Abstract
Basic principles of biology are generally developed, tested, and established for the first time in organisms that are easy to study, convenient to handle and have enough biological merit to generalize the derived inferences. Some of these organisms are given the status of ‘model organism’ provided they fulfill some basic (intrinsic, derived, and community) criteria. The fundamentals of genetics were established through Mendel’s legendary work on garden pea (Pisum sativum) but at the early days of plant genetics maize (Zea mays) was the model system that got popularity. As plant science entered the genomics era and robust genetic manipulation techniques were established in some plant systems, a paradigm shift took place in the selection criteria of plants that can be promoted as ‘model system’. The emergence of Arabidopsis thaliana and rice (Oryza sativa) as ‘model plants’ being the most prominent examples in this regard. During the past 40 years, Arabidopsis has overtaken all others and got established as the most preferred and frequently used model system in plant biology. Rice, on the other hand, has come up a long way to establish itself as a model monocot and it assumes paramount importance especially in the field of agriculture. However, it is also necessary to understand that a handful of model plants cannot answer every biological question. Hence, there exists the potential of expanding the horizon of ‘model plants’ by introducing new entries to keep pace with the ever-expanding knowledge and technology. In fact, with the recent introduction of rapid and low-cost whole-genome sequencing methodologies and precise genome editing technologies, the idea of ‘model organism’ is undergoing a rapid change. Under these circumstances, it seems likely that model plants in the future will be chosen based on their biological relevance rather than the operational ease and historical pedigree.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Alabadı́ D, Oyama T, Yanovsky MJ et al (2001) Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293(5531):880–883
Albertsen HM, Abderrahim H, Cann HM et al (1990) Construction and characterization of a yeast artificial chromosome library containing seven haploid human genome equivalents. Proc Natl Acad Sci 87(11):4256–4260
Amborella Genome Project (2013) The Amborella genome and the evolution of flowering plants. Science 342:1241089
Arioli T, Peng L, Betzner AS et al (1998) Molecular analysis of cellulose biosynthesis in Arabidopsis. Science 279(5351):717–720
Atallah NM, Banks JA (2015) Reproduction and the pheromonal regulation of sex type in fern gametophytes. Front Plant Sci 6:100
Banks JA, Nishiyama T, Hasebe M et al (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332(6032):960–963
Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Philos Trans Royal Soc London B: Biol Sci 274(933):227–274
Bernier G (2013) My favourite flowering image: the role of cytokinin as a flowering signal. J Exp Bot 64(18):5795–5799
Birol I, Raymond A, Jackman SD et al (2013) Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics 29(12):1492–1497
Blilou I, Frugier F, Folmer S et al (2002) The Arabidopsis HOBBIT gene encodes a CDC27 homolog that links the plant cell cycle to progression of cell differentiation. Genes Dev 16(19):2566–2575
Borrill P (2019) Blurring the boundaries between cereal crops and model plants. New Phytol 228(6):1721–1727
Bowman JL (2016) A brief history of Marchantia from Greece to genomics. Plant Cell Physiol 57(2):210–229
Brutnell TP, Wang L, Swartwood K et al (2010) Setaria viridis: a model for C4 photosynthesis. Plant Cell 22(8):2537–2544
Chang C, Bowman JL, DeJohn AW et al (1988) Restriction fragment length polymorphism linkage map for Arabidopsis thaliana. Proc Natl Acad Sci 85(18):6856–6860
Chen F, Dong W, Zhang J et al (2018a) The sequenced angiosperm genomes and genome databases. Front Plant Sci 9:418
Chen R, Xu Q, Liu Y et al (2018b) Generation of transgene-free maize male sterile lines using the CRISPR/Cas9 system. Front Plant Sci 9:1180
