Sink or swim: submergence tolerance and survival strategies in Rorippa and
Arabidopsis
Akman, M.
Publication date
2012
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Citation for published version (APA):
Akman, M. (2012). Sink or swim: submergence tolerance and survival strategies in Rorippa
and Arabidopsis.
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REFERENCES
REFERENCES
Abramoff MD, Magalhaes PJ, Ram SJ. 2004. Image Processing with ImageJ. Biophotonics
International 11: 36-42.
Akman M, Bhikharie A, McLean E, Boonman A, Visser E, Schranz M, Tienderen P. 2012. Wait or Escape? Contrasting submergence tolerance strategies of Rorippa
amphibia, Rorippa sylvestris and their hybrid. Annals of Botany 109: 1263-1276.
Al-Shehbaz IA, Beilstein MA, Kellogg EA. 2006. Systematics and phylogeny of the
Brassicaceae: an overview. Plant Systematics and Evolution 259: 89-120.
Alonso-Blanco C, Aarts MGM, Bentsink L, Keurentjes JJB, Reymond M, Vreugdenhil D, Koornneef M. 2009. What Has Natural Variation Taught Us about Plant
Development, Physiology, and Adaptation? The Plant Cell Online 21(7): 1877-1896.
Armstrong J, Armstrong W. 1999. Phragmites die-back: toxic effects of propionic, butyric
and caproic acids in relation to pH. New Phytologist 142(2): 201-217.
Armstrong W 1980. Aeration in Higher Plants. In: Woolhouse HW ed. Advances in Botanical
Research: Academic Press, 225-332.
Arnell N, Liu C. 2001. Climate Change 2001: hydrology and water resources. in Report
Intergovernmental Panel on Climate Change.
Bailey-Serres J, Fukao T, Gibbs DJ, Holdsworth MJ, Lee SC, Licausi F, Perata P, Voesenek LACJ, van Dongen JT. 2012. Making sense of low oxygen sensing.
Trends in Plant Science 17(3): 129-138.
Bailey-Serres J, Voesenek LACJ. 2008. Flooding stress: acclimations and genetic diversity.
Annual Review of Plant Biology 59: 313-339.
Bailey-Serres J, Voesenek LACJ. 2010. Life in the balance: a signaling network controlling
survival of flooding. Current Opinion in Plant Biology 13: 489-494.
Bannenberg G, Martínez M, Hamberg M, Castresana C. 2009. Diversity of the Enzymatic
Activity in the Lipoxygenase Gene Family of Arabidopsis thaliana. Lipids 44(2): 85-95.
Banti V, Loreti E, Novi G, Santaniello A, Alpi A, Perata P. 2008. Heat acclimation and
cross-tolerance against anoxia in Arabidopsis. Plant, Cell & Environment 31(7): 1029-1037.
Beckett PM, Armstrong W, Justin SHFW, Armstrong J. 1988. On the relative importance
of convective and diffusive gas flows in plant aeration. New Phytologist 110: 463-468.
Benschop JJ, Jackson MB, Gühl K, Vreeburg RAM, Croker SJ, Peeters AJM, Voesenek LACJ. 2005. Contrasting interactions between ethylene and abscisic acid in Rumex
species differing in submergence tolerance. The Plant Journal 44: 756-768.
Bentsink Ln, Jowett J, Hanhart CJ, Koornneef M. 2006. Cloning of DOG1, a quantitative
trait locus controlling seed dormancy in Arabidopsis. Proceedings of the National
Academy of Sciences 103(45): 17042-17047.
Bergelson J, Roux F. 2010. Towards identifying genes underlying ecologically relevant
Bleeker W. 2004. Genetic variation and self-incompatibility within and outside a Rorippa
hybrid zone (Brassicaceae). Plant Systematics and Evolution 246: 35-44.
Bleeker W. 2007. Interspecific hybridization in Rorippa (Brassicaceae): Patterns and
processes. Systematics and Biodiversity 5: 311-319.
Bleeker W, Hurka H. 2001. Introgressive hybridization in Rorippa (Brassicaceae): Gene
flow and its consequences in natural and anthropogenic habitats. Molecular Ecology
10: 2013-2022.
