Plant phenome to genome: a mini-review
Rudi AppelsCentre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia. Email: rudiappels5@gmail.com
Functional Plant Biology 39(7) iii-viii https://doi.org/10.1071/FPv39n7_FO
Published: 12 July 2012
Abstract
Rapid advances in biotechnologies have provided a template for defining the genome–transcriptome–proteome in many plant species and these advances now highlight a particular challenge to link the molecular biology–based studies to changes in the phenome of plant species. Selected examples are provided to review advances in defining environment–phenotype interactions, the genome–transcriptome–proteome in plants and translating research outputs more broadly to society. The specific examples include computer modelling of plant phenotypes and responses to environmental signals, advances in small molecule signal transduction, visualising macromolecules and defining the complex genomes that are important to society. The need to translate research outputs to society more broadly is also discussed.
References
Bao Y, Hu G, Flagel LE, Salmon A, Bezanilla M, Paterson AH, Wang Z, Wendel JF (2011) Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium). Proceedings of the National Academy of Sciences of the United States of America 108, 21 152–21 157.| Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium).Crossref | GoogleScholarGoogle Scholar |
Bayer E, Smith R, Mandel T, Nakayama N, Sauer M, Prusinkiewicz P, Kuhlemeier C (2009) Integration of transport-based models for phyllotaxis and midvein formation. Genes & Development 23, 373–384.
| Integration of transport-based models for phyllotaxis and midvein formation.Crossref | GoogleScholarGoogle Scholar |
Casey BJ, Soliman F, Bath KG, Glatt CE (2010) Imaging genetics and development: challenges and promises. Human Brain Mapping 31, 838–851.
| Imaging genetics and development: challenges and promises.Crossref | GoogleScholarGoogle Scholar |
Crane PR, Friis EM, Chaloner WG (2010) Darwin and the evolution of flowers. Philosophical Transactions Royal Society B 365, 347–350.
| Darwin and the evolution of flowers.Crossref | GoogleScholarGoogle Scholar |
Crisp MD, Cook LG (2009) Explosive radiation or cryptic mass extinction? Interpreting signatures in molecular phylogenies. Evolution 63, 2257–2265.
| Explosive radiation or cryptic mass extinction? Interpreting signatures in molecular phylogenies.Crossref | GoogleScholarGoogle Scholar |
Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Carlson JE, Arumuganathan K, Barakat A, Albert VA, Ma H, de Pamphilis CW (2006) Widespread genome duplications throughout the history of flowering plants. Genome Research 16, 738–749.
| Widespread genome duplications throughout the history of flowering plants.Crossref | GoogleScholarGoogle Scholar |
Deppermann K, Zhang Q, Hinchey TB (2007) ‘Automated seed sampler and methods of sampling, testing and bulking seeds.’ European patent application, EP 1 869 961 A2.
Doležel J Vrána J Šafář J Bartoš J Kubaláková M Šimková H 2012
Fedoroff NV, Battisti DS, Beachy RN, Cooper PJM, Fischhoff DA, Hodges CN, Knauf VC, Lobell D, Mazur BJ, Molden D, Reynolds MP, Ronald PC, Rosegrant MW, Sanchez PA, Vonshak A, Zhu J-K (2010) Radically rethinking agriculture for the 21st century. Science 327, 833–834.
| Radically rethinking agriculture for the 21st century.Crossref | GoogleScholarGoogle Scholar |
Flagel LE, Wendel JF (2010) Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytologist 186, 184–193.
| Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation.Crossref | GoogleScholarGoogle Scholar |
Friis EM, Pedersen KR, Crane PR (2010) Diversity in obscurity: fossil flowers and the early history of angiosperms. Philosophical Transactions Royal Society B 365, 369–382.
| Diversity in obscurity: fossil flowers and the early history of angiosperms.Crossref | GoogleScholarGoogle Scholar |
Fujii S, Hayashi T, Mizuno K (2010) Sucrose synthase is an integral component of the cellulose synthesis machinery. Plant & Cell Physiology 51, 294–301.
| Sucrose synthase is an integral component of the cellulose synthesis machinery.Crossref | GoogleScholarGoogle Scholar |
Gu Y, Kaplinsky N, Bringmann M, Cobb A, Carroll A, Sampathkumar A, Baskin TI, Persson S, Somerville CR (2010) Identification of a cellulose synthase-associated protein required for cellulose biosynthesis. Proceedings of the National Academy of Sciences of the United States of America 107, 12 866–12 871.
| Identification of a cellulose synthase-associated protein required for cellulose biosynthesis.Crossref | GoogleScholarGoogle Scholar |
Guyot R, Yahiaoui N, Feuillet C, Keller B (2004) In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S. Functional & Integrative Genomics 4, 47–58.
