Development of a model system to identify differences in spring and winter oat

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Chawade, Aakash ^a,b   Lindén, Pernilla ^c   Bräutigam, Marcus ^b   Jonsson, Rickard ^d,f   Jonsson, Anders ^b,c   Moritz, Thomas ^c   Olsson, Olof ^a,b,e  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b Crop Tailor AB   (Sweden)

^c SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^d Lantmännen SW Seed AB ^*  (Sweden)

^e LUND UNIVERSITY   (Sweden)

^f Syngenta Seeds AB   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CARBOXYLIC ACID; SUGAR; ELECTROLYTE; SUCROSE;

AGRICULTURAL PARAMETERS; AMINO ACID SEQUENCE; ARTICLE; BREEDING; COLD ACCLIMATIZATION; CONTROLLED STUDY; FLOWER DEVELOPMENT; FLOWERING; FREEZING; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GEOGRAPHIC DISTRIBUTION; NONHUMAN; OAT; PLANT LEAF; PROTEIN ANALYSIS; SEQUENCE ANALYSIS; SPECIES CULTIVATION; SPRING; WINTER; ACCLIMATIZATION; AGRICULTURE; ANALYSIS OF VARIANCE; BIOLOGICAL MODEL; DISCRIMINANT ANALYSIS; FLOWER; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METABOLOME; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEASON;

AVENA; AVENA SATIVA;

ACCLIMATIZATION; AGRICULTURE; ANALYSIS OF VARIANCE; AVENA SATIVA; BREEDING; DISCRIMINANT ANALYSIS; ELECTROLYTES; FLOWERS; FREEZING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; LEAST-SQUARES ANALYSIS; METABOLIC NETWORKS AND PATHWAYS; METABOLOME; MODELS, BIOLOGICAL; PRINCIPAL COMPONENT ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEASONS; SUCROSE;

EID: 84855510815     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029792     Document Type: Article

References (43)