Blokhina O, Virolainen E, Fagerstedt KV. 2003. Antioxidants, Oxidative Damage and
Oxygen Deprivation Stress: a Review. Annals of Botany 91(2): 179-194.
Blom CWPM. 1999. Adaptations to flooding stress: From plant community to molecule.
Plant Biology 1: 261-273.
Branco-Price C, Kaiser KA, Jang CJH, Larive CK, Bailey-Serres J. 2008. Selective
mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. The Plant Journal
56(5): 743-755.
Branco-Price C, Kawaguchi R, Ferreira RB, Bailey-Serres J. 2005. Genome-wide
Analysis of Transcript Abundance and Translation in Arabidopsis Seedlings Subjected to Oxygen Deprivation. Annals of Botany 96(4): 647-660.
Chen L-Q, Qu X-Q, Hou B-H, Sosso D, Osorio S, Fernie AR, Frommer WB. 2012.
Sucrose Efflux Mediated by SWEET Proteins as a Key Step for Phloem Transport.
Science 335(6065): 207-211.
Chen THH, Murata N. 2002. Enhancement of tolerance of abiotic stress by metabolic
engineering of betaines and other compatible solutes. Current Opinion in Plant
Biology 5: 250-257.
Chen X, Huber H, de Kroon H, Peeters AJM, Poorter H, Voesenek LACJ, Visser EJW. 2009. Intraspecific variation in the magnitude and pattern of flooding-induced shoot
elongation in Rumex palustris. Annals of Botany 104: 1057-1067.
Chen X, Visser EJW, de Kroon H, Pierik R, Voesenek LACJ, Huber H. 2011. Fitness
consequences of natural variation in flooding-induced shoot elongation in Rumex
palustris. New Phytologist 190: 409-420.
Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW. 2010. Global Gene Expression
Responses to Waterlogging in Roots and Leaves of Cotton (Gossypium hirsutum
L.). Plant and Cell Physiology 51(1): 21-37.
Colmer TD, Pedersen O. 2007. Underwater photosynthesis and respiration in leaves
of submerged wetland plants: gas films improve CO2 and O2 exchange. New
Phytologist 0(0).
Colmer TD, Voesenek LACJ. 2009. Flooding tolerance: suites of plant traits in variable
environments. Functional Plant Biology 36(8): 665-681.
Cook CDK. 1999. The number and kinds of embryo-bearing plants which have become
aquatic: a survey. Perspectives in Plant Ecology, Evolution and Systematics 2(1): 79-102.
Doerge RW, Churchill GA. 1996. Permutation Tests for Multiple Loci Affecting a
Quantitative Character. Genetics 142(1): 285-294.
REFERENCES
Durack PJ, Wijffels SE, Matear RJ. 2012. Ocean Salinities Reveal Strong Global Water
Cycle Intensification During 1950 to 2000. Science 336(6080): 455-458.
Eastmond PJ, Li Y, Graham IA. 2003. Is trehalose-6-phosphate a regulator of sugar
metabolism in plants? Journal of experimental botany 54(382): 533-537.
Flint J, Mott R. 2001. Finding the molecular basis of quantitative traits: Successes and
pitfalls Nature Reviews Genetics 2(6): 437-445.
Fukao T, Bailey-Serres J. 2008. Submergence tolerance conferred by Sub1A is mediated
by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proceedings of the
National Academy of Sciences 105(43): 16814-16819.
Fukao T, Xu K, Ronald PC, Bailey-Serres J. 2006. A variable cluster of ethylene response
factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18: 2021-2034.
Garg AK, Kim J-K, Owens TG, Ranwala AP, Choi YD, Kochian LV, Wu RJ. 2002.
Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses. Proceedings of the National Academy of Sciences 99: 15898-15903.
Gibbs DJ, Lee SC, Md Isa N, Gramuglia S, Fukao T, Bassel GW, Correia CS, Corbineau F, Theodoulou FL, Bailey-Serres J, Holdsworth MJ. 2011. Homeostatic response
to hypoxia is regulated by the N-end rule pathway in plants. Nature 479(7373): 415-418.