| In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S.Crossref | GoogleScholarGoogle Scholar |
Hamamura Y, Saito C, Awai C, Kurihara D, Miyawaki A, Nakagawa T, Kanaoka MM, Sasaki N, Nakano A, Berger F, Higashiyama T (2011) Live-cell imaging reveals the dynamics of two sperm cells during double fertilization in Arabidopsis thaliana. Current Biology 21, 497–502.
| Live-cell imaging reveals the dynamics of two sperm cells during double fertilization in Arabidopsis thaliana.Crossref | GoogleScholarGoogle Scholar |
Heisler MG, Hamant O, Krupinski P, Uyttewaal M, Ohno C, Jonsson H, Traas J, Meyerowitz EM (2010) Alignment between PIN1 polarity and microtubule orientation in the shoot apical meristem reveals a tight coupling between morphogenesis and auxin transport. PLoS Biology 8, e1000516
| Alignment between PIN1 polarity and microtubule orientation in the shoot apical meristem reveals a tight coupling between morphogenesis and auxin transport.Crossref | GoogleScholarGoogle Scholar |
Higashiyama T (2010) Peptide signaling in pollen–pistil interactions. Plant & Cell Physiology 51, 177–189.
| Peptide signaling in pollen–pistil interactions.Crossref | GoogleScholarGoogle Scholar |
Hirakawa H, Nakamura Y, Kaneko T, Isobe S, Sakai H, Kato T, Hibino T, Sasamoto S, Watanabe A, Yamada M, Nakayama S, Fujishiro T, Kishida Y, Kohara M, Tabata S, Sato S (2011) Survey of the genetic information carried in the genome of Eucalyptus camaldulensis. Plant Biotechnology (Sheffield, England) 28, 471–480.
| Survey of the genetic information carried in the genome of Eucalyptus camaldulensis.Crossref | GoogleScholarGoogle Scholar |
Hu G, Houston NL, Pathak D, Schmidt L, Thelen JJ, Wendel JF (2011) Genomically biased accumulation of seed storage proteins in allopolyploid cotton. Genetics 189, 1103–1115.
| Genomically biased accumulation of seed storage proteins in allopolyploid cotton.Crossref | GoogleScholarGoogle Scholar |
Jaiswal P, Ware D, Ni J, Chang K, Zhao W, Schmidt S, Pan X, Clark K, Teytelman L, Cartinhour S, Stein L, McCouch S (2002) Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics 3, 132–136.
| Gramene: development and integration of trait and gene ontologies for rice.Crossref | GoogleScholarGoogle Scholar |
Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006) Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Research 34, D717–723.
Ji X, Dong B, Shiran B, Talbot JM, Edlington EJ, Hughes T, White GR, Gubler F, Dolferus R (2011) Control of abscisic acid catabolism and abscisic acid homeostasis is important for reproductive stage stress tolerance in cereals. Plant Physiology 156, 647–662.
| Control of abscisic acid catabolism and abscisic acid homeostasis is important for reproductive stage stress tolerance in cereals.Crossref | GoogleScholarGoogle Scholar |
Johnson AAT, Kyriacou B, Callahan DL, Carruthers L, Stangoulis J, Lombi E, Tester M (2011) Constitutive overexpression of the OsNAS gene family reveals single-gene strategies for effective iron- and zinc-biofortification of rice endosperm. PLoS ONE 6, e24476
| Constitutive overexpression of the OsNAS gene family reveals single-gene strategies for effective iron- and zinc-biofortification of rice endosperm.Crossref | GoogleScholarGoogle Scholar |
Joudi M, Ahmadi A, Mohamadi VM, Abbasi A, Vergauwen R, Mohammadi H, Van den Ende W (2012) Comparison of fructan dynamics in two wheat cultivars with different capacities of accumulation and remobilization under drought stress. Physiologia Plantarum 144, 1–12.
| Comparison of fructan dynamics in two wheat cultivars with different capacities of accumulation and remobilization under drought stress.Crossref | GoogleScholarGoogle Scholar |
Khanna R, Kronmiller B, Maszle DR, Coupland G, Holm M, Mizuno T, Wu S-H (2009) The Arabidopsis B-box Zinc finger family. The Plant Cell 21, 3416–3420.
| The Arabidopsis B-box Zinc finger family.Crossref | GoogleScholarGoogle Scholar |
Komori R, Amano Y, Ogawa-Ohnishi M, Matsubayashi Y (2009) Identification of tyrosylprotein sulfotransferase in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 106, 15 067–15 072.