Churchman ML, Brown ML, Kato N et al (2006) SIAMESE, a plant-specific cell cycle regulator, controls endoreplication onset in Arabidopsis thaliana. Plant Cell 18(11):3145–3157
Coudert Y, Périn C, Courtois B et al (2010) Genetic control of root development in rice, the model cereal. Trends Plant Sci 15(4):219–226
Crossa J, Beyene Y, Kassa S et al (2013) Genomic prediction in maize breeding populations with genotyping-by-sequencing. G3: Genes, Genomes Genetics 3(11):1903–1926
D’hont A, Denoeud F, Aury JM et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217
Dewitte W, Riou-Khamlichi C, Scofield S et al (2003) Altered cell cycle distribution, hyperplasia, and inhibited differentiation in Arabidopsis caused by the D-type cyclin CYCD3. Plant Cell 15(1):79–92
Dharmasiri N, Dharmasiri S, Estelle M et al (2005) The F-box protein TIR1 is an auxin receptor. Nature 435(7041):441–445
Dobzhansky T (2013) Nothing in biology makes sense except in the light of evolution. Am Biol Teach 75(2):87–91
Domozych DS (2014) Penium margaritaceum: a unicellular model organism for studying plant cell wall architecture and dynamics. Plan Theory 3(4):543–558
Dong J, MacAlister CA, Bergmann DC (2009) BASL controls asymmetric cell division in Arabidopsis. Cell 137(7):1320–1330
Duan YB, Li J, Qin RY et al (2016) Identification of a regulatory element responsible for salt induction of rice OsRAV2 through ex situ and in situ promoter analysis. Plant Mol Biol 90(1-2):49–62
Feldmann KA, Marks MD (1987) Agrobacterium-mediated transformation of germinating seeds of Arabidopsis thaliana: a non-tissue culture approach. Mol Gen Genet 208(1):1–9
Flavell R (2009) Role of model plant species. Plant Genomics:1–18
Gage JL, Monier B, Giri A et al (2020) Ten years of the maize nested association mapping population: impact, limitations, and future directions. Plant Cell 32(7):2083–2093
Gan D, Zhang J, Jiang H et al (2010) Bacterially expressed dsRNA protects maize against SCMV infection. Plant Cell Rep 29(11):1261–1268
Gazzarrini S, McCourt P (2003) Cross-talk in plant hormone signalling: what Arabidopsis mutants are telling us. Ann Bot 91(6):605–612
Goldstein B, King N (2016) The future of cell biology: emerging model organisms. Trends Cell Biol 26(11):818–824
Hauge BM, Hanley SM, Cartinhour S et al (1993) An integrated genetic/RFLP map of the Arabidopsis thaliana genome. Plant J 3(5):745–754
Hemerly AS, Ferreira P, de Almeida EJ (1993) cdc2a expression in Arabidopsis is linked with competence for cell division. Plant Cell 5(12):1711–1723
Holzinger A, Becker B et al (2015) Desiccation tolerance in the streptophyte green alga Klebsormidium: the role of phytohormones. Commun Integr Biol 8(4):e1059978
Hori K, Maruyama F, Fujisawa T et al (2014) Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat Commun 5(1):1–9
Huala E, Dickerman AW, Garcia-Hernandez M et al (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 29(1):102–105
Hubble E (2005) So much more to know. Science 309:78–102. https://doi.org/10.1126/science.309.5731.78b
Izawa T, Shimamoto K (1996) Becoming a model plant: the importance of rice to plant science. Trends Plant Sci 1(3):95–99
Jackson SA (2016) Rice: the first crop genome. Rice 9(1):1–3
Jacquemin J, Bhatia D, Singh K et al (2013) The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Curr Opin Plant Biol 16(2):147–156
Jiang J (2019) Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosom Res 27(3):153–165
Jiang J, Xing F, Zeng X et al (2018) RicyerDB: a database for collecting rice yield-related genes with biological analysis. Int J Biol Sci 14(8):965
Ju C, Van de Poel B, Cooper ED et al (2015) Conservation of ethylene as a plant hormone over 450 million years of evolution. Nat Plants 1(1):1–7
Kawahara Y, de la Bastide M, Hamilton JP et al (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6(1):1–10
Kim YA, Moon H, Park CJ (2019) CRISPR/Cas9-targeted mutagenesis of Os8N3 in rice to confer resistance to Xanthomonas oryzae pv. oryzae. Rice 12(1):1–3
Koornneef M, Meinke D (2010) The development of Arabidopsis as a model plant. Plant J 61(6):909–921