Groeneveld HW, Voesenek LACJ. 2003. Submergence-induced petiole elongation in
Rumex palustris is controlled by developmental stage and storage compounds. Plant and Soil 253: 115-123.
Guglielminetti L, Perata P, Alpi A. 1995. Effect of anoxia on carbohydrate metabolism in
rice seedlings. Plant Physiology 108: 735-741.
Hattori Y. 2007. A major QTL confers rapid internode elongation in response to water rise in
deepwater rice. Breeding Science 57: 305-314.
Hattori Y. 2008. Mapping of three QTLs that regulate internode elongation in deepwater
rice. Breeding Science 58: 39-46.
Hattori Y, Nagai K, Furukawa S, Song X-J, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H, Matsuoka M, Mori H, Ashikari M. 2009. The
ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460: 1026-1030.
Hinz M, Wilson IW, Yang J, Buerstenbinder K, Llewellyn D, Dennis ES, Sauter M, Dolferus R. 2010. Arabidopsis RAP2.2: An Ethylene Response Transcription
Factor That Is Important for Hypoxia Survival. Plant Physiol. 153(2): 757-772.
Hosmer D, Lemesshow S. 1999. Applied survival analysis. Regression modeling of time to
event data. Wiley series in probability and statistics. (New York, NY, USA: Wiley).
Huynh LN, VanToai T, Streeter J, Banowetz G. 2005. Regulation of flooding tolerance
of SAG12:ipt Arabidopsis plants by cytokinin. Journal of experimental botany
56(415): 1397-1407.
Jackson M, Drew M 1984. Effects of flooding on growth and metabolism of herbaceous
plants. In: TT K ed. Flooding and plant growth. New York: Academic Press, 47–128.
Jackson MB. 1985. Ethylene and responses of plants to soil waterlogging and submergence.
Jackson MB, Ram PC. 2003. Physiological and molecular basis of susceptibility and
tolerance of rice plants to complete submergence. Ann Bot 91: 227-241.
Jagadeeswaran G, Raina S, Acharya BR, Maqbool SB, Mosher SL, Appel HM, Schultz JC, Klessig DF, Raina R. 2007. Arabidopsis GH3-LIKE DEFENSE GENE 1 is
required for accumulation of salicylic acid, activation of defense responses and resistance to Pseudomonas syringae. The Plant Journal 51(2): 234-246.
Jonsell B. 1968. Studies in the North-West European species of Rorippa s. str. Symbolae
Botanicae Upsalienses 19: 1-221.
Jung K-H, Seo Y-S, Walia H, Cao P, Fukao T, Canlas PE, Amonpant F, Bailey-Serres J, Ronald PC. 2010. The Submergence Tolerance Regulator Sub1A Mediates
Stress-Responsive Expression of AP2/ERF Transcription Factors. Plant Physiol. 152(3): 1674-1692.
Keddy PA. 1984. Plant zonation on lakeshores in Nova Scotia: A test of the resource
specialization hypothesis. Journal of Ecology 72: 797-808.
Kende H, van der Knaap E, Cho H-T. 1998. Deepwater rice: A model plant to study stem
elongation. Plant Physiology 118: 1105-1110.
Kiefer E, Heller W, Ernst D. 2000. A simple and efficient protocol for isolation of functional
RNA from plant tissues rich in secondary metabolites. Plant Molecular Biology
Reporter 18(1): 33-39.
Klimesová J, Klimes L. 2007. Bud banks and their role in vegetative regeneration - A
literature review and proposal for simple classification and assessment. Perspectives
in Plant Ecology, Evolution and Systematics 8: 115-129.
Klimesova J, Kocianova A, Martinkova J. 2008. Weeds that can do both tricks: Vegetative
versus generative regeneration of the short-lived root-sprouting herbs Rorippa
palustris and Barbarea vulgaris. Weed Research 48: 131-135.
