Abstract
A cDNA-sequence-related amplified polymorphism (cDNA-SRAP) approach was used to identify relevant genes expressed at the onset of somatic embryo maturation/desiccation in banana (Musa spp. AAB group, Silk subgroup) cv. Manzano. For this, an embryogenic procedure, starting with cell suspensions, was first improved by including a culture period on a free growth-regulator medium for embryo maturation. This produced an up to 95% germination of the coleoptilar embryos. Gene expression patterns were followed through different stages of the process, including immature male flower explants, embryogenic calli, as well as immature, mature and germinated embryos. A total of 151 differentially expressed transcript-derived fragments (TDFs) were detected, sequenced, resulting in the identification of 71 by their similitude to accessions deposited in different data bases. The participation of four of these genes, putatively involved in the banana somatic embryogenesis, was further analyzed by real-time quantitative PCR (q-PCR). This confirmed their preferential expression at the transition from embryo early development to maturation. Noteworthy, tryptophan aminotransferase relate 2 (TAR2), which is involved in the indole-3-pyruvic acid dependent auxin biosynthesis, corresponded to one of the upregulated four genes, suggesting the requirement of this growth regulator at the transition stage. This study opens the path for future in-depth studies of molecular and biochemical events occurring during in vitro somatic embryogenesis in edible bananas.
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References
Bassam BJ, Caetano-Anollés G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83. https://doi.org/10.1016/0003-2697(91)90120-I
Ben-Simhon Z, Judeinstein S, Nadler-Hassar T, Trainin T, Bar-Ya’akov I, Borochov-Neori H, Holland D (2011) A pomegranate (Punica granatum L.) WD40-repeat gene is a functional homologue of Arabidopsis TTG1 and is involved in the regulation of anthocyanin biosynthesis during pomegranate fruit development. Planta 234:865–881. https://doi.org/10.1007/s00425-011-1438-4
Blöchl A, Grenier-de March G, Sourdioux M, Peterbauer T, Richter A (2005) Induction of raffinose oligosaccharide biosynthesis by abscisic acid in somatic embryos of alfalfa (Medicago sativa L.). Plant Sci 168:1075–1082. https://doi.org/10.1016/j.plantsci.2004.12.004
Businge E, Brackmann K, Moritz T, Egertsdotter U (2012) Metabolite profiling reveals clear metabolic changes during somatic embryo development of Norway spruce (Picea abies). Tree Physiol 32:232–244. https://doi.org/10.1093/treephys/tpr142
Chen M, Zhang B, Li C, Kulaveerasingam H, Chew FT, Yu H (2015) TRANSPARENT TESTA GLABRA1: regulates the accumulation of seed storage reserves in. Arabidopsis Plant Physiol 169:391–402. https://doi.org/10.1104/pp.15.00943
Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156–159. https://doi.org/10.1016/0003-2697(87)90021-2
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization analysis in functional genomics research. Bioinformatics 21:3674–3676. https://doi.org/10.1093/bioinformatics/bti610
Côte FX, Domergue R, Monmarson S, Schwendiman J, Teisson C, Escalant JV (1996) Embryogenic cell suspensions from the male flower of Musa AAA cv. Grand nain. Physiol Plantarum 97:285–290. https://doi.org/10.1034/j.1399-3054.1996.970211.x
Deng X-h, Zhang S-n, Hou X-l (2007) Differential expression analysis of bud of Pol CMS and its maintainter line of Brassica rapa ssp. chinensis through SRAP. Acta Horticulturae Sin 34:655
Domergue FGR, Ferrière N, Côte FX (2000) Morphohistological study of the different constituents of a banana (Musa AAA, cv. Grande naine) embryogenic cell suspension. Plant Cell Rep 19:748–754. https://doi.org/10.1007/s002999900188