1. FAO (2008) Food and Agriculture Organization ProdSTAT:FAOSTAT.
2. Thomashow MF, (1999) PLANT COLD ACCLIMATION: Freezing Tolerance Genes and Regulatory Mechanisms. Annu Rev Plant Physiol Plant Mol Biol 50: 571-599.
3. Fowler S, Thomashow MF, (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14: 1675-1690.
4. Vogel JT, Zarka DG, Van Buskirk HA, Fowler SG, Thomashow MF, (2005) Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 41: 195-211.
5. Bohnert HJ, Nelson DE, Jensen RG, (1995) Adaptations to Environmental Stresses. Plant Cell 7: 1099-1111.
6. Sakamoto A, Murata N, (2000) Genetic engineering of glycinebetaine synthesis in plants: current status and implications for enhancement of stress tolerance. J Exp Bot 51: 81-88.
7. Thomashow MF, (2001) So what's new in the field of plant cold acclimation? Lots! Plant Physiol 125: 89-93.
8. Benedict C, Geisler M, Trygg J, Huner N, Hurry V, (2006) Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis. Plant Physiol 141: 1219-1232.
9. Chawade A, Brautigam M, Lindlof A, Olsson O, Olsson B, (2007) Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. BMC Genomics 8: 304.
10. Lindlof A, Brautigam M, Chawade A, Olsson O, Olsson B, (2009) In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control. Bioinformatics 25: 1345-1348.
11. Heather AVB, Thomashow MF, (2006) Arabidopsis transcription factors regulating cold acclimation. Physiologia Plantarum 126: 72-80.
12. Meyer SE, Nelson DL, Carlson SL, (2004) Ecological genetics of vernalization response in Bromus tectorum L. (Poaceae). Ann Bot 93: 653-663.
13. Preston JC, Kellogg EA, (2008) Discrete developmental roles for temperate cereal grass VERNALIZATION1/FRUITFULL-like genes in flowering competency and the transition to flowering. Plant Physiol 146: 265-276.
14. von Zitzewitz J, Szucs P, Dubcovsky J, Yan L, Francia E, et al. (2005) Molecular and structural characterization of barley vernalization genes. Plant Mol Biol 59: 449-467.
15. Danyluk J, Kane NA, Breton G, Limin AE, Fowler DB, et al. (2003) TaVRT-1, a putative transcription factor associated with vegetative to reproductive transition in cereals. Plant Physiol 132: 1849-1860.
16. Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, et al. (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci U S A 100: 6263-6268.
17. Akar T, Francia E, Tondelli A, Rizza F, Stanca AM, et al. (2009) Marker-assisted characterization of frost tolerance in barley (Hordeum vulgare L.). Plant Breeding 128: 381-386.
18. Gulick PJ, Drouin S, Yu Z, Danyluk J, Poisson G, et al. (2005) Transcriptome comparison of winter and spring wheat responding to low temperature. Genome 48: 913-923.
19. Cook D, Fowler S, Fiehn O, Thomashow MF, (2004) A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc Natl Acad Sci U S A 101: 15243-15248.
20. Cunningham SM, Nadeau P, Castonguay Y, Laberge S, Volenec JJ, (2003) Raffinose and Stachyose Accumulation, Galactinol Synthase Expression, and Winter Injury of Contrasting Alfalfa Germplasms. Crop Science 43: 562-570.
21. Kaplan F, Kopka J, Haskell DW, Zhao W, Schiller KC, et al. (2004) Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol 136: 4159-4168.
22. Kaplan F, Kopka J, Sung DY, Zhao W, Popp M, et al. (2007) Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content. Plant J 50: 967-981.
23. Korn M, Gartner T, Erban A, Kopka J, Selbig J, et al. (2010) Predicting Arabidopsis freezing tolerance and heterosis in freezing tolerance from metabolite composition. Mol Plant 3: 224-235.
24. Zuther E, Buchel K, Hundertmark M, Stitt M, Hincha DK, et al. (2004) The role of raffinose in the cold acclimation response of Arabidopsis thaliana. FEBS Lett 576: 169-173.
25. Livingston DP 3rd, (1996) The Second Phase of Cold Hardening: Freezing Tolerance and Fructan Isomer Changes in Winter Cereal Crowns. Crop Science 36: 1568-1573.
26. Livingston DP 3rd, Hincha DK, Heyer AG, (2009) Fructan and its relationship to abiotic stress tolerance in plants. Cell Mol Life Sci 66: 2007-2023.
27. Maruyama K, Takeda M, Kidokoro S, Yamada K, Sakuma Y, et al. (2009) Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A. Plant Physiol 150: 1972-1980.
28. Livingston DP 3rd, Tallury SP, Premkumar R, Owens SA, Olien CR, (2005) Changes in the Histology of Cold-Hardened Oat Crowns during Recovery from Freezing. Crop Science 45: 1545-1558.
29. Livingston DP, Premkumar R, Tallury SP, (2006) Carbohydrate partitioning between upper and lower regions of the crown in oat and rye during cold acclimation and freezing. Cryobiology 52: 200-208.
30. Olien CR, (1964) Freezing processes in the crown of 'Hudson barley' Hordeum vulgare (L. emend. Lamn) Hudson. Crop Science 4: 91-95.
31. Livingston DP 3rd, Elwinger GF, Murphy JP, (2004) Moving beyond the Winter Hardiness Plateau in U.S. Oat Germplasm. Crop Science 44: 1966-1969.
32. Fowler DB, Carles RJ, (1979) Growth, Development, and Cold Tolerance of Fall-acclimated Cereal Grains. Crop Science 19: 915-922.
33. Patterson FL, Schafer JF, (1978) Registration of Norline Oats. Crop Science 18.
34. Brautigam M, Lindlof A, Zakhrabekova S, Gharti-Chhetri G, Olsson B, et al. (2005) Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa. BMC Plant Biol 5: 18.
35. Chawade A, Sikora P, Brautigam M, Larsson M, Vivekanand V, et al. (2010) Development and characterization of an oat TILLING-population and identification of mutations in lignin and beta-glucan biosynthesis genes. BMC Plant Biol 10: 86.
36. Govindachary S, Bukhov NG, Joly D, Carpentier R, (2004) Photosystem II inhibition by moderate light under low temperature in intact leaves of chilling-sensitive and-tolerant plants. Physiol Plant 121: 322-333.
37. Wise RR, Naylor AW, (1987) Chilling-enhanced photooxidation: evidence for the role of singlet oxygen and superoxide in the breakdown of pigments and endogenous antioxidants. Plant Physiol 83: 278-282.
38. Rohde P, Hincha DK, Heyer AG, (2004) Heterosis in the freezing tolerance of crosses between two Arabidopsis thaliana accessions (Columbia-0 and C24) that show differences in non-acclimated and acclimated freezing tolerance. Plant Journal 38: 790-799.
39. Uemura M, Joseph RA, Steponkus PL, (1995) Cold Acclimation of Arabidopsis thaliana (Effect on Plasma Membrane Lipid Composition and Freeze-Induced Lesions). Plant Physiol 109: 15-30.
40. Gullberg J, Jonsson P, Nordstrom A, Sjostrom M, Moritz T, (2004) Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal Biochem 331: 283-295.
41. Schauer N, Steinhauser D, Strelkov S, Schomburg D, Allison G, et al. (2005) GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett 579: 1332-1337.
42. Jonsson P, Johansson AI, Gullberg J, Trygg J, A J, et al. (2005) High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses. Analytical Chemistry 77: 5635-5642.
43. Jonsson P, Johansson ES, Wuolikainen A, Lindberg J, Schuppe-Koistinen I, et al. (2006) Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data-a potential tool for multi-parametric diagnosis. J Proteome Res 5: 1407-1414.