Klok EJ, Wilson IW, Wilson D, Chapman SC, Ewing RM, Somerville SC, Peacock WJ, Dolferus R, Dennis ES. 2002. Expression Profile Analysis of the Low-Oxygen
Response in Arabidopsis Root Cultures. The Plant Cell Online 14(10): 2481-2494.
Koornneef M, Reymond M, Alonso-Blanco C 2011. Natural Variation in Arabidopsis
thaliana; Genetics and Genomics of the Brassicaceae. In: Schmidt R, Bancroft I
eds.: Springer New York, 123-151.
Kreuzwieser J, Hauberg J, Howell KA, Carroll A, Rennenberg H, Millar AH, Whelan J. 2009. Differential Response of Gray Poplar Leaves and Roots Underpins Stress
Adaptation during Hypoxia. Plant Physiology 149(1): 461-473.
Kudahettige NP, Pucciariello C, Parlanti S, Alpi A, Perata P. 2011. Regulatory interplay
of the SUB1A and CIPK15 pathways in the regulation of α-amylase production in flooded rice plants. Plant Biology 13: 611-619.
Lamarck JB, 1802. Hydrogeologie.
Lamarck JB, 1809. Philosophie Zoologique ou Exposition des considérations relative à
l’histoire naturelle des animaux.
Langmead B, Trapnell C, Pop M, Salzberg S. 2009. Ultrafast and memory-efficient
alignment of short DNA sequences to the human genome. Genome Biology 10(3): R25.
REFERENCES
Lasanthi-Kudahettige R, Magneschi L, Loreti E, Gonzali S, Licausi F, Novi G, Beretta O, Vitulli F, Alpi A, Perata P. 2007. Transcript Profiling of the Anoxic Rice
Coleoptile. Plant Physiology 144(1): 218-231.
Lee SC, Mustroph A, Sasidharan R, Vashisht D, Pedersen O, Oosumi T, Voesenek LACJ, Bailey-Serres J. 2011. Molecular characterization of the submergence response of
the Arabidopsis thaliana ecotype Columbia. New Phytologist 190(2): 457-471.
Lenssen JPM, De Kroon H. 2005. Abiotic constraints at the upper boundaries of two Rumex
species on a freshwater flooding gradient. Journal of Ecology 93: 138-147.
Li Y, Roycewicz P, Smith E, Borevitz JO. 2006. Genetics of Local Adaptation in the
Laboratory: Flowering Time Quantitative Trait Loci under Geographic and Seasonal Conditions in Arabidopsis. PLoS ONE 1(1): e105.
Licausi F, Kosmacz M, Weits DA, Giuntoli B, Giorgi FM, Voesenek LACJ, Perata P, van Dongen JT. 2011. Oxygen sensing in plants is mediated by an N-end rule pathway
for protein destabilization. Nature 479(7373): 419-422.
Licausi F, Van Dongen JT, Giuntoli B, Novi G, Santaniello A, Geigenberger P, Perata P. 2010. HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect
anaerobic responses in Arabidopsis thaliana. The Plant Journal 62(2): 302-315.
Lisec J, Meyer RC, Steinfath M, Redestig H, Becher M, Witucka-Wall H, Fiehn O, Törjék O, Selbig J, Altmann T, Willmitzer L. 2008. Identification of metabolic
and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations. The Plant Journal 53(6): 960-972.
Liu F, VanToai T, Moy L, Bock G, Linford L, Quackenbush J. 2005. Global Transcription
Profiling Reveals Comprehensive Insights into Hypoxic Response in Arabidopsis 1 [w]. Plant Physiology 137(3): 1115-1129.
Livak K, Schmittgen T. 2001. Analysis of relative gene expression data using real-time
quantitative PCR and the 2-DDCT Method. Methods in Molecular Biology 25: 402-408.
Loreti E, Poggi A, Novi G, Alpi A, Perata P. 2005. A genome-wide analysis of the effects of
sucrose on gene expression in Arabidopsis seedlings under anoxia. Plant Physiology
137: 1130-1138.
Magnani E, Sjölander K, Hake S. 2004. From Endonucleases to Transcription Factors:
Evolution of the AP2 DNA Binding Domain in Plants. The Plant Cell Online 16(9): 2265-2277.