Krumholz EW, Yang H, Weisenhorn P et al (2012) Genome-wide metabolic network reconstruction of the picoalga Ostreococcus. J Exp Bot 63(6):2353–2362
Kurata N, Yamazaki Y (2006) Oryzabase. An integrated biological and genome information database for rice. Plant Physiol 140(1):12–17
Laibach F. (1943) Arabidopsis thaliana (L.) Heynh. als Objekt für genetische und entwicklungsphysiologische Untersuchungen. Bot Archiv 44: 439-455
Langridge J (1955) Biochemical mutations in the crucifer Arabidopsis thaliana (L.). Heynh Nat 176(4475):260–261
Leutwiler LS, Hough-Evans BR, Meyerowitz EM (1984) The DNA of Arabidopsis thaliana. Mol Gen Genet 194(1):15–23
Li H, Peng Z, Yang X et al (2013) Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet 45(1):43–50
Lou D, Wang H, Liang G et al (2017) OsSAPK2 confers abscisic acid sensitivity and tolerance to drought stress in rice. Front Plant Sci 8:993
McClintock B (1941) The stability of broken ends of chromosomes in Zea mays. Genetics 26(2):234
Mendel, G., 1996. Experiments in plant hybridization (1865). (Verhandlungen des naturforschenden Vereins Brünn.) Available online: www. mendelweb. org/Mendel. html (accessed on 1 January 2013)
Merchant SS, Prochnik SE, Vallon O et al (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848):245–250
Meyerowitz EM (2001a) Prehistory and history of arabidopsis research. Erratum 125(4):2203
Meyerowitz EM (2001b) Prehistory and history of Arabidopsis research. Plant Physiol 125(1):15–19
Ming R, VanBuren R, Wai CM et al (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47(12):1435–1442
Mondal TK, Rawal HC, Chowrasia S et al (2018) Draft genome sequence of first monocot-halophytic species Oryza coarctata reveals stress-specific genes. Sci Rep 8(1):1–3
Nannas NJ, Dawe RK (2015) Genetic and genomic toolbox of Zea mays. Genetics 199(3):655–669
Nagamura Y, Antonio BA, Sato Y et al (2011) Rice TOGO Browser: a platform to retrieve integrated information on rice functional and applied genomics. Plant Cell Physiol 52(2):230–237
Nakamura Y (2018) Rice starch biotechnology: rice endosperm as a model of cereal endosperms. Starch-Stärke 70(1-2):1600375
Narsai R, Castleden I, Whelan J (2010) Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana. BMC Plant Biol 10(1):1–25
Nelson DL, Lehninger AL, Cox MM (2008) Lehninger principles of biochemistry. Macmillan
Nishimura MT, Dangl JL (2010) Arabidopsis and the plant immune system. Plant J 61(6):1053–1066
Nystedt B, Street NR, Wetterbom A et al (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497(7451):579–584
Parker D, Beckmann M, Enot DP et al (2008) Rice blast infection of Brachypodium distachyon as a model system to study dynamic host/pathogen interactions. Nat Protoc 3(3):435
Potuschak T, Lechner E, Parmentier Y et al (2003) EIN3-dependent regulation of plant ethylene hormone signaling by two Arabidopsis F box proteins: EBF1 and EBF2. Cell 115(6):679–689
Prochnik SE, Umen J, Nedelcu AM et al (2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science 329(5988):223–226
Provart NJ, Alonso J, Assmann SM et al (2016) 50 years of Arabidopsis research: highlights and future directions. New Phytol 209(3):921–944
Pruitt RE, Meyerowitz EM (1986) Characterization of the genome of Arabidopsis thaliana. J Mol Biol 187(2):169–183
Rédei GP (1962) Supervital mutants of Arabidopsis. Genetics 47(4):443
Rédei GP (1975) Arabidopsis as a genetic tool. Annu Rev Genet 9(1):111–127
Rédei GP (1992) A heuristic glance at the past of Arabidopsis genetics. Methods Arabidopsis Res 12:1–5
Rine J (2013) A future of the model organism model. Mol Biol Cell 25(5):549–553
Rhoades MM (1984) The early years of maize genetics. Annu Rev Genet 18(1):1–30
Romero FM, Gatica-Arias A (2019) CRISPR/Cas9: development and application in rice breeding. Rice Sci 26(5):265–281
Sakai H, Lee SS, Tanaka T et al (2013) Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol 54(2):e6–e6
Saldivar SS (2016) Cereals: types and composition. In: Caballero B, Finglas P, Toldrá F (eds) 2015 Encyclopedia of food and health (Edited Book). Academic Press