| Identification of tyrosylprotein sulfotransferase in Arabidopsis.Crossref | GoogleScholarGoogle Scholar |
Kramer EM (2004) PIN and AUX/LAX proteins: their role in auxin accumulation. Trends in Plant Science 9, 578–582.
| PIN and AUX/LAX proteins: their role in auxin accumulation.Crossref | GoogleScholarGoogle Scholar |
Leach J, McCouch S, Slezak T, Sasaki T, Wessler S (2002) Why finishing the rice genome matters. Science 296, 45
| Why finishing the rice genome matters.Crossref | GoogleScholarGoogle Scholar |
Leivar P, Quail PH (2011) PIFs: pivotal components in a cellular signaling hub. Trends in Plant Science 16, 19–28.
| PIFs: pivotal components in a cellular signaling hub.Crossref | GoogleScholarGoogle Scholar |
Li N, Zhang D-S, Liu H-S, Yin C-S, Li X-X, Liang W-Q, Yuan Z, Xu B, Chu H-W, Wang J, Wen T-Q, Huang H, Luo D, Ma H, Zhang D-B (2006) The rice Tapetum Degeneration Retardation gene is required for tapetum degeneration and anther development. The Plant Cell 18, 2999–3014.
| The rice Tapetum Degeneration Retardation gene is required for tapetum degeneration and anther development.Crossref | GoogleScholarGoogle Scholar |
Liu L, Liu C, Hou X, Xi W, Shen L, Tao Z, Wang Y, Yu H (2012) FTIP1 is an essential regulator required for florigen transport. PLoS Biology 10, e1001313
| FTIP1 is an essential regulator required for florigen transport.Crossref | GoogleScholarGoogle Scholar |
Matsuzaki Y, Ogawa-Ohnishi M, Mori A, Matsubayashi Y (2010) Secreted peptide signals required for maintenance of root stem cell niche in Arabidopsis. Science 329, 1065–1067.
| Secreted peptide signals required for maintenance of root stem cell niche in Arabidopsis.Crossref | GoogleScholarGoogle Scholar |
McIntyre CL, Seung D, Casu RE, Rebetzke GJ, Shorter R, Xue GP (2012) Genotypic variation in the accumulation of water soluble carbohydrates in wheat. Functional Plant Biology 39, 560–568.
| Genotypic variation in the accumulation of water soluble carbohydrates in wheat.Crossref | GoogleScholarGoogle Scholar |
Meier U (2001) ‘Growth stage of mono- and dicotyledonous plants, second edition.’ (Federal Biological Research Centre for Agriculture and Forestry) Monograph. (Blackwell Wissenschafts-Verlag: Berlin)
Moghaddam MRB, Van den Ende W (2012) Sugars and plant innate immunity. Journal of Experimental Botany
| Sugars and plant innate immunity.Crossref | GoogleScholarGoogle Scholar |
Paiva JA, Prat E, Vautrin S, Santos MD, San-Clemente H, Brommonschenkel S, Fonseca PG, Grattapaglia D, Song X, Ammiraju JS, Kudrna D, Wing RA, Freitas AT, Bergès H, Grima-Pettenati J (2011) Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries. BMC Genomics 12, 137
| Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries.Crossref | GoogleScholarGoogle Scholar |
Paredez AR, Somerville CR, Ehrhardt DW (2006) Visualization of cellulose synthase demonstrates functional association with microtubules. Science 312, 1491–1495.
| Visualization of cellulose synthase demonstrates functional association with microtubules.Crossref | GoogleScholarGoogle Scholar |
Parish RW, Phan HA, Iacuone S, Li SF (2012) Tapetal development and abiotic stress: a centre of vulnerability. Functional Plant Biology 39, 553–559.
| Tapetal development and abiotic stress: a centre of vulnerability.Crossref | GoogleScholarGoogle Scholar |
Powell N, Ji X, Ravash R, Edlington J, Dolferus R (2012) Yield stability for cereals in a changing climate. Functional Plant Biology 39, 539–552.
| Yield stability for cereals in a changing climate.Crossref | GoogleScholarGoogle Scholar |
Price DRG, Gatehouse JA (2008) RNAi-mediated crop protection against insects. Trends in Biotechnology 26, 393–400.
| RNAi-mediated crop protection against insects.Crossref | GoogleScholarGoogle Scholar |
Prusinkiewicz P, Runions A (2012) Computational models of plant development and form. New Phytologist 193, 549–569.