Droc G et al (2013) The Banana Genome Hub. Database https://doi.org/10.1093/database/bat035
Escalant J-V, Teisson C, Cote F (1994) Amplified somatic embryogenesis from male flowers of triploid banana and plantain cultivars (Musa spp.). In Vitro – Plant 30:181–186. https://doi.org/10.1007/bf02823029
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Finn RD et al (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44:D279–D285. https://doi.org/10.1093/nar/gkv1344
Fucile G, Falconer S, Christendat D (2008) Evolutionary diversification of plant shikimate kinase gene duplicates. PLoS Genet 4:e1000292. https://doi.org/10.1371/journal.pgen.1000292
Gaj MD, Zhang S, Harada JJ, Lemaux PG (2005) Leafy cotyledon genes are essential for induction of somatic embryogenesis of Arabidopsis Planta 222:977–988. https://doi.org/10.1007/s00425-005-0041-y
Ganapathi T, Suprasanna P, Bapat V, Kulkarni V, Rao P (1999) Somatic embryogenesis and plant regeneration from male flower buds in banana. Curr Sci 76:1228–1231
Gao Y et al (2018) Tomato SlAN11 regulates flavonoid biosynthesis and seed dormancy by interaction with bHLH proteins but not with MYB proteins Horticulture Res 5:27. https://doi.org/10.1038/s41438-018-0032-3
Garg R, Jain M (2013) RNA-Seq for transcriptome analysis in non-model plants. In: Rose R (ed) Legume genomics. Methods in molecular biology (methods and protocols), vol 1069. Humana Press, Totowa, pp 43–57. https://doi.org/10.1007/978-1-62703-613-9_4
Grapin A, Schwendiman J, Teisson C (1996) Somatic embryogenesis in plantain banana. Vitro - Plant 32:66–71. https://doi.org/10.1007/bf02823133
Harada JJ, Belmonte MF, Kwong RW (2001) Plant embryogenesis (zygotic and somatic). Wiley, Chichester, https://doi.org/10.1002/9780470015902.a0002042.pub2
Huang N, Zhang Y, Xiao X, Huang L, Wu Q, Que Y, Xu L (2015) Identification of smut-responsive genes in sugarcane using cDNA-SRAP. Genet Mol Res 14:6808–6818
Jin F, Hu L, Yuan D, Xu J, Gao W, He L, Yang X, Zhang X (2013) Comparative transcriptome analysis between somatic embryos (SEs) and zygotic embryos in cotton: evidence for stress response functions in SE development. Plant Biotechnol J. https://doi.org/10.1111/pbi.12123
Klimaszewska K, Smith DR (1997) Maturation of somatic embryos of Pinus strobus is promoted by a high concentration of gellan gum. Physiologia Plantarum 100:949–957. https://doi.org/10.1111/j.1399-3054.1997.tb00022.x
Klimaszewska K, bernier-Cardou M, Cyr DR, Sutton BCS (2000) Influence of gelling agents on culture medium gel strength, water availability, tissue water potential, and maturation response in embryogenic cultures of Pinus strobus L. Vitro CellDevBiol-Plant 36:279–286. https://doi.org/10.1007/s11627-000-0051-1
Kong L, Attree SM, Fowke LC (1997) Changes of endogenous hormone levels in developing seeds, zygotic embryos and megagametophytes in Picea glauca. Physiol Plant 101:23–30. https://doi.org/10.1111/j.1399-3054.1997.tb01815.x
Kulkarni VM, Bapat VA (2013) Somatic embryogenesis and plant regeneration from cell suspension cultures of Rajeli (AAB), an endangered banana cultivar. J Plant Biochem Biotechnol 22:132–137. https://doi.org/10.1007/s13562-012-0119-0
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Kumaravel M, Uma S, Backiyarani S, Saraswathi MS, Vaganan MM, Muthusamy M, Sajith KP (2017) Differential proteome analysis during early somatic embryogenesis in Musa spp. AAA cv. Grand Naine Plant Cell Rep 36:163–178. https://doi.org/10.1007/s00299-016-2067-y
Lecouteux CG, Lai FM. McKersie BD (1993) Maturation of alfalfa (Medicago sativa L.) somatic embryos by abscisic acid, sucrose and chilling stress. Plant Sci 94:207–213. https://doi.org/10.1016/0168-9452(93)90021-Q/0168-9452(93)90021-Q