Manzur ME, Grimoldi AA, Insausti P, Striker GG. 2009. Escape from water or remain
quiescent? Lotus tenuis changes its strategy depending on depth of submergence.
Annals of Botany 104(6): 1163-1169.
May A, Berger S, Hertel T, Kock M. 2011. The Arabidopsis thaliana phosphate starvation
responsive gene AtPPsPase1 encodes a novel type of inorganic pyrophosphatase.
Biochimica et Biophysica Acta (BBA) - General Subjects 1810(2): 178-185.
Millenaar FF, Cox MCH, van Berkel YEMdJ, Welschen RAM, Pierik R, Voesenek LAJC, Peeters AJM. 2005. Ethylene-Induced Differential Growth of Petioles
in Arabidopsis. Analyzing Natural Variation, Response Kinetics, and Regulation.
Miller G, Schlauch K, Tam R, Cortes D, Torres MA, Shulaev V, Dangl JL, Mittler R. 2009. The plant NADPH oxidase RBOHD mediates rapid systemic signaling in
response to diverse stimuli. Science signaling 2(84): ra45.
Milly PCD, Wetherald RT, Dunne KA, Delworth TL. 2002. Increasing risk of great floods
in a changing climate. Nature 415: 514-517.
Mitchell-Olds T. 2001. Arabidopsis thaliana and its wild relatives: A model system for
ecology and evolution. Trends in Ecology and Evolution 16: 693-700.
Mommer L, Lenssen JPM, Huber H, Visser EJW, De Kroon H. 2006a. Ecophysiological
determinants of plant performance under flooding: A comparative study of seven plant families. Journal of Ecology 94: 1117-1129.
Mommer L, Pons TL, Visser EJW 2006b. Photosynthetic consequences of phenotypic
plasticity in response to submergence: Rumex palustris as a case study.In. Journal
of experimental botany. 283-290.
Mommer L, Pons TL, Wolters-Arts M, Venema JH, Visser EJW. 2005.
Submergence-Induced Morphological, Anatomical, and Biochemical Responses in a Terrestrial Species Affect Gas Diffusion Resistance and Photosynthetic Performance. Plant
Physiol. 139(1): 497-508.
Mommer L, Visser EJW. 2005. Underwater photosynthesis in flooded terrestrial plants: A
matter of leaf plasticity. Annals of Botany 96: 581-589.
Mustroph A, Lee SC, Oosumi T, Zanetti ME, Yang H, Ma K, Yaghoubi-Masihi A, Fukao T, Bailey-Serres J. 2010. Cross-Kingdom Comparison of Transcriptomic
Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses. Plant Physiology 152(3): 1484-1500.
Mustroph A, Zanetti ME, Jang CJH, Holtan HE, Repetti PP, Galbraith DW, Girke T, Bailey-Serres J. 2009. Profiling translatomes of discrete cell populations resolves
altered cellular priorities during hypoxia in Arabidopsis. Proceedings of the National
Academy of Sciences 106(44): 18843-18848.
Nabben RHM, Blom CWPM, Voesenek LACJ. 1999. Resistance to complete submergence
in Rumex species with different life histories: the influence of plant size and light.
New Phytologist 144(2): 313-321.
Nagai K, Hattori Y, Ashikari M. 2010. Stunt or elongate? Two opposite strategies by which
rice adapts to floods. Journal of Plant Research 123(3): 303-309.
Nakano T, Suzuki K, Fujimura T, Shinshi H. 2006. Genome-wide analysis of the ERF
gene family in Arabidopsis and Rice. Plant Physiol. 140: 411-432.
Nanjo Y, Maruyama K, Yasue H, Yamaguchi-Shinozaki K, Shinozaki K, Komatsu S. 2011. Transcriptional responses to flooding stress in roots including hypocotyl of
soybean seedlings. Plant molecular biology 77(1): 129-144.
Narsai R, Howell KA, Carroll A, Ivanova A, Millar AH, Whelan J. 2009. Defining Core
Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings. Plant Physiology 151(1): 306-322.