| Computational models of plant development and form.Crossref | GoogleScholarGoogle Scholar |
Rapp RA, Udall JA, Wendel JF (2009) Genomic expression dominance in allopolyploids. BMC Biology 7, 18
| Genomic expression dominance in allopolyploids.Crossref | GoogleScholarGoogle Scholar |
Rapp RA, Haigler CH, Flagel L, Hovav RH, Udall JA, Wendel JF (2010) Gene expression in developing fibres of upland cotton (Gossypium hirsutum L.) was massively altered by domestication. BMC Biology 8, 139
| Gene expression in developing fibres of upland cotton (Gossypium hirsutum L.) was massively altered by domestication.Crossref | GoogleScholarGoogle Scholar |
Rasmussen A, Mason MG, De Cuyper C, Brewer PB, Herold S, Agusti J, Geelen D, Greb T, Goormachtig S, Beeckman T, Beveridge CA (2012) Strigolactones suppress adventitious rooting in Arabidopsis and pea. Plant Physiology 158, 1976–1987.
| Strigolactones suppress adventitious rooting in Arabidopsis and pea.Crossref | GoogleScholarGoogle Scholar |
Reinhardt D, Pesce ER, Stieger P, Mandel T, Baltensperger K, Bennett M, Traas J, Friml J, Kuhlemeier C (2003) Regulation of phyllotaxis by polar auxin transport. Nature 426, 255–260.
| Regulation of phyllotaxis by polar auxin transport.Crossref | GoogleScholarGoogle Scholar |
Robinson S, de Reuille PB, Chan J, Bergmann D, Prusinkiewicz P, Coen E (2011) Generation of spatial patterns through cell polarity switching. Science 333, 1436–1440.
| Generation of spatial patterns through cell polarity switching.Crossref | GoogleScholarGoogle Scholar |
Roh , Yul J, Choi JY, Li MS, Jin BR, Je YH (2007) Bacillus thuringiensis as a specific, safe, and effective tool for insect pest control. Journal of Microbiology and Biotechnology 17, 547–559.
Siebner HR, Callicott JH, Sommer T, Mattay VS (2009) From the genome to the phenome and back: linking genes with human brain function and structure using genetically informed neuroimaging. Neuroscience 164, 1–6.
| From the genome to the phenome and back: linking genes with human brain function and structure using genetically informed neuroimaging.Crossref | GoogleScholarGoogle Scholar |
Tilman D, Balzer C, Hill J, Belfort BL (2011) Global food demand and the sustainable intensification of agriculture. Proceedings of the National Academy of Sciences of the United States of America 108, 20 260–20 264.
| Global food demand and the sustainable intensification of agriculture.Crossref | GoogleScholarGoogle Scholar |
Tymowska-Lalanne Z, Kreis M (1998) The plant invertases: physiology, biochemistry, and molecular biology. Advances in Botanical Research 28, 71–117.
| The plant invertases: physiology, biochemistry, and molecular biology.Crossref | GoogleScholarGoogle Scholar |
Volis S, Bohrer G, Oostermeijer G, Van Tienderen P (2005) Regional consequences of local population demography and genetics in relation to habitat management in Gentiana pneumonanthe. Conservation Biology 19, 357–367.
| Regional consequences of local population demography and genetics in relation to habitat management in Gentiana pneumonanthe.Crossref | GoogleScholarGoogle Scholar |
Wabnik K, Kleine-Vehn J, Balla J, Sauer M, Naramoto S, Reinohl V, Merks RMH, Govaerts W, Friml J (2010) Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling. Molecular Systems Biology 6, 447
| Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling.Crossref | GoogleScholarGoogle Scholar |
Webster H, Keeble G, Dell B, Fosu-Nyarko J, Mukai Y, Moolhuijzen P, Bellgard M, Jia J, Kong X, Feuillet C, Choulet F, International Wheat Genome Sequencing Consortium Appels R (2012) Genome-level identification of cell wall invertase genes in wheat for the study of drought tolerance. Functional Plant Biology 39, 569–579.
| Genome-level identification of cell wall invertase genes in wheat for the study of drought tolerance.Crossref | GoogleScholarGoogle Scholar |
Yue G, Zhuang Y, Li Z, Sun L, Zhang J (2008) Differential gene expression analysis of maize leaf at heading stage in response to water-deficit stress. Bioscience Reports 28, 125–134.
| Differential gene expression analysis of maize leaf at heading stage in response to water-deficit stress.Crossref | GoogleScholarGoogle Scholar |
Zhang J, Dell B, Conocono E, Waters I, Setter T, Appels R (2009) Water deficit in wheat: fructan exohydrolase (1-FEH) mRNA expression and relationship to soluble carbohydrate concentration in two varieties. New Phytologist 181, 843–850.
| Water deficit in wheat: fructan exohydrolase (1-FEH) mRNA expression and relationship to soluble carbohydrate concentration in two varieties.Crossref | GoogleScholarGoogle Scholar |