Lelu-Walter M-A et al (2018) High gellan gum concentration and secondary somatic embryogenesis: two key factors to improve somatic embryo development in Pseudotsuga menziesii [Mirb.]. Plant Cell Tiss Organ Cult 132:137–155. https://doi.org/10.1007/s11240-017-1318-0
Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461. https://doi.org/10.1007/s001220100570
Li C, Zhang B, Chen B, Ji L, Yu H (2018) Site-specific phosphorylation of TRANSPARENT TESTA GLABRA1 mediates carbon partitioning in Arabidopsis seeds Nature Commun 9:571. https://doi.org/10.1038/s41467-018-03013-5
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2–∆∆CT. Method Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262
Ma S (1991) Somatic embryogenesis and plant regeneration from cell suspension culture of banana. In: Proceedings of symposium on tissue culture of horticultural crops. Taipei, Taiwan, 8–9 March 1988, pp 181–188
Ma A, Li J, Chen L, Qian W, Fu F, Liu L (2008) Differential display of related genes to seed-coat color by cDNA-SRAP in Brassica napus. L Acta Agron Sin 34:526
Macovei A, Vaid N, Tula S, Tuteja N (2012) A new DEAD-box helicase ATP-binding protein (OsABP) from rice is responsive to abiotic stress. Plant Signal Behav 7:1138–1143. https://doi.org/10.4161/psb.21343
Maldonado-Borges JI, Ku-Cauich JR, Escobedo-GraciaMedrano RM (2013) Annotation of differentially expressed genes in the somatic embryogenesis of Musa and their location in the banana genome. Sci World J 2013:7. https://doi.org/10.1155/2013/535737
Márquez-Martín B, Sesmero R, Quesada MA, Pliego-Alfaro F, Sánchez-Romero C (2011) Water relations in culture media influence maturation of avocado somatic embryos. J Plant Physiol 168:2028–2034. https://doi.org/10.1016/j.jplph.2011.06.008
Menon R (2016) Banana breeding. In: Mohandas S, Ravishankar K (eds) Banana: genomics and transgenic approaches for genetic improvement. Springer, Singapore, pp 13–34. https://doi.org/10.1007/978-981-10-1585-4_2
Miao Q et al (2017) Genome-wide identification and characterization of microRNAs differentially expressed in fibers in a cotton phytochrome A1 RNAi line. PLoS ONE 12:e0179381. https://doi.org/10.1371/journal.pone.0179381
Mishra S, Sanyal I, Amla DV (2012) Changes in protein pattern during different developmental stages of somatic embryos in chickpea. Biol Plant 56:613–619. https://doi.org/10.1007/s10535-012-0124-0
Morel A et al (2014) Early molecular events involved in Pinus pinaster Ait. somatic embryo development under reduced water availability: transcriptomic and proteomic analyses. Physiol Plant 152:184–201. https://doi.org/10.1111/ppl.12158
Nebert DW, Gonzalez FJ (1987) P450 genes: structure, evolution, and regulation annual. Rev Biochem 56:945–993. https://doi.org/10.1146/annurev.bi.56.070187.004501
Nic-Can GI, Loyola-Vargas VM (2016) The role of the auxins during somatic embryogenesis. In: Loyola-Vargas VM, Ochoa-Alejo N (eds) Somatic embryogenesis: fundamental aspects and applications. Springer International Publishing, Cham, pp 171–182. https://doi.org/10.1007/978-3-319-33705-0_10
Podevin N, Krauss A, Henry I, Swennen R, Remy S (2012) Selection and validation of reference genes for quantitative RT-PCR expression studies of the non-model crop Musa. Mol Breed 30:1237–1252. https://doi.org/10.1007/s11032-012-9711-1
Que Y, Xu L, Lin J, Luo J, Xu J, Zheng J, Chen R (2012) cDNA-SRAP and its application in differential gene expression analysis: a case study in Erianthus arundinaceum. J Biomed Biotechnol 2012:8. https://doi.org/10.1155/2012/390107
Remakanthan A, Menon TG, Soniya EV (2014) Somatic embryogenesis in banana (Musa acuminata AAA cv. Grand Naine): effect of explant and culture conditions. Vitro Cell DevBiol-Plant 50:127–136. https://doi.org/10.1007/s11627-013-9546-4
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Schmid J, Amrhein N (1995) Molecular organization of the shikimate pathway in higher plants. Phytochemistry 39:737–749. https://doi.org/10.1016/0031-9422(94)00962-S