Nobuta K, Okrent RA, Stoutemyer M, Rodibaugh N, Kempema L, Wildermuth MC, Innes RW. 2007. The GH3 Acyl Adenylase Family Member PBS3 Regulates
Salicylic Acid-Dependent Defense Responses in Arabidopsis. Plant Physiology
REFERENCES
Normile D. 2008. Reinventing Rice to Feed the World. Science 321(5887): 330-333. Parolin P. 2009. Submerged in darkness: adaptations to prolonged submergence by woody
species of the Amazonian floodplains. Annals of Botany 103(2): 359-376.
Perata P, Alpi A. 1993. Plant responses to anaerobiosis. Plant Science 93: 1-17.
Perata P, Guglielminetti L, Alpi A. 1996. Anaerobic carbohydrate metabolism in wheat
and barley, two anoxia-intolerant cereal seeds. Journal of experimental botany 47: 999-1006.
Pierik R, van Aken JM, Voesenek LACJ. 2009. Is elongation-induced leaf emergence
beneficial for submerged Rumex species? Annals of Botany 103: 353-357.
Ram PC, Singh BB, Singh AK, Ram P, Singh PN, Singh HP, Boamfa I, Harren F, Santosa E, Jackson MB. 2002. Submergence tolerance in rainfed lowland rice:
Physiological basis and prospects for cultivar improvement through marker-aided breeding. Field Crops Research 76: 131-152.
Raskin I, Kende H. 1984. Effect of submergence on translocation, starch content and
amylolytic activity in deep-water rice. Planta 162: 556-559.
Raskin I. 1983. A method for measuring leaf volume, density, thickness, and internal gas
volume. Alexandria, VA, USA: American Society for Horticultural Science.
Rijnders JGHM, Yang Y-Y, Kamiya Y, Takahashi N, Barendse GWM, Blom CWPM, Voesenek LACJ. 1997. Ethylene enhances gibberellin levels and petiole sensitivity
in flooding-tolerant Rumex palustris but not in flooding-intolerant R. acetosa.
Planta 203(1): 20-25.
Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR. Bioinformatics 26(1): 139-140. Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier
T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. 2003. TM4: a free, open-source system for microarray data management and
analysis. Biotechniques 34(2): 374-378.
Sambrook J, Russell DW. 2001. Molecular cloning: A laboratory manual. CSHL Press,
Cold Spring Harbour, NY.
Sasidharan R, Mustroph A. 2011. Plant Oxygen Sensing Is Mediated by the N-End Rule
Pathway: A Milestone in Plant Anaerobiosis. The Plant Cell Online.
Sauter M. 2000. Rice in deep water: “How to take heed against a sea of troubles”.
Naturwissenschaften 87: 289-303.
Schranz ME, Song B-H, Windsor AJ, Mitchell-Olds T. 2007. Comparative genomics in
the Brassicaceae: a family-wide perspective. Current Opinion in Plant Biology 10: 168-175.
Schroder F, Lisso J, Mussig C. 2011. EXORDIUM-LIKE1 Promotes Growth during Low
Carbon Availability in Arabidopsis. Plant Physiology 156(3): 1620-1630.
Setter TL, Laureles EV. 1996. The beneficial effect of reduced elongation growth on
submergence tolerance of rice. Journal of experimental botany 47: 1551-1559.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: A Software Environment for Integrated Models of
Biomolecular Interaction Networks. Genome Research 13(11): 2498-2504.
Silvertown J, Dodd ME, Gowing DJG, Mountford JO. 1999. Hydrologically defined
niches reveal a basis for species richness in plant communities. Nature 400: 61-63.
Singh S, Mackill DJ, Ismail AM. 2009. Responses of SUB1 rice introgression lines to
submergence in the field: Yield and grain quality. Field Crops Research 113: 12-23.
Slater R. 1984. The extraction of total RNA by the detergent and phenol method. Nucleic
acids 2: 101-108.
Smirnoff N, Crawford RMM. 1983. Variation in the Structure and Response to Flooding of
Root Aerenchyma in some Wetland Plants. Annals of Botany 51(2): 237-249.