Settles AM, Holding DR, Tan BC et al (2007) Sequence-indexed mutations in maize using the Uniform Mu transposon-tagging population. BMC Genomics 8(1):1–2
Shi J, Gao H, Wang H et al (2017) ARGOS 8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol J 15(2):207–216
Shoji T, Narita NN, Hayashi K et al (2004) Plant-specific microtubule-associated protein SPIRAL2 is required for anisotropic growth in Arabidopsis. Plant Physiol 136(4):3933–3944
Singh R, Ong-Abdullah M, Low ET et al (2013) Oil palm genome sequence reveals divergence of interfertile species in old and new worlds. Nature 500(7462):335–339
Sohn EJ, Kim ES, Zhao M et al (2003) Rha1, an Arabidopsis Rab5 homolog, plays a critical role in the vacuolar trafficking of soluble cargo proteins. Plant Cell 15(5):1057–1070
Somerville C, Koornneef M (2002) A fortunate choice: the history of Arabidopsis as a model plant. Nat Rev Genet 3(11):883–889
Strable J, Scanlon MJ (2009) Maize (Zea mays): a model organism for basic and applied research in plant biology. Cold Spring Harb Protoc 10:pdb-emo132
Suárez-López P, Wheatley K, Robson F et al (2001) CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410(6832):1116–1120
Szövényi P, Frangedakis E, Ricca M et al (2015) Establishment of Anthoceros agrestis as a model species for studying the biology of hornworts. BMC Plant Biol 15(1):1–7
Thakare D, Zhang J, Wing RA et al (2017) Aflatoxin-free transgenic maize using host-induced gene silencing. Sci Adv 3(3):e1602382
Van Buren R, Bryant D, Edger PP et al (2015) Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 527(7579):508–511
Vij S, Gupta V, Kumar D et al (2006) Decoding the rice genome. BioEssays 28(4):421–432
Wang D, Xia Y, Li X et al (2012a) The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. Nucleic Acids Res 41(D1):D1199–D1205
Wang M, Yan J, Zhao J, Song W, Zhang X, Xiao Y, Zheng Y (2012b) Genome-wide association study (GWAS) of resistance to head smut in maize. Plant Sci 196:125–131
Wang X, Wang H, Liu S et al (2016) Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings. Nat Genet 48(10):1233–1241
Wang P, Hendron RW, Kelly S (2017) Transcriptional control of photosynthetic capacity: conservation and divergence from Arabidopsis to rice. New Phytol 216(1):32–45
Ware D, Jaiswal P, Ni J et al (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Res 30(1):103–105
Wu Y, Messing J (2012) RNA interference can rebalance the nitrogen sink of maize seeds without losing hard endosperm. PLoS One 7(2):e32850
Yan H, Jiang J (2007) Rice as a model for centromere and heterochromatin research. Chromosome Res 15(1):77–84
Yanofsky MF, Ma H, Bowman JL et al (1990) The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346(6279):35–39
Yu Q, Jalaludin A, Han H et al (2015) Evolution of a double amino acid substitution in the 5-enolpyruvylshikimate-3-phosphate synthase in Eleusine indica conferring high-level glyphosate resistance. Plant Physiol 167(4):1440–1447
Zhang X, Henriques R, Lin SS et al (2006) Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method. Nat Protoc 1(2):641
Zhang ZY, Fu FL, Gou L et al (2010) RNA interference-based transgenic maize resistant to maize dwarf mosaic virus. J Plant Biol 53(4):297–305
Zhang J, Zhang X, Chen R (2020) Generation of transgene-free Semidwarf maize plants by gene editing of gibberellin-oxidase20-3 using CRISPR/Cas9. Front Plant Sci 11:1048
Zheng J, Zhang H, Dong S et al (2014) High yield exfoliation of two-dimensional chalcogenides using sodium naphthalenide. Nat Commun 5(1):1–7
Zimin A, Stevens KA, Crepeau MW et al (2014) Sequencing and assembly of the 22-Gb loblolly pine genome. Genetics 196(3):875–890
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Ray, S. et al. (2022). Model Plants in Genomics. In: Singh, R.L., Mondal, S., Parihar, A., Singh, P.K. (eds) Plant Genomics for Sustainable Agriculture. Springer, Singapore. https://doi.org/10.1007/978-981-16-6974-3_9
Download citation
DOI: https://doi.org/10.1007/978-981-16-6974-3_9
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-16-6973-6
Online ISBN: 978-981-16-6974-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)