Shiota H, Satoh R, Watabe K-i, Harada H, Kamada H (1998) C-ABI3, the carrot homologue of the Arabidopsis ABI3, is expressed during both zygotic and somatic embryogenesis and functions in the regulation of embryo-specific ABA-inducible genes. Plant Cell Physiol 39:1184–1193
Sholi NY, Chaurasia A, Agrawal A, Sarin N (2009) ABA enhances plant regeneration of somatic embryos derived from cell suspension cultures of plantain cv. Spambia (Musa sp.). Plant Cell Tiss Organ Cult 99:133–140. https://doi.org/10.1007/s11240-009-9585-z
Stepanova AN et al (2008) TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Cell 133:177–191. https://doi.org/10.1016/j.cell.2008.01.047
Tao Y et al (2008) Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell 133:164–176. https://doi.org/10.1016/j.cell.2008.01.049
Teyssier C et al (2011) Increased gelling agent concentration promotes somatic embryo maturation in hybrid larch (Larix × eurolepsis): a 2-DE proteomic analysis. Physiol Plant 141:152–165. https://doi.org/10.1111/j.1399-3054.2010.01423.x
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Tuteja N, Tuteja R (2004) Prokaryotic and eukaryotic DNA helicases European. J Biochem 271:1835–1848. https://doi.org/10.1111/j.1432-1033.2004.04093.x
Vale EM et al (2014) Comparative proteomic analysis of somatic embryo maturation in Carica papaya L. Proteome Sci 12:37
Vuylsteke M, Peleman JD, van Eijk MJT (2007) AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis. Nat Protocols 2:1399–1413
Yang X, Zhang X (2010) Regulation of somatic embryogenesis in higher plants. Crit Rev Plant Sci 29:36–57
Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL (2012) Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13:134–134. https://doi.org/10.1186/1471-2105-13-134
Zhang B, Schrader A (2017) TRANSPARENT TESTA GLABRA 1-dependent regulation of flavonoid biosynthesis. Plants 6:65. https://doi.org/10.3390/plants6040065
Zhu M, Chen G, Dong T, Wang L, Zhang J, Zhao Z, Hu Z (2015) SlDEAD31,a putative DEAD-box RNA helicase gene, regulates salt and drought tolerance and stress-related genes in tomato. PLoS ONE 10:e0133849. https://doi.org/10.1371/journal.pone.0133849
Acknowledgements
The authors thank the following: Ir. I. Van den Houwe, curator of the Musa International Transit Centre at Katolieke Universiteit, Leuven, Belgium, for the supply of plant material; INIFAP-CIR-SURESTE for the field facilities provided for the conservation of the in situ banana collection launched by the CICY at the INIFAP-Uxmal-Experimental Station, Yucatán, Mexico; Dra. Goreti Campos and MC Angela Ku for their technical help with the scanning electron microscopy. This work was supported by the CONACYT fund for Basic Science Research Project # 0060838 (corresponding author) and Studentship # 378177 awarded to the first author.
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AJEV performed the experimental work, data analysis, and wrote the manuscript; RMEGM designed and outlined the research, interpreted data and wrote the manuscript. JRCK collaborated in in vitro cultures development, greenhouse acclimatization and transfer to the field. FAVF participated in data interpretation and in editing the manuscript.
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Communicated by Maria Margarida Oliveira.
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Enríquez-Valencia, A.J., Vázquez-Flota, F.A., Ku-Cauich, J.R. et al. Differentially expressed genes during the transition from early to late development phases in somatic embryo of banana (Musa spp. AAB group, Silk subgroup) cv. Manzano. Plant Cell Tiss Organ Cult 136, 289–302 (2019). https://doi.org/10.1007/s11240-018-1514-6
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DOI: https://doi.org/10.1007/s11240-018-1514-6