Smith AM, Zeeman SC. 2006. Quantification of starch in plant tissues. Nature protocols 1:
1342-1345.
Smyth G 2005. Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit
S, Irizarry R, Huber W eds. Bioinfor-matics and Computational Biology Solutions
using R and Bioconductor, R. New York: Springer, 397{420.
Sosnova M, van Diggelen R, Klimesova J. 2010. Distribution of clonal growth forms in
wetlands. Aquatic Botany 92: 33-39.
Stael S, Rocha AG, Robinson AJ, Kmiecik P, Vothknecht UC, Teige M. 2011. Arabidopsis
calcium-binding mitochondrial carrier proteins as potential facilitators of mitochondrial ATP-import and plastid SAM-import. FEBS Letters 585(24): 3935-3940.
Stepanova AN, Yun J, Likhacheva AV, Alonso JM. 2007. Multilevel Interactions between
Ethylene and Auxin in Arabidopsis Roots. Plant Cell 19(7): 2169-2185.
Stift M, Bregman R, Oostermeijer JGB, van Tienderen PH. 2010. Other tetraploid
species and conspecific diploids as sources of genetic variation for an autotetraploid.
American Journal of Botany 97(11): 1858-1866.
Stift M, Luttikhuizen PC, Visser EJW, Van Tienderen PH. 2008. Different flooding
responses in Rorippa amphibia and Rorippa sylvestris, and their modes of expression in F1 hybrids. New Phytologist 180: 229-239.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular
Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. . Molecular Biology and Evolution 28: 2731-2739.
Tang H, Bowers J, Wang X, Ming R, Alam M, Paterson A. 2008. Synteny and Collinearity
in Plant Genomes. Science 320: 486-488.
Thevelein JM, Hohmann S. 1995. Trehalose synthase: guard to the gate of glycolysis in
yeast? Trends in Biochemical Sciences 20(1): 3-10.
Thomson CJ, ArmstrongW,Waters I, Greenway H. 1990. Aerenchyma formation and
associated oxygen movement in seminal and nodal roots of wheat. Plant, Cell & Environment 13: 395–403.
van Dongen JT, Frohlich A, Ramirez-Aguilar SJ, Schauer N, Fernie AR, Erban A, Kopka J, Clark J, Langer A, Geigenberger P. 2009. Transcript and metabolite
profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants. Annals of Botany 103(2): 269-280.
REFERENCES
Van Eck WHJM, Van De Steeg HM, Blom CWPM, De Kroon H. 2004. Is tolerance
to summer flooding correlated with distribution patterns in river floodplains? A comparative study of 20 terrestrial grassland species. Oikos 107: 393-405.
Van Leur H, Raaijmakers CE, Van Dam NM. 2008. Reciprocal interactions between
the cabbage root fly (Delia radicum) and two glucosinolate phenotypes of
Barbarea vulgaris. Entomologia Experimentalis et Applicata 128: 312-322.
Vashisht D, Hesselink A, Pierik R, Ammerlaan JMH, Bailey-Serres J, Visser EJW, Pedersen O, van Zanten M, Vreugdenhil D, Jamar DCL, Voesenek LACJ, Sasidharan R. 2011. Natural variation of submergence tolerance among Arabidopsis
thaliana accessions. New Phytologist 190: 299-310.
Vervuren PJA, C. W. P. M. Blom H. de Kroon. 2003. Extreme flooding events on the Rhine
and the survival and distribution of riparian plant species. Journal of Ecology 91: 135-146.
Vidoz ML, Loreti E, Mensuali A, Alpi A, Perata P. 2010. Hormonal interplay during
adventitious root formation in flooded tomato plants. The Plant Journal 63(4): 551-562.
Voesenek L, Banga M, Rijnders J, Visser EJW, Blom C. 1996. Hormone sensitivity and
plant adaptations to flooding. Folia Geobotanica 31: 47-56.
Voesenek L, Banga M, Thier RH, Mudde CM, Harren F, Barendse G, Blom C. 1993.
