et al. The homeotic gene Ph DEF regulates production of volatiles in petunia flowers by activating EOBI and EOBII. The Plant Cell. 2025;37:koaf027. https://doi.org/10.1093/plcell/koaf027
11. Wang L, Yu S, Tong C, Zhao Y, Liu Y, Song C, et al. Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol. 2014;15:R39. https://doi.org/10.1186/gb-2014-15-2-r39
12. Wei X, Wang L, Yu J, Zhang Y, Li D, Zhang X. Genome-wide identification and analysis of the MADS-box gene family in sesame. Gene. 2015;569:66-76. https://doi.org/10.1016/j.gene.2015.05.018.
13. Kumar K, Srivastava H, Das A, Tribhuvan KU, Durgesh K, Joshi R, et al. Identification and characterization of MADS box gene family in pigeonpea for their role during floral transition. 3 Biotech. 2021;11:105. https://doi.org/10.1007/s13205-020-02605-7
14. Saitou N, Nei M. The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence. J Mol Evol. 1986;24:189-204. https://doi.org/10.1007/BF02099966
15. Alvarez-Buylla ER, Benítez M, Corvera-Poiré A, Cador ÁC, De Folter S, De Buen AG, et al. Flower development. Arabidopsis Book. 2010;8:e0127. https://doi.org/10.1199/tab.0127
16. Pamei I, Makandar R. Comparative transcriptome provides a new insight into floral regulation and defense response against phytoplasma in sesame (Sesamum indicum L.). Plant Mol Biol Reporter. 2022;40:446-57. https://doi.org/10.1007/s11105-022-01335-9
17. Ahrens U, Seemüller E. Detection of plant pathogenic mycoplasma like organisms by a polymerase chain reaction that amplifies a sequence of 16S rRNA gene. Phytopathol. 1992;82:828-32. https://doi.org/10.1094/Phyto-82-828
18. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods. 2001;25:402-8. https://doi.org/10.1006/meth.2001.1262
19. Weigel D, Meyerowitz EM. The ABCs of floral homeotic genes. Cell. 1994;78:203-9. https://doi.org/10.1016/0092-8674(94)90291-7
20. Theissen G, Saedler H. Floral quartets. Nature. 2001;409:469-71, https://doi.org/10.1038/35054172
21. Smaczniak C, Immink RG, Angenent GC, Kaufmann K. Developmental and evolutionary diversity of plant MADS-domain factors: Insights from recent studies. Development. 2012;139:3081- 98. https://doi.org/10.1242/dev.074674
22. Coen ES, Romero JM, Doyle S, Elliot R, Murphy G, Carpenter R. Floricaula: A homeotic gene required for flower development in Antirrhinum majus. Cell. 1990;63:1311-22. https://doi.org/10.1016/0092-8674(90)90426-F
23. Ma N, An Y, Li J, Wang L. Cloning and characterization of a homologue of the FLORICAULA/LEAFY gene in Ficus carica L., FcLFY, and its role in flower bud differentiation. Sci Hortic. 2020;261:109014. https://doi.org/10.1016/j.scienta.2019.109014
24. Lopes FL, Galvan-Ampudia C, Landrein B. WUSCHEL in the shoot apical meristem: Old player, new tricks. J Exp Bot. 2021;72:1527-35. https://doi.org/10.1093/jxb/eraa572
25. Laux T, Mayer KF, Berger J, Jürgens G. The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis. Development. 1996;122:87-96. https://doi.org/10.1242/dev.122.1.87
26. Lee J, Lee I. Regulation and function of SOC1, a flowering pathway integrator. J Exp Bot. 2010;61:2247-54. https://doi.org/10.1093/jxb/erq098
27. Levin JZ, Meyerowitz EM. UFO: An Arabidopsis gene involved in both floral meristem and floral organ development. Plant Cell. 1995;7:529-48. https://doi.org/10.1105/tpc.7.5.529
28. Theissen G, Becker A, Di Rosa A, Kanno A, Kim JT, Munster T, et al. A short history of MADS-box genes in plants. Plant Mol Biol. 2000;42:115-49. https://doi.org/10.1023/A:1006332105728
29. Jofuku KD, Den Boer BG, Van Montagu M, Okamuro JK. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell. 1994;6:1211-25. https://doi.org/10.1105/tpc.6.9.1211
30. Chi Y, Huang F, Liu H, Yang S, Yu D. An APETALA1-like gene of soybean regulates flowering time and specifies floral organs. J Plant Physiol. 2011;168:2251-9. https://doi.org/10.1016/j.jplph.2011.08.007
31. Irish VF, Sussex I. Function of the Apetala-1 gene during Arabidopsis floral development. Plant Cell. 1990;2:741-53. https://doi.org/10.1105/tpc.2.8.741
32. Saedler H, Huijser P. Molecular biology of flower development in Antirrhinum majus (snapdragon). Gene. 1993;135:239-43. https://doi.org/10.1016/0378-1119(93)90071-a
33. Tröbner W, Ramirez L, Motte P, Hue I, Huijser P, Lönnig WE, et al. GLOBOSA: A homeotic gene which interacts with DEFICIENS in the control of Antirrhinum floral organogenesis. EMBO J. 1992;11:4693-704. https://doi.org/10.1002/j.1460-2075.1992.tb05574.x
34. Souer E, Rebocho AB, Bliek M, Kusters E, De Bruin RA, Koes R. Patterning of inflorescences and flowers by the F-Box protein double top and the leafy homolog aberrant leaf and flower of petunia. Plant Cell. 2008;20:2033-48. https://doi.org/10.1105/tpc.108.060871
35. Kaufmann K, Wellmer F, Muiño JM, Ferrier T, Wuest SE, Kumar V, et al. Orchestration of floral initiation by APETALA1. Science. 2010;328:85-9. https://doi.org/10.1126/science.1185244
36. Wuest SE, O’Maoileidigh DS, Rae L, Kwasniewska K, Raganelli A, Hanczaryk K, et al. Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA. Proc of the Natl Acad of Sci. 2012;109:13452-7. https://doi.org/10.1073/pnas.120707510
37. Mizukami Y, Ma H. Determination of Arabidopsis floral meristem identity by AGAMOUS. Plant Cell. 1997;9:393-408. https://doi.org/10.1105/tpc.9.3.393
38. Pinyopich A, Ditta GS, Savidge B, Liljegren SJ, Baumann E, Wisman E, et al. Assessing the redundancy of MADS-box genes during carpel and ovule development. Nature. 2003;424:85-8. https://doi.org/10.1038/nature01741
39. Cao L, Liu D, Jiang F, Wang B, Wu Y, Che D, et al. Heterologous expression of LiSEP3 from oriental Lilium hybrid ‘sorbonne’ promotes the flowering of Arabidopsis thaliana L. Mol Biotech. 2022;64:1120-9. https://doi.org/10.1007/s12033-022-00492-2
Year
Month