Submergence-Induced Ethylene Synthesis, Entrapment, and Growth in Two Plant Species with Contrasting Flooding Resistances. Plant Physiology 103(3): 783-791.
Voesenek L, Sman AJM, Harren FJM, Blom C. 1991. Ethylene and flooding resistance:
An integration of plant hormone physiology and plant ecology.
Voesenek LACJ, Benschop JJ, Bou J, Cox MCH, Groeneveld HW, Millenaar FF, Vreeburg RAM, Peeters AJM. 2003. Interactions between plant hormones
regulate submergence induced shoot elongation in the flooding tolerant dicot Rumex
palustris. Annals of Botany 91: 205-211.
Voesenek LACJ, Blom CWPM. 1989. Growth responses of Rumex species in relation to
submergence and ethylene. Plant, Cell & Environment 12(4): 433-439.
Voesenek LACJ, Colmer TD, Pierik R, Millenaar FF, Peeters AJM. 2006. How plants
cope with complete submergence. New Phytologist 170: 213-226.
Voesenek LACJ, Rijnders JHGM, Peeters AJM, van de Steeg HM, de Kroon H. 2004. Plant hormones regulate fast shoot elongation under water: from genes to
communities. Ecology: 16-27.
Voorrips RE. 2002. MapChart: Software for the Graphical Presentation of Linkage Maps
and QTLs. Journal of Heredity 93(1): 77-78.
Vreeburg RAM, Benschop JJ, Peeters AJM, Colmer TD, Ammerlaan AHM, Staal M, Elzenga TM, Staals RHJ, Darley CP, McQueen-Mason SJ, Voesenek LACJ. 2005. Ethylene regulates fast apoplastic acidification and expansin A transcription
during submergence-induced petiole elongation in Rumex palustris. The Plant
Journal 43: 597-610.
Vriezen WH, De Graaf B, Mariani C, Voesenek LACJ. 2000. Submergence induces
expansin gene expression in tolerant Rumex palustris and not in flooding-intolerant R. acetosa. Planta 210(6): 956-963.
Wang H, Tian C-e, Duan J, Wu K. 2008. Research progresses on GH3s, one family of
primary auxin-responsive genes. Plant Growth Regulation 56(3): 225-232.
Wang S, Basten CJ, Z.-B. Z. 2011. Windows QTL Cartographer 2.5. Department of
Statistics, North Carolina State University, Raleigh, NC.
Weigel D, Mott R. 2009. The 1001 Genomes Project for Arabidopsis thaliana. Genome
Biology 10(5): 1-5.
Wilson IW, Schiff CL, Hughes DE, Somerville SC. 2001. Quantitative Trait Loci Analysis
of Powdery Mildew Disease Resistance in the Arabidopsis thaliana Accession Kashmir-1. Genetics 158(3): 1301-1309.
Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker JR, Berry CC, Chory J. 2004. Light-Response Quantitative Trait Loci Identified with Composite Interval
and eXtreme Array Mapping in Arabidopsis thaliana. Genetics 167(2): 907-917.
Xu K. 2006. Sub1A is an ethylene-response-factor-like gene that confers submergence
tolerance to rice. Nature 442: 705-708.
Xu K, Mackill D. 1996. A major locus for submergence tolerance mapped on rice chromosome
9. Molecular Breeding 2(3): 219-224.
Yang Y, Xu R, Ma C-j, Vlot AC, Klessig DF, Pichersky E. 2008. Inactive Methyl
Indole-3-Acetic Acid Ester Can Be Hydrolyzed and Activated by Several Esterases Belonging to the AtMES Esterase Family of Arabidopsis. Plant Physiology 147(3): 1034-1045.
Young MD, Wakefield MJ, Smyth GK, Oshlack A 2010. Gene ontology analysis for
RNA-seq: accounting for selection bias.In: BioMed Central Ltd.
Zhang G, Chen M, Chen X, Xu Z, Guan S, Li L-C, Li A, Guo J, Mao L, Ma Y. 2008.
Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.). Journal of experimental botany 59(15): 4095-4107.
